@article {1546926, title = {A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution}, journal = {bioRxiv}, year = {2023}, abstract = {Genomes contain conserved non-coding sequences that perform important biological functions, such as gene regulation. We present a phylogenetic method, PhyloAcc-C, that associates nucleotide substitution rates with changes in a continuous trait of interest. The method takes as input a multiple sequence alignment of conserved elements, continuous trait data observed in extant species, and a background phylogeny and substitution process. Gibbs sampling is used to assign rate categories (background, conserved, accelerated) to lineages and explore whether the assigned rate categories are associated with increases or decreases in the rate of trait evolution. We test our method using simulations and then illustrate its application using mammalian body size and lifespan data previously analyzed with respect to protein coding genes. Like other studies, we find processes such as tumor suppression, telomere maintenance, and p53 regulation to be related to changes in longevity and body size. In addition, we also find that skeletal genes, and developmental processes, such as sprouting angiogenesis, are relevant. The R/C++ software package implementing our method is available under an open source license from\ https://github.com/phyloacc/PhyloAcc-C.}, url = {https://www.biorxiv.org/content/10.1101/2023.10.04.560937v1.abstract}, author = {Gemmell, Patrick and Sackton, Timothy B and Edwards, Scott V and Liu, Jun S} } @article {1546921, title = {Ancient duplication, coevolution, and selection at the MHC class IIA and IIB genes of birds}, journal = {Frontiers in Immunology}, year = {2023}, pages = {1250824}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10641522/}, author = {Minias, Piotr and Edwards, Scott V and Babik, Wies{\l}aw} } @article {1546906, title = {PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts on targeted lineages accounting for gene tree discordance}, journal = {Molecular Biology and Evolution}, volume = {40}, year = {2023}, pages = {msad195}, abstract = {An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here, we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations, and show that PhyloAcc-GT is a robust tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.}, url = {https://academic.oup.com/mbe/article/40/9/msad195/7259332}, author = {Yan, Han and Hu, Zhirui and Thomas, Gregg WC and Edwards, Scott V and Sackton, Timothy B and Liu, Jun S} } @article {1546901, title = {Episodic population fragmentation and gene flow reveal a trade-off between heterozygosity and allelic richness}, journal = {Molecular Ecology}, year = {2023}, abstract = {In episodic environments like deserts, populations of some animal species exhibit irregular fluctuations such that populations are alternately large and connected or small and isolated. Such dynamics are typically driven by periodic resource pulses due, for example, to large but infrequent rainfall events. The repeated population bottlenecks resulting from fragmentation should lower genetic diversity over time, yet species undergoing these fluctuations appear to maintain high levels of genetic diversity. To resolve this apparent paradox, we simulated a metapopulation of constant size undergoing repeat episodes of fragmentation and change in gene flow to mimic outcomes experienced by mammals in an Australian desert. We show that episodic fragmentation and gene flow have contrasting effects on two measures of genetic diversity: heterozygosity and allelic richness. Specifically, fragmentation into many, small subpopulations, coupled with periods of infrequent gene flow, preserves allelic richness at the expense of heterozygosity. In contrast, fragmentation into a few, large subpopulations maintains heterozygosity at the expense of allelic richness. The strength of the trade-off between heterozygosity and allelic richness depends on the amount of gene flow and the frequency of gene flow events. Our results imply that the type of genetic diversity maintained among species living in strongly fluctuating environments will depend on the way populations fragment, with our results highlighting different mechanisms for maintaining allelic richness and heterozygosity in small, fragmented populations.}, url = {https://onlinelibrary.wiley.com/doi/full/10.1111/mec.17174}, author = {Hill, Peta and Dickman, Chris R and Dinnage, Russell and Duncan, Richard P and Edwards, Scott V and Greenville, Aaron and Sarre, Stephen D and Stringer, Emily J and Wardle, Glenda M and Gruber, Bernd} } @article {1546896, title = {Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers}, journal = {Proceedings of the National Academy of Sciences}, volume = {120}, year = {2023}, pages = {e2307340120}, abstract = {Echolocation, the detection of objects by means of sound waves, has evolved independently in diverse animals. Echolocators include not only mammals such as toothed whales and yangochiropteran and rhinolophoid bats but also\ Rousettus\ fruit bats, as well as two bird lineages, oilbirds and swiftlets. In whales and yangochiropteran and rhinolophoid bats, positive selection and molecular convergence has been documented in key hearing-related genes, such as\ prestin\ (SLC26A5), but few studies have examined these loci in other echolocators. Here, we examine patterns of selection and convergence in echolocation-related genes in echolocating birds and\ Rousettus\ bats. Fewer of these loci were under selection in\ Rousettus\ or birds compared with classically recognized echolocators, and elevated convergence (compared to outgroups) was not evident across this gene set. In certain genes, however, we detected convergent substitutions with potential functional relevance, including convergence between\ Rousettus\ and classic echolocators in\ prestin\ at a site known to affect hair cell electromotility. We also detected convergence between Yangochiroptera, Rhinolophidea, and oilbirds in TMC1, an important mechanosensory transduction channel in vertebrate hair cells, and observed an amino acid change at the same site within the pore domain. Our results suggest that although most proteins implicated in echolocation in specialized mammals may not have been recruited in birds or\ Rousettus\ fruit bats, certain hearing-related loci may have undergone convergent functional changes. Investigating adaptations in diverse echolocators will deepen our understanding of this unusual sensory modality.}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.2307340120}, author = {Sadanandan, Keren R and Ko, Meng-Ching and Low, Gabriel W and Gahr, Manfred and Edwards, Scott V and Hiller, Michael and Sackton, Timothy B and Rheindt, Frank E and Sin, Simon Yung Wa and Baldwin, Maude W} } @article {1546886, title = {Mitogenomics clarifies the position of the Nearctic magpies (Pica hudsonia and Pica nuttalli) within the Holarctic magpie radiation}, journal = {Current Zoology}, year = {2023}, pages = {zoad048}, abstract = {Partial separation of a peripheral population may lead to its divergence and, potentially, speciation due to genetic drift followed by selection and geographic isolation. This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verified directly. The two Nearctic allopatric species of magpies (Aves, Corvidae: Pica) serve as a good example of these problems. The Black-billed magpie Pica hudsonia is widely distributed in North America, whereas the Yellow-billed Magpie Pica nuttalli is endemic to restricted range in California. Their relationships with Palearctic species have been little studied. We obtained complete mitochondrial genomes of both Nearctic magpie species, along with the Eurasian Magpie (Pica pica) and the Oriental Magpie (Pica serica), 20 mitogenomes in total. Phylogenetic analysis reveals a basal position of P. serica, and P. pica as a sister clade to the two Nearctic species. P. hudsonia and P. nuttalli form reciprocal monophyletic subclades, showing recent divergence between and within them. Our data show that the Nearctic magpie lineage diverged from the common ancestor with P. pica, with a single migration wave via the Beringia. Within the Nearctic, we hypothesize a peripatric mode of speciation among Pica taxa due to divergence and separation of the small marginal population in California below the Sierra-Nevada mountains. Diversifying amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for heat-tolerance. Considering the clear phenotypic differences between P. hudsonia and P. nuttalli, our data, showing their reciprocal monophylies and genetic distinctness, is consistent with the two-species taxonomy.}, url = {https://academic.oup.com/cz/advance-article/doi/10.1093/cz/zoad048/7336799}, author = {Kryukov, Alexy P and Kryukov, Kirill A and Collier, Kathleen and Fang, Bohao and Edwards, Scott V} } @article {1544311, title = {Whole-genome analyses reveal past population fluctuations and low genetic diversities of the North Pacific albatrosses}, journal = {Molecular Biology and Evolution}, volume = {40}, year = {2023}, pages = {msad155}, abstract = {Throughout the Plio-Pleistocene, climate change has impacted tropical marine ecosystems substantially, with even more severe impacts predicted in the Anthropocene. Although many studies have clarified demographic histories of seabirds in polar regions, the history of keystone seabirds of the tropics is unclear, despite the prominence of albatrosses (Diomedeidae, Procellariiformes) as the largest and most threatened group of oceanic seabirds. To understand the impact of climate change on tropical albatrosses, we investigated the evolutionary and demographic histories of all four North Pacific albatrosses and their prey using whole-genome analyses. We report a striking concordance in demographic histories among the four species, with a notable dip in effective population size at the beginning of the Pleistocene and a population expansion in the Last Glacial Period when sea levels were low, which resulted in increased potential coastal breeding sites. Abundance of the black-footed albatross dropped again during the Last Glacial Maximum, potentially linked to climate-driven loss of breeding sites and concordant genome-derived decreases in its major prey. We find very low genome-wide (π \< 0.001) and adaptative genetic diversities across the albatrosses, with genes of the major histocompatibility complex close to monomorphic. We also identify recent selective sweeps at genes associated with hyperosmotic adaptation, longevity, and cognition and memory. Our study has shed light on the evolutionary and demographic histories of the largest tropical oceanic seabirds and provides evidence for their large population fluctuations and alarmingly low genetic diversities.}, url = {https://academic.oup.com/mbe/article/40/7/msad155/7218901}, author = {Huynh, Stella and Cloutier, Alison and Chen, Guoling and Tsz, David and Chan, Chung and Lam, Derek Kong and Huyvaert, Kathryn P and Sato, Fumio and Edwards, Scott V. and Sin, Simon Yung Wa} } @article {1544306, title = {Short branch attraction in phylogenomic inference under the multispecies coalescent}, journal = {Frontiers in Ecology and Evolution}, volume = {11}, year = {2023}, abstract = {Accurate reconstruction of species trees often relies on the quality of input gene trees estimated from molecular sequences. Previous studies suggested that if the sequence length is fixed, the maximum likelihood may produce biased gene trees which subsequently mislead inference of species trees. Two key questions need to be answered in this context: what are the scenarios that may result in consistently biased gene trees? and for those scenarios, are there any remedies that may remove or at least reduce the misleading effects of consistently biased gene trees? In this article, we establish a theoretical framework to address these questions. Considering a scenario where the true gene tree is a 4-taxon star tree T SS SS *=() 1 234 ,, , with two short branches leading to the species S1 and S2, we demonstrate that maximum likelihood significantly favors the wrong bifurcating tree [(S1, S2), S3, S4] grouping the two species S1 and S2 with short branches. We name this inconsistent behavior short branch attraction, which may occur in real-world data involving a 4-taxon bifurcating gene tree with a short internal branch. If no mutation occurs along the internal branch, which is likely if the internal branch is short, the 4-taxon bifurcating tree is equivalent to the 4-taxon star tree and thus will suffer the same misleading effect of short branch attraction. Theoretical and simulation results further demonstrate that short branch attraction may occur in gene trees and species trees of arbitrary size. Moreover, short branch attraction is primarily caused by a lack of phylogenetic information in sequence data, suggesting that converting short internal branches to polytomies in the estimated gene trees can significantly reduce artifacts induced by short branch attraction. KEYWORDS coalescent methods, species trees, gene trees, multispecies coalescent model, long branch attraction, short branch attraction}, url = {http://scholar.sdpublishers.info/id/eprint/2463/}, author = {Liu, Liang and Liu, Yu and Wu, Shaoyuan and Arnold, Jonathan and Whalen, Christopher and Davis, Charles and Edwards, Scott V.} } @article {1544301, title = {Multiple Instances of Adaptive Evolution in Aquaporins of Amphibious Fishes}, journal = {Biology}, volume = {12}, year = {2023}, pages = {846}, abstract = {

Aquaporins (AQPs) are a highly diverse family of transmembrane proteins involved in osmotic regulation that played an important role in the conquest of land by tetrapods. However, little is known about their possible implication in the acquisition of an amphibious lifestyle in actinopterygian fishes. Herein, we investigated the molecular evolution of AQPs in 22 amphibious actinopterygian fishes by assembling a comprehensive dataset that was used to (1) catalogue AQP paralog members and classes; (2) determine the gene family birth and death process; (3) test for positive selection in a phylogenetic framework; and (4) reconstruct structural protein models. We found evidence of adaptive evolution in 21 AQPs belonging to 5 different classes. Almost half of the tree branches and protein sites that were under positive selection were found in the AQP11 class. The detected sequence changes indicate modifications in molecular function and/or structure, which could be related to adaptation to an amphibious lifestyle. AQP11 orthologues appear to be the most promising candidates to have facilitated the processes of the water-to-land transition in amphibious fishes. Additionally, the signature of positive selection found in the AQP11b stem branch of the Gobiidae clade suggests a possible case of exaptation in this clade.

Keywords:\ 

aquaporin;\ amphibious fishes;\ adaptive evolution;\ emersion

}, url = {https://www.mdpi.com/2079-7737/12/6/846}, author = {Lorente-Martinez, Hector and Agorreta, Ainhoa and Irisarri, Iker and Zardoya, Rafael and Edwards, Scott V. and San Mauro, Diego} } @article {1544296, title = {Testosterone coordinates gene expression across different tissues to produce carotenoid-based red ornamentation}, journal = {Molecular Biology and Evolution}, volume = {40}, year = {2023}, pages = {msad056}, abstract = {Carotenoid pigments underlie most of the red, orange, and yellow visual signals used in mate choice in vertebrates. However, many of the underlying processes surrounding the production of carotenoid-based traits remain unclear due to the complex nature of carotenoid uptake, metabolism, and deposition across tissues. Here, we leverage the ability to experimentally induce the production of a carotenoid-based red plumage patch in the red-backed fairywren (Malurus melanocephalus), a songbird in which red plumage is an important male sexual signal. We experimentally elevated testosterone in unornamented males lacking red plumage to induce the production of ornamentation and compared gene expression in both the liver and feather follicles between unornamented control males, testosterone-implanted males, and naturally ornamented males. We show that testosterone upregulates the expression of\ CYP2J19, a gene known to be involved in ketocarotenoid metabolism, and a putative carotenoid processing gene (ELOVL6) in the liver, and also regulates the expression of putative carotenoid transporter genes in red feather follicles on the back, including\ ABCG1.\ In black feathers, carotenoid-related genes are downregulated and melanin genes upregulated, but we find that carotenoids are still present in the feathers. This may be due to the activity of the carotenoid-cleaving enzyme BCO2 in black feathers. Our study provides a first working model of a pathway for carotenoid-based trait production in free-living birds, implicates testosterone as a key regulator of carotenoid-associated gene expression, and suggests hormones may coordinate the many processes that underlie the production of these traits across multiple tissues.}, url = {https://academic.oup.com/mbe/article/40/4/msad056/7076405}, author = {Khalil, Sarah and Enbody, Erik D. and Frankl-Vilches, Caroline and Welklin, Joseph F. and Koch, Rebecca E. and Toomey, Matthew B. and Sin, Simon Yung Wa and Edwards, Scott V. and Gahr, Manfred and Schwabl, Hubert and Hubert, Michael S. and Karubian, Jordan} } @article {1544291, title = {Whole-genome phylogeography of the blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome}, journal = {Molecular Ecology}, volume = {32}, year = {2023}, pages = {1248-1270}, abstract = {Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here, we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue-faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within\ E. cyanotis\ across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3{\textendash}1.7\ Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome; and in\ E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination-suppressed portion of the neo-Z (~37.2\ Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral-Z. Yet, the new PAR (~17.4\ Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16604}, author = {Burley, John T. and Orzechowski, Sophia CM and Sin, Simon Yung Wa and Edwards, Scott V} } @article {1544286, title = {Genetic basis and evolution of structural color polymorphism in an Australian songbird}, journal = {bioRxiv}, year = {2023}, abstract = {Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaption under differential selection. Some island birds have melanic plumage differing from the color of mainland conspecifics, a trait proposed as an insular adaptation. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genomes to investigate the genetic basis of melanism by comparing the blue and black\ M. leucopterus\ subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene\ ASIP\ and four candidate genes that may contribute to feather nanostructure development. We also detected signatures of a selective sweep in genomic regions containing\ ASIP\ and\ SCUBE2\ not in the black subspecies, as predicted by earlier work, but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This re-evolution was likely driven by a pre-existing female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.}, url = {https://www.biorxiv.org/content/10.1101/2023.09.03.556140v1}, author = {Sin, Simon Yung Wa and Ke, Fushi and Chen, Guoling and Guoling, Pei-Yu and Enbody, Erik and Karubian, Jordan and Webster, Michael S. and Edwards, Scott V.} } @article {1512046, title = {Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles }, journal = {Animals}, volume = {13}, year = {2023}, pages = {471}, abstract = {

Abstract

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles{\textemdash}lizards and snakes{\textemdash}recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.

Keywords:\ 

anonymous loci;\ GC content;\ genome size;\ isochores;\ karyotype;\ natural history;\ reduced representation;\ repetitive elements;\ sex determination and chromosomes;\ target capture;\ ultraconserved elements

}, url = {https://www.mdpi.com/2076-2615/13/3/471}, author = {Card, Daren C. and Jennings, W. Bryan and Edwards, Scott V.} } @article {1512041, title = {Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene}, journal = {PLoS genetics}, volume = {19}, year = {2023}, pages = {e1010551}, abstract = {Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl\ Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20{\textendash}50\%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of\ G.\ gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.}, url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010551}, author = {Wu, Meng Yue and Forcina, Giovanni and Low, Gabriel Weijie and Sadanandan, Keren R. and Gwee, Chyi Yin and van Grouw, Hein and Wu, Shaoyuan and Edwards, Scott V. and Baldwin, Maude W. and Rheindt, Frank E.} } @article {1512036, title = {Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves: Climacteris)}, journal = {Biological Journal of the Linnean Society}, volume = {138}, year = {2023}, pages = {249-273}, abstract = {The Carpentarian barrier across north-eastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modelling of brown and black-tailed treecreepers (Climacteris picumnus\ and\ Climacteris melanurus), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (Fst = 0.91), and revealed a signature of a recent selective sweep in\ C. picumnus.\ A variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7{\textendash}2.8 Mya. Palaeoecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the past ~600 kyr and that the area of interspecific range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.}, url = {https://academic.oup.com/biolinnean/article/138/3/249/7022154}, author = {Edwards, Scott V. and Tonini, Jo{\~a}o F R and Mcinerney, Nancy and Welch, Corey and Beerli, Peter} } @book {1477301, title = {Species Tree Inference: A Guide to Methods and Applications}, year = {2023}, publisher = {Princeton University Press}, organization = {Princeton University Press}, address = {Princeton}, abstract = {An up-to-date reference book on phylogenetic methods and applications for evolutionary biologists The increasingly widespread availability of genomic data is transforming how biologists estimate evolutionary relationships among organisms and broadening the range of questions that researchers can test in a phylogenetic framework. Species Tree Inference brings together many of today{\textquoteright}s leading scholars in the field to provide an incisive guide to the latest practices for analyzing multilocus sequence data. This wide-ranging and authoritative book gives detailed explanations of emerging new approaches and assesses their strengths and challenges, offering an invaluable context for gauging which procedure to apply given the types of genomic data and processes that contribute to differences in the patterns of inheritance across loci. It demonstrates how to apply these approaches using empirical studies that span a range of taxa, timeframes of diversification, and processes that cause the evolutionary history of genes across genomes to differ. By fully embracing this genomic heterogeneity, Species Tree Inference illustrates how to address questions beyond the goal of estimating phylogenetic relationships of organisms, enabling students and researchers to pursue their own research in statistically sophisticated ways while charting new directions of scientific discovery.}, url = {https://books.google.com/books?hl=en\&lr=\&id=5YeJEAAAQBAJ\&oi=fnd\&pg=PR1\&dq=info:_dzXwIHuYkwJ:scholar.google.com\&ots=QCmNoaTyRt\&sig=f3885Z75pXu9Rk5u04DE9c96FE8$\#$v=onepage\&q\&f=false}, author = {Blischak, Paul D. and Brown, Jeremy M and Cao, Zhen and Cloutier, Alison and Cobb, Kerry and DiGiacomo, Alexandria A and Eaton, Deren AR and Edwards, Scott V and Gallivan, Kyle A and Gates, Daniel J and Grayson, Phil and Liu, Xinhao and McKenzie, Patrick F and Mirarab, Siavash and Molloy, Erin and Mount, Genevieve G and Nakhleh, Luay and Oaks, Jamie R and Ogilvie, Huw A and Pease, James B and Pilson, Diana and Sackton, Timothy B and Smith, Stacey D and Smith, Stephen A and Waight, Emiko M and Sol{\'\i}s-Lemus, Claudia and Swofford, David L and Thompson, Coleen E and Walker, Joseph F and Warnow, Tandy and Weinheimer, Ellen I and Wilgenbusch, James C and Wolfe, Andrea D and Yan, Zhi} } @article {1546956, title = {Museum Genomics}, journal = {Annual Review of Genetics}, volume = {55}, year = {2022}, pages = {633-659}, abstract = {Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth{\textquoteright}s biodiversity. Museum genomics{\textemdash}genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations{\textemdash}has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.}, url = {https://www.annualreviews.org/doi/abs/10.1146/annurev-genet-071719-020506}, author = {Card, Daren C and Shapiro, Beth and Giribet, Gonzalo and Moritz, Craig and Edwards, Scott V} } @article {1546936, title = {Development of the visual system in social poison frog tadpoles}, journal = {bioRxiv}, year = {2022}, abstract = {The ways in which animals sense the world around them change throughout development. Young of many species have absent or limited visual capabilities, but still make complex decisions about individuals with whom they interact. Poison frog tadpoles display complex social behaviors that have been suggested to rely on vision despite a century of research indicating tadpoles have poorly-developed visual systems. Here, we examined visual system development in tadopoles of the Mimetic Poison Frog (Ranitomeya imitator)\ that use begging displays to stimulate egg feeding from their mothers. Neural activation in the retina increased in begging metamorphic tadpoles, but not in begging pre-metamorphic tadpoles. Molecular profiling of active eye neurons during begging identified numerous differentially expressed development-related transcripts, suggesting that developmental stage, not begging, was driving gene expression profiles. Using the neural tracer neurobiotin, we found that connections between the eye and brain proliferate during metamorphosis, with little retinotectal connections in recently-hatched tadpoles. To assess visual capabilities of tadpoles, we used a light/dark preference assay in early, middle, and late stages. All tadpoles showed a preference for the dark side, but the strength of preference increased with developmental stage and eyes were not required for this behavior. Taken together, these data indicate visual ontology of poison frog tadpoles is similar to that of other frogs, with poor visual capabilities at hatching and immense morphological and physiological changes occurring during metamorphosis. More broadly, this highlights the importance of multimodal cues, including photodetection via the pineal structure, in tadpole social interactions.}, url = {https://www.biorxiv.org/content/10.1101/2022.10.18.512729v1.abstract}, author = {Butler, Julie M and McKinney, Jordan and Ludington, Sarah C and Mabogunje, Moremi and Singh, Devraj and Edwards, Scott V and O{\textquoteright}Connell, Lauren A} } @article {1512031, title = {Structure and evolution of the squamate major histocompatibility complex as revealed by two Anolis lizard genomes}, journal = {Frontiers in Genetics}, volume = {13}, year = {2022}, abstract = {The major histocompatibility complex (MHC) is an important genomic region for adaptive immunity and has long been studied in ecological and evolutionary contexts, such as disease resistance and mate and kin selection. The MHC has been investigated extensively in mammals and birds but far less so in squamate reptiles, the third major radiation of amniotes. We localized the core MHC genomic region in two squamate species, the green anole (Anolis carolinensis) and brown anole (A. sagrei), and provide the first detailed characterization of the squamate MHC, including the presence and ordering of known MHC genes in these species and comparative assessments of genomic structure and composition in MHC regions. We find that the\ Anolis\ MHC, located on chromosome 2 in both species, contains homologs of many previously-identified mammalian MHC genes in a single core MHC region. The repetitive element composition in anole MHC regions was similar to those observed in mammals but had important distinctions, such as higher proportions of DNA transposons. Moreover, longer introns and intergenic regions result in a much larger squamate MHC region (11.7 Mb and 24.6\ Mb in the green and brown anole, respectively). Evolutionary analyses of MHC homologs of anoles and other representative amniotes uncovered generally monophyletic relationships between species-specific homologs and a loss of the peptide-binding domain exon 2 in one of two\ mhc2β\ gene homologs of each anole species. Signals of diversifying selection in each anole species was evident across codons of\ mhc1, many of which appear functionally relevant given known structures of this protein from the green anole, chicken, and human. Altogether, our investigation fills a major gap in understanding of amniote MHC diversity and evolution and provides an important foundation for future squamate-specific or vertebrate-wide investigations of the MHC.}, url = {https://www.frontiersin.org/articles/10.3389/fgene.2022.979746/full}, author = {Card, Daren C and Van Camp, Andrew G. and Santonastaso, Trenten and Jensen-Seaman, Michael I. and Anthony, Nicola M. and Edwards, Scott V.} } @article {1512026, title = {Development of the visual system in social poison frog tadpoles}, journal = {bioRxiv}, year = {2022}, abstract = {The ways in which animals sense the world around them change throughout development. Young of many species have absent or limited visual capabilities, but still make complex decisions about individuals with whom they interact. Poison frog tadpoles display complex social behaviors that have been suggested to rely on vision despite a century of research indicating tadpoles have poorly-developed visual systems. Here, we examined visual system development in tadopoles of the Mimetic Poison Frog (Ranitomeya imitator)\ that use begging displays to stimulate egg feeding from their mothers. Neural activation in the retina increased in begging metamorphic tadpoles, but not in begging pre-metamorphic tadpoles. Molecular profiling of active eye neurons during begging identified numerous differentially expressed development-related transcripts, suggesting that developmental stage, not begging, was driving gene expression profiles. Using the neural tracer neurobiotin, we found that connections between the eye and brain proliferate during metamorphosis, with little retinotectal connections in recently-hatched tadpoles. To assess visual capabilities of tadpoles, we used a light/dark preference assay in early, middle, and late stages. All tadpoles showed a preference for the dark side, but the strength of preference increased with developmental stage and eyes were not required for this behavior. Taken together, these data indicate visual ontology of poison frog tadpoles is similar to that of other frogs, with poor visual capabilities at hatching and immense morphological and physiological changes occurring during metamorphosis. More broadly, this highlights the importance of multimodal cues, including photodetection via the pineal structure, in tadpole social interactions.}, url = {https://www.biorxiv.org/content/10.1101/2022.10.18.512729v1.abstract}, author = {McKinney, Jordan and Ludington, Sarah C. and Mabogunje, Moremi and Singh, Devraj and Edwards, Scott V. and O{\textquoteright}Connell, Lauren A.} } @article {1512021, title = {PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts and associations with binary traits under gene tree discordance}, journal = {bioRxiv}, year = {2022}, abstract = {

An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype to phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity to detect rate shifts across genomic regions. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target-lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. In summary, PhyloAcc-GT is a useful tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.

}, url = {https://www.biorxiv.org/content/10.1101/2022.12.23.521765v1.abstract}, author = {Yan, Han and Hu, Zhirui and Thomas, Gregg and Edwards, Scott V. and Sackton, Timothy B. and Liu, Jun S.} } @article {1477376, title = {Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird}, journal = {Genetics}, volume = {220}, year = {2022}, pages = {iyab210}, abstract = {Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird species thus far. Here, we assembled a high-quality genome and nasal epithelium transcriptome of the Leach{\textquoteright}s storm-petrel (Oceanodroma leucorhoa) to extensively characterize their OR repertoire. Using a depth-of-coverage-assisted counting method, we estimated over 160 intact OR genes (\~{}500 including OR fragments). This method reveals the highest number of intact OR genes and the lowest proportion of pseudogenes compared to other waterbirds studied, and suggests that rates of OR gene duplication vary between major clades of birds, with particularly high rates in passerines. OR expression patterns reveal two OR genes (OR6-6 and OR5-11) highly expressed in adults, and four OR genes (OR14-14, OR14-12, OR10-2, and OR14-9) differentially expressed between age classes of storm-petrels. All four genes differentially expressed between age classes were more highly expressed in chicks compared to adults, suggesting that OR genes may exhibit ontogenetic specializations. Three highly differentially expressed OR genes also had high copy number ratios, suggesting that expression variation may be linked to copy number in the genome. We provide better estimates of OR gene number by using a copy number-assisted counting method, and document ontogenetic changes in OR gene expression that may be linked to olfactory specialization. These results provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds.}, url = {https://academic.oup.com/genetics/article/220/2/iyab210/6458329}, author = {Yung Wa Sin, Simon and Cloutier, Alison and Nevitt, Gabrielle and Edwards, Scott V} } @article {1477371, title = {The evolutionary history and mechanistic basis of female ornamentation in a tropical songbird}, journal = {Evolution}, volume = {76}, year = {2022}, pages = {1720-1736}, abstract = {Ornamentation, such as the showy plumage of birds, is widespread among female vertebrates, yet the evolutionary pressures shaping female ornamentation remain uncertain. In part this is due to a poor understanding of the mechanistic route to ornamentation in females. To address this issue, we evaluated the evolutionary history of ornament expression in a tropical passerine bird, the White-shouldered Fairywren, whose females, but not males, strongly vary between populations in occurrence of ornamented black-and-white plumage. We first use phylogenomic analysis to demonstrate that female ornamentation is derived and that female ornamentation evolves independently of changes in male plumage. We then use exogenous testosterone in a field experiment to induce partial ornamentation in naturally unornamented females. By sequencing the transcriptome of experimentally induced ornamented and natural feathers, we identify genes expressed during ornament production and evaluate the degree to which female ornamentation in this system is associated with elevated testosterone, as is common in males. We reveal that some ornamentation in females is linked to testosterone and that sexes differ in ornament-linked gene expression. Lastly, using genomic outlier analysis we identify a candidate melanogenesis gene that lies in a region of high genomic divergence among populations that is also differentially expressed in feather follicles of different female plumages. Taken together, these findings are consistent with sex-specific selection favoring the evolution of female ornaments and demonstrate a key role for testosterone in generating population divergence in female ornamentation through gene regulation. More broadly, our work highlights similarities and differences in how ornamentation evolves in the sexes.}, url = {https://academic.oup.com/evolut/article/76/8/1720/6966201}, author = {Enbody, Erik D and Sin, Simon YW and Boersma, Jordan and Edwards, Scott V and Ketaloya, Serena and Schwabl, Hubert and Webster, Michael S and Karubian, Jordan} } @article {1477361, title = {A unifying framework for estimating generation time in age-structured populations: implications for phylogenetics and conservation biology}, journal = {The American Naturalist}, volume = {200}, year = {2022}, pages = {48-62}, abstract = {Generation time is a measure of the pace of life and is used to describe processes in population dynamics and evolution. We show that three commonly used mathematical definitions of generation time in age-structured populations can produce different estimates of up to several years for the same set of life history data. We present and prove a mathematical theorem that reveals a general order relation among the definitions. Furthermore, the exact population growth rate at the time of sampling influences estimates of generation time, which calls for attention. For phylogenetic estimates of divergence times between species, included demographic data should be collected when the population growth rate for each species is most common and typical. In conservation biology, demographic data should be collected during phases of population decline in declining species, contrary to common recommendations to use predisturbance data. The results can be used to improve the International Union for Conservation of Nature{\textquoteright}s recommendation in parameterizing models for evaluating threat categories of threatened species and to avoid underestimating extinction risk.}, url = {https://www.journals.uchicago.edu/doi/epdf/10.1086/719667}, author = {Jonasson, Johan and H{\"a}rk{\"o}nen, Tero and Sundqvist, Lisa and Edwards, Scott V and Hardingm Karin C} } @article {1477356, title = {Whole-genome phylogeography of the blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome}, journal = {Molecular Ecology}, year = {2022}, abstract = {

Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here, we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue-faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within\ E. cyanotis\ across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3{\textendash}1.7\ Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome; and in\ E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination-suppressed portion of the neo-Z (~37.2\ Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral-Z. Yet, the new PAR (~17.4\ Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.

}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16604}, author = {Burley, John T and Orzechowski, Sophia CM and Yung Wa Sin, Simon and Edwards, Scott V} } @article {1477331, title = {An automated work-flow for pinniped surveys: A new tool for monitoring population dynamics}, journal = {Frontiers in Ecology and Evolution}, volume = {10}, year = {2022}, abstract = {Detecting changesinpopulation trends dependsontheaccuracyofestimated mean population growth rates and thus the quality of input data. However, monitoring wildlife populations poses economic and logistic challenges especially in complex and remote habitats. Declines in wildlife populations can remain undetected for years unless effective monitoring techniques are developed, guiding appropriate management actions. We developed an automated survey workflow using unmanned aerial vehicles (drones) to quantify the number and size of individual animals, using the wellstudied Scandinavian harbour seal (Phoca vitulina) as a model species. We compared ground-based counts using telescopes with manual flights, using a zoom photo/video, and pre-programmed flights producing orthomosaic photo maps. We used machine learning to identify and count both pups and older seals and we present a new method for measuring body size automatically. We evaluate the population{\textquoteright}s reproductive success using drone data, historical counts and predictions from a Leslie matrix population model. The most accurate and time-efficient results were achieved by performing pre-programmed flights where individual seals are identified by machine learning and their body sizes are measured automatically. The accuracy of the machine learning detector was 95{\textendash}97\% and the classification error was 4.6 {\textpm} 2.9 for pups and 3.1 {\textpm} 2.1 for older seals during good light conditions. There was a clear distinction between the body sizes of pups and older seals during breeding time. We estimated 320 pups in the breeding season 2021 with the drone, which is well beyond the expected number, based on historical data on pup production. The new high quality data from the drone survey confirms earlier indications of a deteriorating reproductive rate in this important harbour seal colony. We show that aerial drones and machine learning are powerful tools for monitoring wildlife in inaccessible areas which can be used to assess annual recruitment and seasonal variations in body condition.}, author = {Infantes, Eduardo and Carroll, Daire and Silva, Willian TAF and H{\"a}rk{\"o}nen, Tero and Edwards, Scott V and Harding, Karin C} } @article {1477321, title = {Passerine birds}, journal = {Current Biology}, volume = {32}, year = {2022}, pages = {R1149-R1154}, abstract = {Passeriformes, more commonly known as perching birds or passerines, are the most species-rich group of birds. Totaling nearly 6500 species, approximately two out of every three bird species is a passerine. Passerines are globally distributed and are among the most abundant birds at nearly every terrestrial location on Earth. Owing to their diversity, abundance and cosmopolitan distribution, passerines are among the most familiar of all birds and have figured prominently in both human culture and science. For example, humans have long been captivated by the beautiful songs of many passerines (such as the Common Nightingale (Luscinia megarhynchos) in Europe and the Wood Thrush (Hylocichla mustelina) of North America), and it is common in some cultures {\textemdash} although globally discouraged as ecologically damaging, especially when birds are captured directly from the wild {\textemdash} to keep passerines as pets. Nevertheless, the vocal prowess and frequent ability to thrive in captivity have made passerines important models for lab-based research ranging from neurobiology to genetics. In contrast, the diversity and accessibility of many passerine birds in the wild continue to make them among the best animal models for field-based studies of behavioral ecology, evolution, mating systems, life history, disease resistance, ecological and evolutionary responses to climate change, among many other fields.}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0960982222013835}, author = {Schmitt, C Jonathan and Edwards, Scott V} } @article {1477316, title = {Effects of Plastic Ingestion on Blood Chemistry, Gene Expression and Body Condition in Wedge-Tailed Shearwaters (Ardenna Pacifica)}, journal = {bioRxiv}, year = {2022}, pages = {2022.11. 26.517527}, abstract = {

ABSTRACT

Plastic pollution is a global threat and affects almost every marine ecosystem. The amount of plastic in the ocean has increased substantially over the past decade, posing a mounting threat to biodiversity. Seabirds, typically top predators in marine food chains, have been negatively affected by plastic pollution. Here we focused on documenting the sublethal effects of plastic in Wedge-tailed Shearwaters (Ardenna pacifica, WTSH) on the island of Maui, Hawai{\textquoteright}i. Through analyses of blood chemistry, gene expression, morphometrics and stomach contents, we documented the effects of plastic ingestion on adult WTHS from 3 established colonies. We detected a negative relationship between body weight and the presence of plastic in regurgitated stomach contents. Genes associated with metabolic, biosynthetic pathways, inflammatory responses and ribosome function were upregulated in lighter birds. Birds that had ingested plastic tended to be lighter in weight, in comparison to birds that did not have plastic and tended to weight more. Furthermore, there were 43 genes differentiating males and females that did not have plastic compared to only 11 genes differentiating males and females that had ingested plastic. There was also a marginal negative relationship between lighter birds and blood urea nitrogen levels. We also hope that the morphometric measurements, blood parameters and gene expression data we collected contributes to a database that will be used for future studies on understanding anthropogenic effects on seabird body condition.

}, url = {https://www.biorxiv.org/content/10.1101/2022.11.26.517527v1}, author = {Mejia, Nicole and Termignoni Garcia, Flavia and Learned, Jennifer and Penniman, Jay and Edwards, Scott V} } @article {1429568, title = {Evolution of the DAN gene family in vertebrates}, journal = {Developmental Biology}, volume = {482}, year = {2022}, pages = {34-43}, abstract = {The DAN\ gene family\ (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in\ limb bud\ formation and digitation, kidney formation and\ morphogenesis\ and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the\ monophyly\ of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our\ phylogenetic\ results revealed the presence of two new DAN gene lineages; one is only retained in\ cephalochordates, whereas the other one (GREM3) was only identified in\ cartilaginous fish, holostean fish, and\ coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2,\ SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0012160621002475}, author = {Opazo, Juan C. and Hoffman, Federico G. and Zavala, Kattina and Edwards, Scott V.} } @article {1429566, title = {The Earth BioGenome Project 2020: Starting the clock}, journal = {Proceedings of the National Academy of Sciences}, volume = {119}, year = {2022}, abstract = {November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project{\textquoteright}s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP{\textquoteright}s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.}, url = {https://www.pnas.org/content/119/4/e2115635118.short}, author = {Lewin, Harris A. and Richards, Stephen and Aiden, Erez Lieberman and Allende, Miguel L. and Archibaldg, John M. and B{\'a}lint, Mikl{\'o}s and Barker, Katharine B. and Baumgartner, Bridget and Belov, Katherine and Bertorelle, Giorgio and Blaxter, Mark L. and Cai, Jing and Caperello, Nicolette D. and Carlson, Keith and Castilla-Rubio, Juan Carlos and Chaw, Shu-Miaw and Chen, Lei and Childers, Anna K. and Coddington, Jonathan A. and Conde, Dalia A. and Corominas, Monserrat and Crandall, Ketih A. and Crawford, Andrew J. and Federica di Palma and Durbin, Richard and Ebenezerer, ThankGod E. and Edwards, Scott V. and Fedrigo, Oliver and Flicek, Paul and Formenti, Giulio and Gobbs, Richard A. and Gilbert, M. Thomas P. and Goldstein, Melissa M. and Graves, Jennifer Marshall and Greeley, Henry T. and Grigoriev, Igor V. and Hackett, Kevin J. and Hall, eil and Haussler, David and Helgen, Kristofer M. and Hogg, Carolyn J. and Isobe, Sachiko and Jacobse, Kjetill Sigurd and Janke, Aaxel and Jarvis, Erich D. and Johnson, Warren E. and Jones, Steven J. M. and Karlsson, Elinor K. and Kersey, Paul J. and Kim, Jin-Hyong and Kress, W. John and Lawniczak, Mara K. N. and Leebens-Mack, James H. and Li, Xueyan and Kerstin Lindblad-Toh and Liu, Xin and Lopez, Jose V. and Marques-Boet, Tomas and Mazard, Sophie and Mazet, Jona A. K. and Mazzoni, Camila J. and Myers, Eugene W. and O{\textquoteright}Neill, Rachel J. and Paez, Ssayde and Park, Hyun and Robison, Gene E. and Roquet, Cristina and Ryder, Oliver A. and Sabir, Jamal S. M. and Shaffer, H. Bradley and Shank, Timothy M. and Sherkow, Jacob S. and Soltis, Pamela S. and Tag, Boping and Tedersoo, Leho and Uliano-Silva, Marcela and Wang, Kun and Wei, Xiaofeng and Wetzer, Regina and Wilson, Julia L. and Xu, Xun and Yang, Huanming and Yoder, Anne D. and Zhang, Guojie} } @article {1429565, title = {Why sequence all eukaryotes?}, journal = {Proceedings of the National Academy of Sciences}, volume = {119}, year = {2022}, abstract = {Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes{\textemdash}about 2 million species{\textemdash}should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine. genome j diversity j ecology j evolution j conservation}, url = {https://www.pnas.org/content/pnas/119/4/e2115636118.full.pdf}, author = {Mark Blaxter and Archibald, John M. and Childers, Anna K. and Coddington, Jonathan A. and Crandall, Keith A. and Di Palma, Frederica and Durbin, Richard and Edwards, Scott V. and Graves, Jennifer A. M. and Hackett, Kevin J. and Hall, Neil and Jarvis, Erich D, and Johnson, Rebecca N. and Karlsson, Elinor K. and Kress, W. John and Kuraku, Shigehiro and Lawniczak, Mara K. N. and Kerstin Lindblad-Toh and Lopez, Jose V. and Moran, Nancy A. and Robinson, Gene E. and Ryder, Oliver A. and Shapiro, Beth and Soltis, Pamela S. and Warnow, Tandy and Zhag, Guojie and Lewin, Harris A.} } @article {1429562, title = {Understanding the evolution of viviparity using intraspecific variation in reproductive mode and transitional forms of pregnancyBiological Reviews}, journal = {Biological Reviews}, year = {2022}, abstract = {How innovations such as vision, flight and pregnancy evolve is a central question in evolutionary biology. Examination of transitional (intermediate) forms of these traits can help address this question, but these intermediate phenotypes are very rare in extant species. Here we explore the biology and evolution of transitional forms of pregnancy that are midway between the ancestral state of oviparity (egg-laying) and the derived state, viviparity (live birth). Transitional forms of pregnancy occur in only three vertebrates, all of which are lizard species that also display intraspecific variation in reproductive phenotype. In these lizards (Lerista bougainvillii,\ Saiphos equalis, and\ Zootoca vivipara), geographic variation of three reproductive forms occurs within a single species: oviparity, viviparity, and a transitional form of pregnancy. This phenomenon offers the valuable prospect of watching {\textquoteleft}evolution in action{\textquoteright}. In these species, it is possible to conduct comparative research using different reproductive forms that are not confounded by speciation, and are of relatively recent origin. We identify major proximate and ultimate questions that can be addressed in these species, and the genetic and genomic tools that can help us understand how transitional forms of pregnancy are produced, despite predicted fitness costs. We argue that these taxa represent an excellent prospect for understanding the major evolutionary shift between egg-laying and live birth, which is a fundamental innovation in the history of animals.}, url = {https://onlinelibrary.wiley.com/doi/full/10.1111/brv.12836}, author = {Whittington, Camilla M. and Van Dyke, James U. and Liang, Stephanie QT and Edwards, Scott V. and Shine, Richard and Grueber, Catherine E.} } @article {1429560, title = {Comparative Population Genomics of Cryptic Speciation and Adaptive Divergence in Bicknell{\textquoteright}s and Gray-Cheeked Thrushes (Aves: Catharus bicknelli and Catharus minimus)}, journal = {Genome Biology and Evolution}, volume = {14}, year = {2022}, pages = {evab255}, abstract = {Cryptic speciation may occur when reproductive isolation is recent or the accumulation of morphological differences between sister lineages is slowed by stabilizing selection preventing phenotypic differentiation. In North America, Bicknell{\textquoteright}s Thrush (Catharus bicknelli) and its sister species, the Gray-cheeked Thrush (Catharus minimus), are parapatrically breeding migratory songbirds, distinguishable in nature only by subtle differences in song and coloration, and were recognized as distinct species only in the 1990s. Previous molecular studies have estimated that the species diverged approximately 120,000{\textendash}420,000 YBP and found very low levels of introgression despite their similarity and sympatry in the spring (prebreeding) migration. To further clarify the history, genetic divergence, genomic structure, and adaptive processes in C. bicknelli and C. minimus, we sequenced and assembled highcoverage reference genomes of both species and resequenced genomes from population samples of C. bicknelli, C. minimus, and two individuals of the Swainson{\textquoteright}s Thrush (Catharus ustulatus). The genome of C. bicknelli exhibits markedly higher abundances of transposable elements compared with other Catharus and chicken. Demographic and admixture analyses confirm moderate genome-wide differentiation (Fst 0.10) and limited gene flow between C. bicknelli and C. minimus, but suggest a more recent divergence than estimates based on mtDNA. We find evidence of rapid evolution of the Z-chromosome and elevated divergence consistent with natural selection on genomic regions near genes involved with neuronal processes in C. bicknelli. These genomes are a useful resource for future investigations of speciation, migration, and adaptation in Catharus thrushes. Key words: transposable element, speciation, selective sweeps, divergence time, effective population size.}, url = {https://academic.oup.com/gbe/article/14/1/evab255/6432041}, author = {Termignoni-Garcia, Flavia and Kirchman, Jeremy J. and Kirchman, Jeremy and Clark, Jonathan and Edwards, Scott V.} } @article {1429559, title = {The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics}, journal = {Genome Biology and Evolution}, volume = {14}, year = {2022}, pages = {evab176}, abstract = {

Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong {\textquotedblleft}sense of place,{\textquotedblright} comparative phylogeography offers abundant {\textquotedblleft}place-based{\textquotedblright} educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.

Gott Earth projection,\ whole-genome sequencing,\ landscape genomics,\ place-based education,\ indigenous knowledge

}, url = {https://academic.oup.com/gbe/article/14/1/evab176/6339579}, author = {Edwards, Scott V. and Robin, VV and Ferrand, Nuno and Moritz, Craig} } @article {1429556, title = {Museum genomics}, journal = {Annual Review of Genetics}, volume = {55}, year = {2021}, pages = {633-59}, abstract = {Anthropocene, ancient DNA, cryogenic collections, museomics, museum curation, natural history collections Abstract Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth{\textquoteright}s biodiversity. Museum genomics{\textemdash}genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations{\textemdash}has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.}, url = {https://pgl.soe.ucsc.edu/card21.pdf}, author = {Card, Daren C. and Shapiro, Beth and Girabet, Gonzalo and Moritz, Craig and Edwards, Scott V.} } @article {1429555, title = {What have we learned from the first 500 avian genomes?}, journal = {Annual Review of Ecology, Evolution, and Systematics}, volume = {52}, year = {2021}, pages = {611-639}, abstract = {

The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500{\textemdash}approximately 5\% of bird diversity{\textemdash}placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.

Keywords

comparative genomics,\ phylogenomics,\ genome evolution,\ Aves,\ a posteriori marker selection,\ chromosomes

}, url = {https://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-012121-085928}, author = {Bravo, Gustavo A. and Schmitt, C. Jonathan and Edwards, Scott V.} } @article {1429554, title = {Early origin of sweet perception in the songbird radiation}, journal = {Science}, volume = {373}, year = {2021}, pages = {226-231}, abstract = {Seeing a bird eat nectar from a flower is a common sight in our world. The ability to detect sugars, however, is not ancestral in the bird lineage, where most species were carnivorous. Toda\ et al.\ looked at receptors within the largest group of birds, the passerines or songbirds, and found that the emergence of sweet detection involved a single shift in a receptor for umami (see the Perspective by Barker). This ancient change facilitated sugar detection not just in nectar feeding birds, but also across the songbird group, and in a way that was different from, though convergent with, that in hummingbirds.}, url = {https://www.science.org/doi/10.1126/science.abf6505}, author = {Toda, Yassuka and Ko, Meng-Ching and Miller, Eliot T. and Rico-Guevara, Alejandro and Nakagita, Tomoya and Sakakibara, Ayano and Uemura, Kana and Sackton, Timothy and Hayakawa, Takashi and Sin, Simon Yung Wa and Ishimaru, Yoshiro and Misaka, Takumi and Oteiza, Pablo and James Crall and Edwards, Scott V. and Buttemer, William and Matsumura, Shuichi and Baldwin, Maude W.} } @article {1429508, title = {slimr: An R package for integrating data and tailor-made population genomic simulations over space and time}, journal = {bioRxiv}, year = {2021}, abstract = {Software for realistically simulating complex population genomic processes is revolutionizing our understanding of evolutionary processes, and providing novel opportunities for integrating empirical data with simulations. However, the integration between simulation software and software designed for working with empirical data is currently not well developed. In particular, SLiM 3.0, which is one of the most powerful population genomic simulation frameworks for linking evolutionary dynamics with ecological patterns and processes is a standalone scripting language with limited data manipulation abilities. Here we present slimr, an R package designed to create a available under aCC-BY-NC-ND 4.0 International license. (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made bioRxiv preprint doi: https://doi.org/10.1101/2021.08.05.455258; this version posted August 6, 2021. The copyright holder for this preprint seamless link between SLiM 3.0 and the R development environment, with its powerful data manipulation and analysis tools. ● We show how slimr, in combination with SliM, facilitates smooth integration between genetic data, ecological data and simulation in a single environment. The package enables pipelines that begin with data reading, cleaning, and manipulation, proceed to constructing empirically-based parameters and initial conditions for simulations, then to running numerical simulations, and finally to retrieving simulation results in a format suitable for comparisons with empirical data {\textendash} aided by advanced analysis and visualization tools provided by R (such as ABC and deep learning). ● We demonstrate the use of slimr with an example from our own work on the landscape population genomics of desert mammals, highlighting the advantage of having a single integrated tool for both data analysis and simulation. ● slimr makes the powerful simulation ability of SliM 3.0 directly accessible to R users, allowing integrated simulation projects that incorporate empirical data without the need to switch between software environments. This should provide more opportunities for evolutionary biologists and ecologists to use realistic simulations to better understand the interplay between ecological and evolutionary processes. slimr is available at https://rdinnager.github.io/slimr/. Keywords: population genomics; simulation; landscape genomics; evolution; ecology; evolutionary ecology; application; software}, url = {https://www.biorxiv.org/content/10.1101/2021.08.05.455258v1}, author = {Sarre, Stephen D. and Duncan, Richard P. and Dickman, Christpher D. and Edwards, Scott V. and Greeville, Aaron and Wardle, Glenda and Gruber, Berd} } @article {1408853, title = {Author Correction: Dense sampling of bird diversity increases power of comparative genomics}, journal = {Nature}, volume = {592}, year = {2021}, pages = {E24-E24}, abstract = {In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU-029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU-029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.}, url = {https://www.nature.com/articles/s41586-021-03473-8}, author = {Feng, Shaohong and Stiller, Josefin and Deng, Yuan and Armstrong, Joel and Fang, Qi and Reeve, Andrew Hard and Xie, Duo and Chen, Guangji and Guo, Chunxue and Faircloth, Brant C. and Peterson, Bent and Wang, Zongji and Zhou, Qi and Diekhans, Mark and Chen, Wanjun and Andreu-S{\'a}nchez, Sergio and Margaryan, Ashot and Howard, Jason Travis and Parent, Carole and Pacheco, George and Sinding, Mikkel-Holger S. and Puetz, Lara and Cavill, Emily and Riberiro, {\^A}ngela M, and Eckhart, Leopold and Fjelds{\r a}, Jon and Hosner, Peter A. and Brumfield, Robb T. and Christidis, Les and Bertelsen, Mads F. and Sicheritz-Ponten, Thomaws and Tietze, Dieter Thomas and Robertson, Bruce C. and Song, Gang and Borgia, Gerald and Clarmunt, Santiago and Lovette, Irby J. and Cowen, Saul J. and Njoroge, Peter and Dumbacher, John Philip and Ryder, Oliver A. and Fuchs, J{\'e}r{\^o}me and Bunce, Michael and Burt, David W. and Cracraft, Joel and Meng, Guanliang and Hackett, Shannon J. and Ryan, Peter G and J{\o}nsson, Knud Andreas and Jamieson, Ian G. and R da Fonseca, Rute and Braun, Edward L. and Houde, Peters and Mirarab, Siavash and Suh, Alexander and Hansson, Bengt and Ponnikas, Suvi and Sigeman, Hanna and Stervander, Martin and Frandsen, Paul B and van der Zwan, Henriette and van der Sluis, Rencia and Visser, Carina and Balakrishnan, Christopher N. and Andrew G. Clark and Fitzpatrick, John W. and Bowman, Reed and Chen, Nancy and Cloutier, Alison and Timothy B. Sackton and Edwards, Scott V. and Foote, Dustin J. and Shakya, Subir B. and Sheldon, Frederick H. and Vignal, Alain and Soares, Andr{\'e} ER and Shapiro, Beth and Gonz{\'a}lez-Sol{\'\i}s, Jacob and Ferrer-Obiol, Joan and Rozas, Julio and Riutort, Marta and Tigano, Anna and Friesen, Vicki and Dal{\'e}n, Love and Urrutia, Araxi O. and Sz{\'e}kely, Tam{\'a}s and Liu, Yang and Campana, Michael G. and Corvel, Andr{\'e} and Gemmell, Neil J. and Gemmell, Nicolas and Mouritsen, Henrik and Thiele, Nadine and Delmore, Kira and Liedvogel, Miriam and Franke, Andre and Hoeppner, Marc P. and Mil{\'a}, Borja and Ketterson, Ellen D. and Fidler, Andrew Eric and Friis, Guillermo and Parody-Merino, {\'A}ngela M. and Battley, Phil F. and Cox, Murray P. and Costa Barroso Lima, Nicholas and Prosdocimi, Francisco and Parchman, Thomas Lee and Schlinger, Barney A. and Loiselle, Bette A. and Blake, John G. and Haw, John G. and Lim, Chuan and Day, Lainy B. and Fuxjager, Matthew J. and Baldwin, Maude W. and Braun, Michael J. and Wirthlin, Morgan and Rebecca B. Dikow and Ryder, T. Brandt and Camenisch, Glauco and Keller, Lukas F and Jeffrey M. DaCosta and Hauber, Mark E. and Louder, Matthew IM and Witt, Christopher C. and McGuire, Jimmy A. and Mudge, Joann and Megna, Libby C. and Carling, Matthew D. and Wang, Biao and Taylor, Scott A. and Del-Rio, Glaucia and Aleixo, Alexandre and Ribeiro Vasconcelos, Ana Tereza and Mello, Claudio V. and Li, Qiye and Yang, Huanming and Wang, Jian and Lei, Fumin and Carsten Rahbek and Gilbert, M. Thomas P. and Graves, Gary R. and Jarvis, Erich D. and Paten, Benedict and Zhang, Guojie} } @article {1408852, title = {Demographic history, not mating system, explains signatures of inbreeding and inbreeding depression in a large outbred population}, journal = {The American Naturalist}, volume = {197}, year = {2021}, pages = {658-676}, abstract = {Inbreeding depression is often found in small, inbred populations, but whether it can be detected in and have evolutionary consequences for large, wide-ranging populations is poorly known. Here, we investigate the possibility of inbreeding in a large population to determine whether mild levels of inbreeding can still have genetic and phenotypic consequences and how genomically widespread these effects can be. We apply genome-wide methods to investigate whether individual and parental heterozygosity is related to morphological, growth, or life-history traits in a pelagic seabird, Leach{\textquoteright}s storm-petrel (Oceanodroma leucorhoa). Examining 560 individuals as part of a multiyear study, we found a substantial effect of maternal heterozygosity on chick traits: chicks from less heterozygous (relatively inbred) mothers were significantly smaller than chicks from more heterozygous (noninbred) mothers. We show that these heterozygosity-fitness correlations were due to general genome-wide effects and demonstrate a correlation between heterozygosity and inbreeding, suggesting inbreeding depression. We used population genetic models to further show that the variance in inbreeding was probably due to past demographic events rather than the current mating system and ongoing mate choice. Our findings demonstrate that inbreeding depression can be observed in large populations and illustrate how the integration of genomic techniques and fieldwork can elucidate its underlying causes.}, url = {https://www.journals.uchicago.edu/doi/full/10.1086/714079?af=R}, author = {Sin, Simon Yung Wa and Hoover, Brian A. and Nevitt, Gabrielle A. and Edwards, Scott V.} } @article {1408851, title = {Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant}, journal = { Molecular Biology and Evolution}, volume = {38}, year = {2021}, pages = {263-273}, abstract = {Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that\ C.\ mantchuricum\ has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in\ C.\ mantchuricum\ with that of its closely related sister species, the Blue eared pheasant (C.\ auritum) for which the conservation concern is low. There were detrimental genetic consequences across all\ C.\ mantchuricum\ genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.}, url = {https://academic.oup.com/mbe/article/38/1/263/5898204?login=true}, author = {Wang, Pengcheng and Burley, John T. and Liu, Yang and Chang, Jiang and Chen, De and Lu, Qi and Li, Shou-Hsien and Zhou, Xuming and Edwards, Scott V. and Zhang, Zhengwang} } @article {1408850, title = {Early origin of sweet perception in the songbird radiation}, journal = {Science}, volume = {373}, year = {2021}, pages = {226-231}, abstract = {Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large evolutionary radiation containing nearly half of all living birds. We demonstrate sugar responses across species with diverse diets, uncover critical sites underlying carbohydrate detection, and identify the molecular basis of sensory convergence between songbirds and nectar-specialist hummingbirds. This early shift shaped the sensory biology of an entire radiation, emphasizing the role of contingency and providing an example of the genetic basis of convergence in avian evolution.}, url = {https://science.sciencemag.org/content/373/6551/226}, author = {Toda, Yasuka and Ko, Meng-Ching and Liang, Qiaoyi and Miller, Eliot T. and Rico-Guevara, Alejandro and Nakagita, Tomoya and Sakakibara, Ayano and Uemura, Kana and Sackton, Timothy and Hayakawa, Takashi and Sin, Simon Yung Wa and Ishimaru, Yoshiro and Misaka, Takumi and Oteiza, Pablo and James Crall and Edwards, Scott V. and Buttemer, William and Matsumura, Shuichi and Baldwin, Maude W.} } @article {1408849, title = {A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum}, journal = {Proceedings of the National Academy of Sciences}, volume = {118}, year = {2021}, abstract = {The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum) from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At \~{}1.06 gigabases (Gb), the\ P. ornatum\ genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of TEs; increased net deletion bias in TEs; drastic reduction in intron lengths; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of Piwi-interacting RNA (piRNA)-based TE-silencing pathway genes in germline cells. Transcriptomes from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in\ Platyplectrum. Genome skimming of two closely related frog species (Lechriodus fletcheri\ and\ Limnodynastes fletcheri) confirms a reduction in TEs as a major driver of genome reduction in\ Platyplectrum\ and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The\ P. ornatum\ genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and vertebrates generally.}, url = {https://www.pnas.org/content/118/11/e2011649118}, author = {Lamichhaney, Sangeet and Catullo, Renee and Keogh, Keogh and Clulow, Simon and Edwards, Scott V.} } @proceedings {edwards2020bicycling, title = {Bicycling, Birding and $\#$BLM across America in a Summer of Chaos}, volume = {4}, year = {2020}, publisher = {Pensoft Publishers}, abstract = {From 6 June to 20 August, 2020, I undertook a 76-day, ~3800 mile bicycle trip across the United States from the Atlantic to the Pacific oceans. In this talk I will share with you some of the amazing people, landscapes and birds I encountered, mostly in rural towns and along blue highways. The gradually changing birdscape, both in sight and sound, underscored the sensitive ecological gradients to which birds respond, as well as the ability of some species to thrive in agricultural monocultures. Rivers large and small regularly benchmarked my progress, as well as the western journey of Lewis \& Clark over 200 years ago. The recent incidents in the US involving African Americans as targets of white violence inexorably caused me to festoon my bicycle with $\#$BlackLivesMatter ($\#$BLM) signs and share my experiences on social media. I encountered a variety of reactions, often positive and occasionally sharply negative, in a sea of generosity and extraordinary kindness as I wheeled my way through towns on the brink of collapse, vast private ranches and the occasional city. Rural America exhibits an abundance of loyalty and empathy for local communities, yet it is sometimes hard for Americans {\textendash} myself included {\textendash} to empathize with people they have never met in person. Two imperatives I took away, with ramifications for both biodiversity and political stability, were the need to somehow bring divergent communities together and to encourage empathy at the national level, among communities that otherwise experience each other only on TV.}, url = {https://biss.pensoft.net/article/59303/}, author = {Edwards, Scott V.} } @article {sin2020novo, title = {De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration}, journal = {G3: Genes, Genomes, Genetics}, volume = {10}, year = {2020}, pages = {3541{\textendash}3548}, publisher = {Genetics Society of America}, author = {Sin, Simon Yung Wa and Lu, Lily and Edwards, Scott V.} } @article {feng2020dense, title = {Dense sampling of bird diversity increases power of comparative genomics}, journal = {Nature}, volume = {587}, year = {2020}, pages = {252{\textendash}257}, publisher = {Nature Publishing Group}, author = {Feng, Shaohong and Stiller, Josefin and Deng, Yuan and Armstrong, Joel and Fang, Qi and Reeve, Andrew Hart and Xie, Duo and Chen, Guangji and Guo, Chunxue and Faircloth, Brant C and others} } @article {hedrick2020digitization, title = {Digitization and the future of natural history collections}, journal = {BioScience}, volume = {70}, year = {2020}, pages = {243{\textendash}251}, publisher = {Oxford University Press}, author = {Hedrick, Brandon P and Heberling, J Mason and Emily K Meineke and Turner, Kathryn G and Grassa, Christopher J and Park, Daniel S and Kennedy, Jonathan and Clarke, Julia A and Cook, Joseph A and Blackburn, David C and others} } @article {corbett2020evidence, title = {Evidence for the Pleistocene Arc Hypothesis from genome-wide SNPs in a Neotropical dry forest specialist, the Rufous-fronted Thornbird (Furnariidae: Phacellodomus rufifrons)}, journal = {Molecular Ecology}, volume = {29}, year = {2020}, pages = {4457{\textendash}4472}, author = {Corbett, Eamon C and Bravo, Gustavo A and Schunck, Fabio and Naka, Luciano N and Silveira, Lu{\'{\i}s F and Edwards, Scott V.} } @article {harvey2020evolution, title = {The evolution of a tropical biodiversity hotspot}, journal = {Science}, volume = {370}, year = {2020}, pages = {1343{\textendash}1348}, publisher = {American Association for the Advancement of Science}, author = {Harvey, Michael G and Bravo, Gustavo A and Claramunt, Santiago and Cuervo, Andr{\'e}s M and Derryberry, Graham E and Battilana, Jaqueline and Seeholzer, Glenn F and McKay, Jessica Shearer and O{\textquoteright}Meara, Brian C and Faircloth, Brant C and others} } @article {dierickx2020genetic, title = {Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark}, journal = {Proceedings of the Royal Society B}, volume = {287}, year = {2020}, pages = {20192613}, publisher = {The Royal Society}, author = {Dierickx, Elisa G and Sin, Simon Yung Wa and van Veelen, H Pieter J and Brooke, M de L and Liu, Yang and Edwards, Scott V. and Martin, Simon H} } @article {edwards2020genomics, title = {Genomics of adaptation and acclimation: from field to lab and back}, journal = {National Science Review}, volume = {7}, year = {2020}, pages = {128{\textendash}128}, publisher = {Oxford University Press}, author = {Edwards, Scott V.} } @article {bakker2020global, title = {The Global Museum: natural history collections and the future of evolutionary science and public education}, journal = {PeerJ}, volume = {8}, year = {2020}, pages = {e8225}, publisher = {PeerJ Inc.}, author = {Bakker, Freek T and Antonelli, Alexandre and Clarke, Julia A and Cook, Joseph A and Edwards, Scott V. and Ericson, Per GP and Faurby, S{\o}ren and Ferrand, Nuno and Gelang, Magnus and Gillespie, Rosemary G and others} } @article {rannala2020multi, title = {The multi-species coalescent model and species tree inference}, journal = {Phylogenetics in the Genomic Era}, year = {2020}, pages = {3{\textendash}3}, publisher = {No commercial publisher| Authors open access book}, author = {Rannala, Bruce and Edwards, Scott V. and Leach{\'e}, Adam and Yang, Ziheng} } @article {jiang2020multispecies, title = {The Multispecies Coalescent Model Outperforms Concatenation across Diverse Phylogenomic Data Sets}, journal = {Systematic Biology}, year = {2020}, author = {Jiang, Xiaodong and Edwards, Scott V. and Liu, Liang} } @article {smith2020phylogenetics, title = {Phylogenetics is the New Genetics (for Most of Biodiversity)}, journal = {Trends in Ecology \& Evolution}, year = {2020}, publisher = {Elsevier}, author = {Smith, Stacey D and Pennell, Matthew W and Dunn, Casey W. and Edwards, Scott V.} } @article {termignoni2020prospects, title = {Prospects for sociogenomics in avian cooperative breeding and parental care}, journal = {Current Zoology}, volume = {66}, year = {2020}, pages = {293{\textendash}306}, publisher = {Oxford University Press}, author = {Termignoni-Garcia, Flavia and Louder, Matthew IM and Balakrishnan, Christopher N and O{\textquoteright}Connell, Lauren and Edwards, Scott V.} } @inbook {edwards2020speciation, title = {Speciation}, booktitle = {The Theory of Evolution: Principles, Concepts, and Assumptions}, year = {2020}, pages = {296}, publisher = {University of Chicago Press}, organization = {University of Chicago Press}, author = {Edwards, Scott V. and Robin Hopkins and Mallet, James} } @article {gemmell2020tuatara, title = {The tuatara genome reveals ancient features of amniote evolution}, journal = {Nature}, volume = {584}, year = {2020}, pages = {403{\textendash}409}, publisher = {NATURE PUBLISHING GROUP}, author = {Gemmell, Neil J and Rutherford, Kim and Prost, Stefan and Tollis, Marc and Winter, David and Macey, J Robert and Adelson, David L and Suh, Alexander and Bertozzi, Terry and Grau, Jose H and others} } @article {YOUNG20193681, title = {Attenuated Fgf Signaling Underlies the Forelimb Heterochrony in the Emu Dromaius novaehollandiae}, journal = {Current Biology}, volume = {29}, year = {2019}, pages = {3681 - 3691.e5}, abstract = {Summary Powered flight was fundamental to the establishment and radiation of birds. However, flight has been lost multiple times throughout avian evolution. Convergent losses of flight within the ratites (flightless paleognaths, including the emu and ostrich) often coincide with reduced wings. Although there is a wealth of anatomical knowledge for several ratites, the genetic mechanisms causing these changes remain debated. Here, we use a multidisciplinary approach employing embryological, genetic, and genomic techniques to interrogate the mechanisms underlying forelimb heterochrony in emu embryos. We show that the initiation of limb formation, an epithelial to mesenchymal transition (EMT) in the lateral plate mesoderm (LPM) and myoblast migration into the LPM, occur at equivalent stages in the emu and chick. However, the emu forelimb fails to subsequently proliferate. The unique emu forelimb expression of Nkx2.5, previously associated with diminished wing development, initiates after this stage (concomitant with myoblast migration into the LPM) and is therefore unlikely to cause this developmental delay. In contrast, RNA sequencing of limb tissue reveals significantly lower Fgf10 expression in the emu forelimb. Artificially increasing Fgf10 expression in the emu LPM induces ectodermal Fgf8 expression and a limb bud. Analyzing open chromatin reveals differentially active regulatory elements near Fgf10 and Sall-1 in the emu wing, and the Sall-1 enhancer activity is dependent on a likely Fgf-mediated Ets transcription factor-binding site. Taken together, our results suggest that regulatory changes result in lower expression of Fgf10 and a concomitant failure to express genes required for limb proliferation in the early emu wing bud.}, keywords = {avian, Development, emu, Evolution, Fgf signaling, limb, loss of flight, paleognath, powered-flight, ratite}, issn = {0960-9822}, doi = {https://doi.org/10.1016/j.cub.2019.09.014}, url = {http://www.sciencedirect.com/science/article/pii/S0960982219311741}, author = {John J. Young and Phil Grayson and Edwards, Scott V. and Clifford J. Tabin} } @book {1230492, title = {Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model}, year = {2019}, pages = {211-239}, publisher = {Humana}, organization = {Humana}, address = {New York, NY}, abstract = {The multispecies coalescent (MSC) model provides a compelling framework for building phylogenetic trees from multilocus DNA sequence data. The pure MSC is best thought of as a special case of so-called {\textquotedblleft}multispecies network coalescent{\textquotedblright} models, in which gene flow is allowed among branches of the tree, whereas MSC methods assume there is no gene flow between diverging species. Early implementations of the MSC, such as {\textquotedblleft}parsimony{\textquotedblright} or {\textquotedblleft}democratic vote{\textquotedblright} approaches to combining information from multiple gene trees, as well as concatenation, in which DNA sequences from multiple gene trees are combined into a single {\textquotedblleft}supergene,{\textquotedblright} were quickly shown to be inconsistent in some regions of tree space, in so far as they converged on the incorrect species tree as more gene trees and sequence data were accumulated. The anomaly zone, a region of tree space in which the most frequent gene tree is different from the species tree, is one such region where many so-called {\textquotedblleft}coalescent{\textquotedblright} methods are inconsistent. Second-generation implementations of the MSC employed Bayesian or likelihood models; these are consistent in all regions of gene tree space, but Bayesian methods in particular are incapable of handling the large phylogenomic data sets currently available. Two-step methods, such as MP-EST and ASTRAL, in which gene trees are first estimated and then combined to estimate an overarching species tree, are currently popular in part because they can handle large phylogenomic data sets. These methods are consistent in the anomaly zone but can sometimes provide inappropriate measures of tree support or apportion error and signal in the data inappropriately. MP-EST in particular employs a likelihood model which can be conveniently manipulated to perform statistical tests of competing species trees, incorporating the likelihood of the collected gene trees on each species tree in a likelihood ratio test. Such tests provide a useful alternative to the multilocus bootstrap, which only indirectly tests the appropriateness of competing species trees. We illustrate these tests and implementations of the MSC with examples and suggest that MSC methods are a useful class of models effectively using information from multiple loci to build phylogenetic trees.}, url = {https://link.springer.com/protocol/10.1007/978-1-4939-9074-0_7}, author = {Liu, Liang and Anderson, Christian and Pearl, Dennis and Edwards, Scott} } @article {1230430, title = {Endless forms of sexual selection}, journal = {PeerJ}, volume = {7}, year = {2019}, abstract = {In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a {\textquotedblleft}stock-taking{\textquotedblright} workshop on sexual selection and conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the {\textquoteleft}aesthetic sense{\textquoteright} proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate {\textquoteleft}null model{\textquoteright} of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.}, url = {https://peerj.com/preprints/27584/}, author = {Lindsay, Willow R. and Andersson, Staffan and Bererhi, Badreddine and H{\"o}glund, Jacob and Johnsen, Arild and Kvarnemo, Charlotta and Leder, Erica H. and Lifjel, Jan T. and Ninnes, Calum E. and Olsson, Mats and Parker, Geoff A. and Pizzari, Tomasso and Qvarnstr{\"o}m, Anna and Safran, Rebecca J. and Svensson, Ola and Edwards, Scott V.} } @article {1230428, title = {The Global Museum: natural history collections and the future of evolutionary biology and public education}, journal = {PeerJ}, volume = {7}, year = {2019}, abstract = {Natural history museums are unique spaces for interdisciplinary research and for educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the {\textquoteleft}Global Museum{\textquoteright}) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science; inform biomimetic design; and even provide solutions to climate change, global health and food security challenges. As institutions, they are incubators for cutting-edge research in biology and simultaneously protect core infrastructure for present and future societal needs. In this perspective, we discuss challenges to the realization of the full potential of natural history collections and museums to serve society. After reviewing collections and types of museums, including local and global efforts, we discuss the value of specimens and the importance of observations. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this. We also explore ways in which improved infrastructure will allow higher quality science and increased opportunities for interdisciplinary research and communication, as well as new uses of collections. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow{\textquoteright}s technologies and hence further increasing the relevance of natural history museums.}, url = {https://peerj.com/preprints/27666/}, author = {Bakker, Freek T. and Antonelli, Alexandre and Clarke, Julia A. and Cook, Joseph A. and Edwards, Scott V. and Ericson, Per GP and Faurby, S{\o}ren and Ferrand, Nuno and Gelang, Magnus and Gillespie, Rosemary G. and Irestedt, Martin and Lundin, Kennet and Larsson, Ellen and Matos-Marav{\'\i}, P{\'a}vel and M{\"u}ller, Johannes and von Proschwitz, Ted and Roderick, George K. and Schliep, Alexander and Wahlberg, Niklas and Wiedenhoeft, John and K{\"a}llersj{\"o}, Mari} } @article {1230426, title = {Genomics of hosts-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales}, journal = {PeerJ}, year = {2019}, abstract = {Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed to the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of hostpathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.27734v1 | CC BY 4.0 Open Access | rec: 15 May 2019, publ: 15 May 2019 scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.}, url = {https://peerj.com/preprints/27734.pdf}, author = {N{\"a}pflin, Kathrin and Becks, Lutz and Bensch, Staffan and Ellis, Vincenzo A. and Hafer-Hahmann, Nina and Harding, Karin C. and Lind{\'e}n, Sara K. and O{\textquoteright}Connor, Emily A. and Olsen, Morten T. and Roved, Jacob and Timothy B. Sackton and Schultz, Alison J. and Venkatakrishnan, Vignesh and Videvall, Elin and Westerdahl, Helena and Winternitz, Jamie C. and Edwards, Scott V.} } @article {1230424, title = {Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution}, journal = {Philosophical Transactions of the Royal Society B}, volume = {374}, year = {2019}, pages = {20180248}, abstract = {Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current {\textquoteleft}genomics gold rush{\textquoteright} in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep {\textquoteleft}vertical{\textquoteright}, natural history knowledge with {\textquoteleft}horizontal{\textquoteright} knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa.}, url = {https://royalsocietypublishing.org/doi/full/10.1098/rstb.2018.0248}, author = {Lamichhaney, Sangeet and Card, Daren C. and Grayson, Philip and Tonini, Jo{\~a} F. R. and Bravo, Gustavo A. and N{\"a}pflin, Kathrin and Termignoni-Garcia, Flavia and Torres, Christopher and Burbrink, Frank and Clarke, Julia A. and Timothy B. Sackton and Edwards, Scott V.} } @article {1230421, title = {Evolutionary dynamics of sex chromosomes of paleognathous birds}, journal = {Genome Biology \& Evolution}, volume = {11}, year = {2019}, pages = {2376-2390}, abstract = {Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over \>100\ Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.}, url = {https://academic.oup.com/gbe/article/11/8/2376/5536880}, author = {Xu, Luohao and Sin, Simon Y. W. and Phil Grayson and Edwards, Scott V. and Timothy B. Sackton} } @article {1230419, title = {Avian MHC Evolution in the Era of Genomics: Phase 1.0}, journal = {Cells8}, year = {2019}, pages = {1152}, abstract = {Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.}, url = {https://www.mdpi.com/2073-4409/8/10/1152}, author = {O{\textquoteright}Connor, Emily A. and Westerdahl, Helena and Burri, Reto and Edwards, Scott V.} } @article {CloutierA.SacktonT.B.GraysonP.ClampM.BakerA.J.2019, title = {Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone}, journal = {Systematic Biology}, volume = {10.1101/26}, year = {2019}, author = {Cloutier, A. and Sackton, T. B. and Grayson, P. and Clamp, M. and Baker, A. J. and Edwards, S. V.} } @article {Hu2019, title = {Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees}, journal = {Molecular Biology and Evolution}, volume = {36}, year = {2019}, month = {mar}, pages = {1086-1100}, issn = {0737-4038}, doi = {10.1093/molbev/msz049}, url = {https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msz049/5372678}, author = {Hu, Zhirui and Sackton, Timothy B and Edwards, Scott V. and Liu, Jun S}, editor = {Pond, Sergei Kosakovsky} } @article {Sackton2019, title = {Convergent regulatory evolution and loss of flight in paleognathous birds.}, journal = {Science (New York, N.Y.)}, volume = {364}, year = {2019}, month = {apr}, pages = {74{\textendash}78}, publisher = {American Association for the Advancement of Science}, abstract = {A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.}, issn = {1095-9203}, doi = {10.1126/science.aat7244}, url = {http://www.ncbi.nlm.nih.gov/pubmed/30948549}, author = {Sackton, Timothy B and Phil Grayson and Cloutier, Alison and Hu, Zhirui and Liu, Jun S and Wheeler, Nicole E and Gardner, Paul P and Clarke, Julia A and Baker, Allan J and Clamp, Michele and Edwards, Scott V.} } @article {Bravo, title = {Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics}, journal = {PeerJ}, volume = {7}, year = {2019}, pages = {e6399}, abstract = {Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are}, doi = {10.7717/peerj.6399}, url = {https://peerj.com/articles/6399.pdf}, author = {Bravo, Gustavo A and Antonelli, Alexandre and Bacon, Christine D and Bartoszek, Krzysztof and Blom, Mozes P K and Huynh, Stella and Jones, Graham and Knowles, L Lacey and Lamichhaney, Sangeet and Marcussen, Thomas and Morlon, H{\'e}l{\`e}ne and Nakhleh, Luay K and Oxelman, Bengt and Pfeil, Bernard and Schliep, Alexander and Wahlberg, Niklas and Werneck, Fernanda P and Wiedenhoeft, John and Willows-Munro, Sandi and Edwards, Scott V.} } @article {LiuL.ZhangJ.RheindtF.R.LeiF.QuY.WangY.ZhangY.SullivanC.NieW.WangJ.YangF.ChenJ.EdwardsS.V.MengJ.2018, title = {Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification}, journal = {Proceedings of the National Academy of Sciences}, volume = {114}, year = {2018}, pages = {E9433{\textendash}E9434}, author = {Liu, L. and Zhang, J. and Rheindt, F. R. and Lei, F. and Qu, Y. and Wang, Y. and Zhang, Y. and Sullivan, C. and Nie, W. and J. Wang and Yang, F. and Chen, J. and Edwards, S. V. and Meng, J. and Wu, S.} } @article {Antonelli2018, title = {Conceptual and empirical advances in Neotropical biodiversity research}, journal = {PeerJ}, volume = {6}, year = {2018}, month = {oct}, pages = {e5644}, abstract = {\textlessp\textgreaterThe unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of {\textquotedblleft}trans-disciplinary biogeography,{\textquotedblright} which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow{\textquoteright}s ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.\textless/p\textgreater}, issn = {2167-8359}, doi = {10.7717/peerj.5644}, url = {https://peerj.com/articles/5644}, author = {Antonelli, Alexandre and Ariza, Mar{\'\i}a and Albert, James and Andermann, Tobias and Azevedo, Josu{\'e} and Bacon, Christine and Faurby, S{\o}ren and Guedes, Thais and Hoorn, Carina and Lohmann, L{\'u}cia G. and Matos-Marav{\'\i}, P{\'a}vel and Ritter, Camila D. and Sanmart{\'\i}n, Isabel and Silvestro, Daniele and Tejedor, Marcelo and ter Steege, Hans and Tuomisto, Hanna and Werneck, Fernanda P. and Zizka, Alexander and Edwards, Scott V.} } @article {Lewin2018, title = {Earth BioGenome Project: Sequencing life for the future of life}, journal = {Proceedings of the National Academy of Sciences}, volume = {115}, year = {2018}, month = {apr}, pages = {4325{\textendash}4333}, abstract = {Increasing our understanding of Earth{\textquoteright}s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet{\textquoteright}s organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth{\textquoteright}s eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project{\textquoteright}s goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.}, keywords = {access and benefit sharing, Biodiversity, data science, genome sequencing, Genomics}, issn = {0027-8424}, doi = {10.1073/pnas.1720115115}, url = {http://www.ncbi.nlm.nih.gov/pubmed/29686065 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5924910 http://www.pnas.org/lookup/doi/10.1073/pnas.1720115115}, author = {Lewin, Harris A. and Robinson, Gene E. and Kress, W. John and Baker, William J. and Coddington, Jonathan and Crandall, Keith A. and Durbin, Richard and Edwards, Scott V. and Forest, F{\'e}lix and Gilbert, M. Thomas P. and Goldstein, Melissa M. and Grigoriev, Igor V. and Hackett, Kevin J. and Haussler, David and Jarvis, Erich D. and Johnson, Warren E. and Aristides Patrinos and Richards, Stephen and Castilla-Rubio, Juan Carlos and van Sluys, Marie-Anne and Soltis, Pamela S. and Xu, Xun and Yang, Huanming and Zhang, Guojie} } @article {Hoover2018, title = {Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach{\textquoteright}s storm-petrels (Oceanodroma leucorhoa)}, journal = {Molecular Ecology}, volume = {27}, year = {2018}, month = {aug}, pages = {3371{\textendash}3385}, abstract = {Studies of MHC-based mate choice in wild populations often test hypotheses on species exhibiting female choice and male-male competition, which reflects the general prevalence of females as the choosy sex in natural systems. Here, we examined mutual mate-choice patterns in a small burrow-nesting seabird, the Leach{\textquoteright}s storm-petrel (Oceanodroma leucorhoa), using the major histocompatibility complex (MHC). The life history and ecology of this species are extreme: both partners work together to fledge a single chick during the breeding season, a task that requires regularly travelling hundreds of kilometres to and from foraging grounds over a 6- to 8-week provisioning period. Using a 5-year data set unprecedented for this species (n\ =\ 1078 adults and 925 chicks), we found a positive relationship between variation in the likelihood of female reproductive success and heterozygosity at Ocle-DAB2, a MHC class IIB locus. Contrary to previous reports rejecting disassortative mating as a mechanism for maintaining genetic polymorphism in this species, here we show that males make significant disassortative mate-choice decisions. Variability in female reproductive success suggests that the most common homozygous females (Ocle-DAB2*01/Ocle-DAB2*01) may be physiologically disadvantaged and, therefore, less preferred as lifelong partners for choosy males. The results from this study support the role of mate choice in maintaining high levels of MHC variability in a wild seabird species and highlight the need to incorporate a broader ecological framework and sufficient sample sizes into studies of MHC-based mating patterns in wild populations in general.}, keywords = {heterozygosity, Major Histocompatibility Complex, mate choice, seabirds, sexual selection}, issn = {09621083}, doi = {10.1111/mec.14801}, url = {http://www.ncbi.nlm.nih.gov/pubmed/30010226 http://doi.wiley.com/10.1111/mec.14801}, author = {Hoover, Brian and Alcaide, Miguel and Jennings, Sarah and Sin, Simon Yung Wa and Edwards, Scott V. and Nevitt, Gabrielle A.} } @article {Schmitt2019, title = {Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, volume = {374}, year = {2018}, month = {jan}, pages = {20170387}, abstract = {Natural history museums and the specimen collections they curate are vital scientific infrastructure, a fact as true today as it was when biologists began collecting and preserving specimens over 200 years ago. The importance of museum specimens in studies of taxonomy, systematics, ecology and evolutionary biology is evidenced by a rich and abundant literature, yet creative and novel uses of specimens are constantly broadening the impact of natural history collections on biodiversity science and global sustainability. Excellent examples of the critical importance of specimens come from their use in documenting the consequences of environmental change, which is particularly relevant considering the alarming rate at which we now modify our planet in the Anthropocene. In this review, we highlight the important role of bird, mammal and amphibian specimens in documenting the Anthropocene and provide examples that underscore the need for continued collection of museum specimens.This article is part of the theme issue {\textquoteright}Biological collections for understanding biodiversity in the Anthropocene{\textquoteright}.}, keywords = {Anthropocene, climate change, contamination, emergent disease, museum specimens}, issn = {0962-8436}, doi = {10.1098/rstb.2017.0387}, url = {http://www.ncbi.nlm.nih.gov/pubmed/30455205 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC6282080 http://www.royalsocietypublishing.org/doi/10.1098/rstb.2017.0387}, author = {Schmitt, C. Jonathan and Cook, Joseph A. and Zamudio, Kelly R. and Edwards, Scott V.} } @article {Tang2018, title = {Rapid diversification and hybridization have shaped the dynamic history of the genus Elaenia.}, journal = {Molecular phylogenetics and evolution}, volume = {127}, year = {2018}, month = {oct}, pages = {522{\textendash}533}, abstract = {Multi-locus data have proven invaluable in phylogenetic reconstruction and species delimitation. However, the mixed genetic signal from different loci can make inference of evolutionary history challenging and may produce incongruences depending on analytical and marker choice. Aside from incomplete lineage sorting (ILS) following diversification events that have had little time for deep differentiation, the most common causes of incongruent phylogenies are genetic introgression confounding a bifurcating evolutionary trajectory. In this study, we used multi-locus analytical approaches on sequence data of nine loci from 80 individuals of over 20 Neotropical Elaenia flycatcher species to examine the systematics, molecular phylogeny and species limits of this complex genus. Our results provide a robust phylogeny and estimates of species limits within Elaenia, but point to important cases of incongruences among phylogenies based on different analytical approaches. Simulations and estimates of divergence times provide reasonable explanations for the incongruent placement of some Elaenia taxa, pointing to multiple cases of both ILS and introgression within the genus. Molecular dating of major evolutionary events revealed intensive diversification during the Pleistocene, suggesting a central role of climate oscillations in the evolution of Elaenia flycatchers.}, keywords = {Elaenia flycatchers, incomplete lineage sorting, introgression, phylogenetic incongruence, Pleistocene climate oscillations}, issn = {1095-9513}, doi = {10.1016/j.ympev.2018.05.008}, url = {https://linkinghub.elsevier.com/retrieve/pii/S105579031730667X http://www.ncbi.nlm.nih.gov/pubmed/29758274}, author = {Tang, Qian and Edwards, Scott V. and Rheindt, Frank E} } @article {Ezaz2018, title = {Editorial: Evolutionary Feedbacks Between Population Biology and Genome Architecture}, journal = {Frontiers in Genetics}, volume = {9}, year = {2018}, month = {aug}, pages = {329}, publisher = {Frontiers}, keywords = {CNVs, microRNA, natural selection, Nearly neutral theory, Transposable Element (TE), vertebrate}, issn = {1664-8021}, doi = {10.3389/fgene.2018.00329}, url = {https://www.frontiersin.org/article/10.3389/fgene.2018.00329/full}, author = {Ezaz, Tariq and Edwards, Scott V.} } @article {Wu2018, title = {Genome-scale DNA sequence data and the evolutionary history of placental mammals}, journal = {Data in Brief}, volume = {18}, year = {2018}, month = {jun}, pages = {1972{\textendash}1975}, abstract = {We present a genomic data set comprised of the coding DNA sequences of 5162 loci from 90 vertebrate species, including 82 mammals. The loci were aligned with their protein sequences. The aligned protein sequences were then back translated into their original DNA sequences. The alignments were further filtered to remove individual sequences from each alignment exhibiting long branches or other unusual features. The data is deposited in figshare (http://figshare.com/articles/cds\_5162.zip/6031190) and will be useful as a test data set for large-scale phylogenomic analysis.}, keywords = {alignment, Mammal, phylogenomics}, issn = {23523409}, doi = {10.1016/j.dib.2018.04.094}, url = {http://www.ncbi.nlm.nih.gov/pubmed/29904704 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5998303 https://linkinghub.elsevier.com/retrieve/pii/S2352340918304475}, author = {Shaoyuan Wu and Edwards, Scott and Liu, Liang} } @article {Perry2018, title = {Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome}, journal = {Genome Biology and Evolution}, volume = {10}, year = {2018}, month = {aug}, pages = {2110{\textendash}2129}, abstract = {Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.}, issn = {1759-6653}, doi = {10.1093/gbe/evy157}, url = {http://www.ncbi.nlm.nih.gov/pubmed/30060036 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC6110522 https://academic.oup.com/gbe/article/10/8/2110/5061318}, author = {Perry, Blair W and Card, Daren C and McGlothlin, Joel W and Pasquesi, Giulia I M and Adams, Richard H and Schield, Drew R and Hales, Nicole R and Corbin, Andrew B and Demuth, Jeffery P and Hoffmann, Federico G and Vandewege, Michael W and Schott, Ryan K and Bhattacharyya, Nihar and Chang, Belinda S W and Casewell, Nicholas R and Whiteley, Gareth and Reyes-Velasco, Jacobo and Mackessy, Stephen P and Gamble, Tony and Storey, Kenneth B and Biggar, Kyle K and Passow, Courtney N and Kuo, Chih-Horng and McGaugh, Suzanne E and Bronikowski, Anne M and de Koning, A P Jason and Edwards, Scott V. and Pfrender, Michael E and Minx, Patrick and Brodie, Edmund D and Brodie, Edmund D and Warren, Wesley C and Castoe, Todd A}, editor = {O{\textquoteright}Connell, Mary} } @article {Campbell-Staton2018, title = {Physiological and regulatory underpinnings of geographic variation in reptilian cold tolerance across a latitudinal cline}, journal = {Molecular Ecology}, volume = {27}, year = {2018}, month = {may}, pages = {2243{\textendash}2255}, abstract = {Understanding the mechanisms that produce variation in thermal performance is a key component to investigating climatic effects on evolution and adaptation. However, disentangling the effects of local adaptation and phenotypic plasticity in shaping patterns of geographic variation in natural populations can prove challenging. Additionally, the physiological mechanisms that cause organismal dysfunction at extreme temperatures are still largely under debate. Using the green anole, Anolis carolinensis, we integrate measures of cold tolerance (CTmin ), standard metabolic rate, heart size, blood lactate concentration and RNAseq data from liver tissue to investigate geographic variation in cold tolerance and its underlying mechanisms along a latitudinal cline. We found significant effects of thermal acclimation and latitude of origin on variation in cold tolerance. Increased cold tolerance correlates with decreased rates of oxygen consumption and blood lactate concentration (a proxy for oxygen limitation), suggesting elevated performance is associated with improved oxygen economy during cold exposure. Consistent with these results, co-expression modules associated with blood lactate concentration are enriched for functions associated with blood circulation, coagulation and clotting. Expression of these modules correlates with thermal acclimation and latitude of origin. Our findings support the oxygen and capacity-limited thermal tolerance hypothesis as a potential contributor to variation in reptilian cold tolerance. Moreover, differences in gene expression suggest regulation of the blood coagulation cascade may play an important role in reptilian cold tolerance and may be the target of natural selection in populations inhabiting colder environments.}, keywords = {adaptation, Anolis, metabolism, physiology, RNAseq, thermal tolerance}, issn = {09621083}, doi = {10.1111/mec.14580}, url = {http://www.ncbi.nlm.nih.gov/pubmed/29633453 http://doi.wiley.com/10.1111/mec.14580}, author = {Campbell-Staton, Shane C. and Bare, Anna and Jonathan B. Losos and Edwards, Scott V. and Cheviron, Zachary A.} } @article {Ghanem2017, title = {Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum}, journal = {Journal of Clinical Microbiology}, volume = {56}, year = {2017}, month = {oct}, abstract = {\textlessp\textgreater \textlessnamed-content content-type="genus-species"\textgreaterMycoplasma gallisepticum\textless/named-content\textgreater is the most virulent and economically important \textlessnamed-content content-type="genus-species"\textgreaterMycoplasma\textless/named-content\textgreater species for poultry worldwide. Currently, \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater strain differentiation based on sequence analysis of 5 loci remains insufficient for accurate outbreak investigation. Recently, whole-genome sequences (WGS) of many human and animal pathogens have been successfully used for microbial outbreak investigations. However, the massive sequence data and the diverse properties of different genes within bacterial genomes results in a lack of standard reproducible methods for comparisons among \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater whole genomes. Here, we proposed the development of a core genome multilocus sequence typing (cgMLST) scheme for \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater strains and field isolates. For development of this scheme, a diverse collection of 37 \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater genomes was used to identify cgMLST targets. A total of 425 \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater conserved genes (49.85\% of \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater genome) were selected as core genome targets. A total of 81 \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater genomes from 5 countries on 4 continents were typed using \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater cgMLST. Analyses of phylogenetic trees generated by cgMLST displayed a high degree of agreement with geographical and temporal information. Moreover, the high discriminatory power of cgMLST allowed differentiation between \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater strains of the same outbreak. \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation among \textlessnamed-content content-type="genus-species"\textgreaterM. gallisepticum\textless/named-content\textgreater isolates. cgMLST provides stable and expandable nomenclature, allowing for comparison and sharing of typing results among laboratories worldwide. cgMLST offers an opportunity to harness the tremendous power of next-generation sequencing technology in applied avian mycoplasma epidemiology at both local and global levels. \textless/p\textgreater}, keywords = {cgMLST, genomes, Mycoplasma gallisepticum, strain typing, whole-genome sequence}, issn = {0095-1137}, doi = {10.1128/JCM.01145-17}, url = {http://www.ncbi.nlm.nih.gov/pubmed/29070657 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5744223 https://jcm.asm.org/lookup/doi/10.1128/JCM.01145-17}, author = {Ghanem, Mostafa and Wang, Leyi and Yan Zhang and Edwards, Scott and Lu, Amanda and Ley, David and El-Gazzar, Mohamed}, editor = {Fenwick, Brad} } @article {Chattopadhyay2017, title = {Gene flow during glacial habitat shifts facilitates character displacement in a Neotropical flycatcher radiation}, journal = {BMC Evolutionary Biology}, volume = {17}, year = {2017}, month = {dec}, pages = {210}, publisher = {BioMed Central}, abstract = {Pleistocene climatic fluctuations are known to be an engine of biotic diversification at higher latitudes, but their impact on highly diverse tropical areas such as the Andes remains less well-documented. Specifically, while periods of global cooling may have led to fragmentation and differentiation at colder latitudes, they may {\textendash} at the same time {\textendash} have led to connectivity among insular patches of montane tropical habitat with unknown consequences on diversification. In the present study we utilized \~5.5~kb of DNA sequence data from eight nuclear loci and one mitochondrial gene alongside diagnostic morphological and bioacoustic markers to test the effects of Pleistocene climatic fluctuations on diversification in a complex of Andean tyrant-flycatchers of the genus Elaenia. Population genetic and phylogenetic approaches coupled with coalescent simulations demonstrated disparate levels of gene flow between the taxon chilensis and two parapatric Elaenia taxa predominantly during the last glacial period but not thereafter, possibly on account of downward shifts of montane forest habitat linking the populations of adjacent ridges. Additionally, morphological and bioacoustic analyses revealed a distinct pattern of character displacement in coloration and vocal traits between the two sympatric taxa albiceps and pallatangae, which were characterized by a lack of gene flow. Our study demonstrates that global periods of cooling are likely to have facilitated gene flow among Andean montane Elaenia flycatchers that are more isolated from one another during warm interglacial periods such as the present era. We also identify a hitherto overlooked case of plumage and vocal character displacement, underpinning the complexities of gene flow patterns caused by Pleistocene climate change across the Andes.}, keywords = {Animal Systematics/Taxonomy/Biogeography, Entomology, evolutionary biology, general, Genetics and Population Dynamics, Life Sciences}, issn = {1471-2148}, doi = {10.1186/s12862-017-1047-3}, url = {https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-017-1047-3}, author = {Chattopadhyay, Balaji and Garg, Kritika M. and Gwee, Chyi Yin and Edwards, Scott V. and Rheindt, Frank E.} } @article { ISI:000408536000010, title = {Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary}, journal = {PNAS}, volume = {114}, year = {2017}, month = {AUG 29}, pages = {E7282-E7290}, issn = {0027-8424}, doi = {10.1073/pnas.1616744114}, url = {http://www.pnas.org/content/114/35/E7282}, author = {Liu, Liang and Zhang, Jin and Rheindt, Frank E. and Lei, Fumin and Qu, Yanhua and Wang, Yu and Zhang, Yu and Sullivan, Corwin and Nie, Wenhui and Wang, Jinhuan and Yang, Fengtang and Chen, Jinping and Edwards, Scott V. and Meng, Jin and Shaoyuan Wu} } @article { ISI:000408307600010, title = {Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient}, journal = {Molecular Ecology}, volume = {26}, year = {2017}, month = {SEP}, pages = {4483-4496}, issn = {0962-1083}, doi = {10.1111/mec.14224}, author = {Termignoni-Garcia, Flavia and Jaramillo-Correa, Juan P. and Chable-Santos, Juan and Liu, Mark and Shultz, Allison J. and Edwards, Scott V. and Escalante-Pliego, Patricia} } @article { ISI:000399738700034, title = {Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird}, journal = {Ecology and Evolution}, volume = {7}, year = {2017}, month = {APR}, pages = {2370-2381}, issn = {2045-7758}, doi = {10.1002/ece3.2819}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.2819/full}, author = {Tigano, Anna and Shultz, Allison J. and Edwards, Scott V. and Robertson, Gregory J. and Friesen, Vicki L.} } @article {Edwards2017, title = {Conserved Nonexonic Elements : A Novel Class of Marker for Phylogenomics}, journal = {Systematic Biology}, volume = {66}, year = {2017}, pages = {1028{\textendash}1044}, abstract = {Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather
than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and \~{}3600{\textendash}\~{}3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignmentswas superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the
passerine+falcon clade,was resolved differently and with moderate (\>70\%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.}, doi = {10.1093/sysbio/syx058}, url = {https://academic.oup.com/sysbio/article/66/6/1028/3868964/Conserved-Nonexonic-Elements-A-Novel-Class-of}, author = {Edwards, Scott V. and Cloutier, Alison C and Baker, Allan J} } @article { ISI:000406840100036, title = {Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard}, journal = {Science}, volume = {357}, year = {2017}, month = {AUG 4}, pages = {495-497}, abstract = {Extreme environmental perturbations offer opportunities to observe the effects of natural selection in wild populations. During the winter of 2013-2014, the southeastern United States endured an extreme cold event. We used thermal performance, transcriptomics, and genome scans to measure responses of lizard populations to storm-induced selection. We found significant increases in cold tolerance at the species{\textquoteright} southern limit. Gene expression in southern survivors shifted toward patterns characteristic of northern populations. Comparing samples before and after the extreme winter, 14 genomic regions were differentiated in the surviving southern population; four also exhibited signatures of local adaptation across the latitudinal gradient and implicate genes involved in nervous system function. Together, our results suggest that extreme winter events can rapidly produce strong selection on natural populations at multiple biological levels that recapitulate geographic patterns of local adaptation.}, issn = {0036-8075}, doi = {10.1126/science.aam5512}, author = {Campbell-Staton, Shane C. and Cheviron, Zachary A. and Rochette, Nicholas and Catchen, Julian and Jonathan B. Losos and Edwards, Scott V.} } @inbook {961266, title = {Comparative genomics as a foundation for evo-devo studies in birds}, booktitle = {Methods in Molecular Biology: Avian and Reptilian Developmental Biology}, year = {2017}, publisher = {Humana Press}, organization = {Humana Press}, address = {New York}, abstract = {

Developmental genomics is a rapidly growing field and high quality genomes are a useful foundation for comparative developmental studies. A genome streamlines and simplifies the development of primers used to isolate putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, micro RNAs (miRNAs) or short hairpin RNAs(shRNA) forRNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and in recent years, even guide RNAs (gRNAs) for CRISPR knockouts. A high quality genome also forms an essential reference onto which the data from numerous assays and experiments, including ChIPseq, ATAC-seq, and RNA-seq, can be mapped. Finally, much can be gleaned from comparative genomics alone, including identification of highly conserved putative regulatory regions. This chapter provides an overview of laboratory and bioinformatics protocols for DNA extraction, library preparation, library quantification and genome assembly, from fresh or frozen tissue to a draft avian genome. Generating a high quality draft genome can provide a developmental research group with excellent resources for their study organism, opening the doors to many additional assays and experiments.

}, author = {Phil Grayson and Simon Y W Sin and Tim Sackton and Edwards, S. V.} } @article { ISI:000388312300006, title = {Climate-mediated adaptation after mainland colonization of an ancestrally subtropical island lizard, Anolis carolinensis}, journal = {Journal of Evolutionary Biology}, volume = {29}, year = {2016}, month = {NOV}, pages = {2168-2180}, abstract = {Climate-mediated evolution plays an integral role in species migration and range expansion. Gaining a clearer understanding of how climate affects demographic history and adaptation provides fundamental insight into the generation of intra-and interspecific diversity. In this study, we used the natural colonization of the green anole (Anolis carolinensis) from the island of Cuba to mainland North America to investigate the role of evolution at the niche, phenotypic and genetic levels after long-term establishment in a novel environment. The North American green anole occupies a broader range of thermal habitats than its Cuban sister species. We documented niche expansion in the mainland green anole, mediated primarily through adaptation to winter temperatures. Common garden experiments strongly suggest a genetic component to differences in thermal performance found between populations in different temperature regimes. Analysis of geographic variation in population structure based on 53 486 single nucleotide variants from RAD loci revealed increased genetic isolation between populations in different vs. similar thermal environments. Selection scans for environment-allele correlations reveal 19 genomic loci of known function that may have played a role in the physiological adaptation of A. carolinensis to temperate environments on the mainland.}, issn = {1010-061X}, doi = {10.1111/jeb.12935}, author = {Campbell-Staton, S. C. and Edwards, S. V. and Losos, J. B.} } @article {1070871, title = {SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)}, journal = {Ecology and Evolution}, volume = {6}, year = {2016}, pages = {7475{\textendash}7489}, abstract = {Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen-induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre-epizootic western US birds, introduced birds from Hawaii and the eastern United States, post-epizootic eastern birds, and western birds sampled across a similar time span. We found 14\% and 7\% reductions in nucleotide diversity, respectively, in Hawaiian and pre-epizootic eastern birds relative to pre-epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre-epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.2444/abstract}, author = {Shultz, A. J. and Baker, A. J. and Hill, G. E. and Nolan, P. M. and Edwards, S. V.} } @inbook {905731, title = {Inferring species trees}, booktitle = {Encyclopedia of Evolutionary Biology}, volume = {4}, year = {2016}, pages = {236-244}, publisher = {Elsevier Inc.}, organization = {Elsevier Inc.}, address = {New York}, author = {Edwards, S. V.}, editor = {Kliman, R.} } @article {905711, title = {Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics}, journal = {Molecular Phylogenetics and Evolution}, volume = {94}, year = {2016}, pages = {447-462}, abstract = {
In recent articles published in
Molecular Phylogenetics and Evolution
, Mark Springer and John Gatesy (S\&G)
present numerous criticisms of recent implementations and testing of the multispecies coalescent (MSC)
model in phylogenomics, popularly known as {\textquoteleft}{\textquoteleft}species tree{\textquotedblright} methods. After pointing out errors in align-
ments and gene tree rooting in recent phylogenomic data sets, particularly in Song et al. (2012) on mam-
mals and Xi et al. (2014) on plants, they suggest that these errors seriously compromise the conclusions
of these studies. Additionally, S\&G enumerate numerous perceived violated assumptions and deficiencies
in the application of the MSC model in phylogenomics, such as its assumption of neutrality and in par-
ticular the use of transcriptomes, which are deemed inappropriate for the MSC because the constituent
exons often subtend large regions of chromosomes within which recombination is substantial. We
acknowledge these previously reported errors in recent phylogenomic data sets, but disapprove of
S\&G{\textquoteright}s excessively combative and taunting tone. We show that these errors, as well as two nucleotide
sorting methods used in the analysis of
Amborella
, have little impact on the conclusions of those papers.
Moreover, several concepts introduced by S\&G and an appeal to {\textquoteleft}{\textquoteleft}first principles{\textquotedblright} of phylogenetics in an
attempt to discredit MSC models are invalid and reveal numerous misunderstandings of the MSC.
Contrary to the claims of S\&G we show that recent computer simulations used to test the robustness
of MSC models are not circular and do not unfairly favor MSC models over concatenation. In fact, although
both concatenation and MSC models clearly perform well in regions of tree space with long branches and
little incomplete lineage sorting (ILS), simulations reveal the erratic behavior of concatenation when sub-
jected to data subsampling and its tendency to produce spuriously confident yet conflicting results in
regions of parameter space where MSC models still perform well. S\&G{\textquoteright}s claims that MSC models explain
little or none (0{\textendash}15\%) of the observed gene tree heterogeneity observed in a mammal data set and that
MSC models assume ILS as the only source of gene tree variation are flawed. Overall many of their crit-
icisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the
MSC, which in turn is a special case of emerging network models in phylogenomics. We reiterate that
there is enormous promise and value in recent implementations and tests of the MSC and look forward
to its increased use and refinement in phylogenomics.
}, isbn = {1055-7903}, author = {Edwards, Scott V. and Zhenxiang Xi and Axel Janke and Faircloth, Brant C and McCormack, John E and Glenn, Travis C and Bojian Zhong and Shaoyuan Wu and Emily Moriarty Lemmon and Lemmon, Alan R} } @article {905726, title = {Phylogenomic subsampling: a brief review}, journal = {Zoologica Scripta}, volume = {45}, year = {2016}, month = {Oct 2016}, pages = {63-74}, author = {Edwards, S. V.} } @article {905716, title = {Reticulation, divergence, and the phylogeography{\textendash}phylogenetics continuum}, journal = {Proceedings of the National Academy of Sciences}, volume = {113}, number = {29}, year = {2016}, pages = {8025-8032}, publisher = {National Academy of Sciences}, abstract = {
Phylogeography, and its extensions into comparative phylogeogra-
phy, have their roots in the layering of gene trees across geography,
a paradigm that was greatly facilitated by the nonrecombining, fast
evolution provided by animal mtDNA. As phylogeography moves
into the era of next-generation sequencing, the specter of reticula-
tion at several levels
{\textemdash}
within loci and genomes in the form of re-
combination and across populations and species in the form of
introgression
{\textemdash}
has raised its head with a prominence even greater
than glimpsed during the nuclear gene PCR era. Here we explore the
theme of reticulation in comparative phylogeography, speciation
analysis, and phylogenomics, and ask how the centrality of gene
trees has fared in the next-generation era. To frame these issues,
we first provide a snapshot of multilocus phylogeographic studies
across the Carpentarian Barrier, a prominent biogeographic barrier
dividing faunas spanning the monsoon tropics in northern Australia.
We find that divergence across this barrier is evident in most spe-
cies, but is heterogeneous in time and demographic history, often
reflecting the taxonomic distinctness of lineages spanning it. We
then discuss a variety of forces generating reticulate patterns in
phylogeography, including introgression, contact zones, and the
potential selection-driven outliers on next-generation molecular
markers. We emphasize the continued need for demographic models
incorporating reticulation at the level of genomes and populations,
and conclude that gene trees, whether explicit or implicit, should
continue to play a role in the future of phylogeography.
}, author = {Edwards, Scott V. and Potter, Sally and Schmitt, C. Jonathan and Bragg, Jason G. and Moritz, Craig} } @article { ISI:000357951500013, title = {Major Histocompatibility Complex Genes Map to Two Chromosomes in an Evolutionarily Ancient Reptile, the Tuatara Sphenodon punctatus}, journal = {G3-Genes, Genomes, Genetics}, volume = {5}, year = {2015}, month = {JUL 1}, pages = {1439-1451}, publisher = {GENETICS SOCIETY AMERICA}, type = {Article}, address = {9650 ROCKVILLE AVE, BETHESDA, MD 20814 USA}, abstract = {Major histocompatibility complex (MHC) genes are a central component of the vertebrate immune system and usually exist in a single genomic region. However, considerable differences in MHC organization and size exist between different vertebrate lineages. Reptiles occupy a key evolutionary position for understanding how variation in MHC structure evolved in vertebrates, but information on the structure of the MHC region in reptiles is limited. In this study, we investigate the organization and cytogenetic location of MHC genes in the tuatara (Sphenodon punctatus), the sole extant representative of the early-diverging reptilian order Rhynchocephalia. Sequencing and mapping of 12 clones containing class I and II MHC genes from a bacterial artificial chromosome library indicated that the core MHC region is located on chromosome 13q. However, duplication and translocation of MHC genes outside of the core region was evident, because additional class IMHC genes were located on chromosome 4p. We found a total of seven class I sequences and 11 class II beta sequences, with evidence for duplication and pseudogenization of genes within the tuatara lineage. The tuatara MHC is characterized by high repeat content and low gene density compared with other species and we found no antigen processing or MHC framework genes on the MHC gene-containing clones. Our findings indicate substantial differences in MHC organization in tuatara compared with mammalian and avian MHCs and highlight the dynamic nature of the MHC. Further sequencing and annotation of tuatara and other reptile MHCs will determine if the tuatara MHC is representative of nonavian reptiles in general.}, keywords = {comparative genomics, MHC class I, MHC class II, reptilia}, issn = {2160-1836}, doi = {10.1534/g3.115.017467}, author = {Miller, Hilary C. and O{\textquoteright}Meally, Denis and Ezaz, Tariq and Amemiya, Chris and Marshall-Graves, Jennifer A. and Edwards, Scott} } @article {905741, title = {Comment on {\textquotedblleft}Statistical binning enables an accurate coalescent-based estimation of the avian tree{\textquotedblright}}, journal = {Science}, volume = {350}, number = {6257}, year = {2015}, month = {October 9, 2015}, pages = {171}, abstract = {

Mirarab et al. (Research Article, 12 December 2014, p. 1250463) introduced statistical binning to improve the signal in phylogenetic methods using the multispecies coalescent model. We show that all forms of binning{\textemdash}na{\"\i}ve, statistical, and weighted statistical{\textemdash}display poor performance and are statistically inconsistent in large regions of parameter space, unlike unbinned sequence data used with species tree methods.

}, author = {Liu, Liang and Edwards, Scott V.} } @article {905736, title = {Estimating phylogenetic trees from genome-scale data}, journal = {Annals of the New York Academy of Sciences}, volume = {1360}, year = {2015}, pages = {36{\textendash}53}, abstract = {

The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as {\textquotedblleft}species tree{\textquotedblright} methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data.

}, keywords = {anomaly zone, bias{\textendash}variance dilemma, isochore, recombination, Transcriptome}, isbn = {1749-6632}, author = {Liu, Liang and Zhenxiang Xi and Shaoyuan Wu and Charles C. Davis and Edwards, Scott V.} } @article {905751, title = {Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation}, journal = {Evolutionary Applications}, volume = {8}, number = {7}, year = {2015}, note = {

Cn1ffTimes Cited:1Cited References Count:100

}, month = {Aug}, pages = {662-678}, abstract = {

Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions. Despite multiple studies, the taxonomic status and extent of gene flow between the main breeding populations of Black-footed Albatross (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still controversial. Here, we employ double digest RADseq to quantify the extent of genomewide divergence and gene flow in this species. Our genomewide data set of 9760 loci containing 3455 single nucleotide polymorphisms yielded estimates of genetic diversity and gene flow that were generally robust across seven different filtering and sampling protocols and suggest a low level of genomic variation ( per site=similar to 0.00002-0.00028), with estimates of effective population size (N-e=similar to 500-15881) falling far below current census size. Genetic differentiation was small but detectable between Japan and Hawaii (F-ST approximate to 0.038 0.049), with no F-ST outliers. Additionally, using museum specimens, we found that effect sizes of morphological differences by sex or population rarely exceeded 4\%. These patterns suggest that the Hawaiian and Japanese populations exhibit small but significant differences and should be considered separate management units, although the evolutionary and adaptive consequences of this differentiation remain to be identified.

}, keywords = {atlantic salmon, avian phylogeography, black-footed albatross, colonization history, conservation genomics, double digest radseq, Gene Flow, genetic diversity, hybrid zone, integrative taxonomy, izu-torishima, microsatellite markers, midway island, mitochondrial-DNA, phoebastria nigripes, population differentiation, population-structure, snp discovery, subspecies, white-capped albatrosses}, isbn = {1752-4571}, author = {Dierickx, E. G. and Shultz, A. J. and Sato, F. and Hiraoka, T. and Edwards, S. V.} } @article {905746, title = {Next-generation sequencing and the expanding domain of phylogeography}, journal = {Folia Zoologica}, volume = {64}, number = {3}, year = {2015}, pages = {187-206}, abstract = {

Phylogeography is experiencing a revolution brought on by next-generation sequencing methods. A historical survey of the
phylogeographic literature suggests that phylogeography typically incorporates new questions, expanding on its classical domain, when new
technologies offer novel or increased numbers of molecular markers. A variety of methods for subsampling genomic variation, including
restriction site associated DNA sequencing (Rad-seq) and other next generation approaches, are proving exceptionally useful in helping
to define major phylogeographic lineages within species as well as details of historical demography. Next-generation methods are also
blurring the edges of phylogeography and related fields such as association mapping of loci under selection, and the emerging paradigm
is one of simultaneously inferring both population history across geography and genomic targets of selection. However, recent examples,
including some from our lab on Anolis lizards and songbirds, suggest that genome subsampling methods, while extremely powerful for the
classical goals of phylogeography, may fail to allow phylogeography to fully achieve the goals of this new, expanded domain. Specifically,
if genome-wide linkage disequilibrium is low, as is the case in many species with large population sizes, most genome subsampling
methods will not sample densely enough to detect selected variants, or variants closely linked to them. We suggest that whole-genome
resequencing methods will be essential for allowing phylogeographers to robustly identify loci involved in phenotypic divergence and
speciation, while at the same time allowing free choice of molecular markers and further resolution of the demographic history of species.

}, keywords = {association mapping, bird, demographic history, genotype-by-sequencing, natural selection, rad-seq}, isbn = {0139-7893}, author = {Edwards, Scott V. and Schultz, Allison and Campbell-Staton, Shane} } @article {905756, title = {Physical Mapping and Refinement of the Painted Turtle Genome ( Chrysemys picta ) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation}, journal = {Genome Biology and Evolution}, volume = {7}, number = {7}, year = {2015}, pages = {2038-2050}, abstract = {
Comparative genomics continues illuminating amniote genome evolution, but for man
y lineages our understanding remains incom-plete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemyspicta{\textemdash}CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochro-mosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully
conserved macrochromosomes for greater than 300 Myr. C-banding re
vealed large heterochromatic blocks in the centromeric region
of only few chromosomes. The nucleolar-org
anizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles
and lizards the NOR maps to nonhomologous sex-chromosomes, t
hus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromere s of five chromosomes, whereas others were widespread in the CPI
genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five ch romosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the inde-pendent evolution of vertebrate sex-determining mechanisms.
}, keywords = {chicken, chromosomal rearrangements, clone mapping, Evolution, genome and chromosome, genotypic sex determination, Human, nonmodel vertebrates, physical molecular cytogenetic bac, temperature-dependent and, translocations and inversions, turtles}, author = {Badenhorst, Daleen and Hillier, LaDeana W. and Literman, Robert and Montiel, Eugenia Elisabet and Radhakrishnan, Srihari and Shen, Yingjia and Minx, Patrick and Janes, Daniel E. and Warren, Wesley C. and Edwards, Scott V. and Valenzuela, Nicole} } @article {RN126, title = {Feather Development Genes and Associated Regulatory Innovation Predate the Origin of Dinosauria}, journal = {Molecular Biology and Evolution}, volume = {32}, year = {2015}, pages = {23-28}, type = {Journal Article}, abstract = {
The evolution of avian feathers have recently been illuminated by fossils and the
identification of genes involved in feather patterning and morphogenesis.
However, molecular studies have focused mainly on protein-coding genes.
Using comparative genomics and more than 600,000 conserved regulatory
elements, we show that patterns of genome evolution in the vicinity of feather genes
are consistent with a major role for regulatory innovation in the evolution of feathers. Rates
of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86\% of such regulatory elements were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near IGFB P2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.
}, issn = {0737-4038}, doi = {10.1093/molbev/msu309}, url = {://WOS:000350050200003}, author = {Lowe, Craig B. and Clarke, Julia A. and Baker, Allan J. and Haussler, David and Edwards, Scott V.} } @article {RN125, title = {Plumage color and pathogen-induced gene expression in a wild bird}, journal = {Behavioral Ecology}, volume = {26}, year = {2015}, pages = {1100-1110}, type = {Journal Article}, issn = {1045-2249}, doi = {10.1093/beheco/arv055}, url = {https://www.researchgate.net/profile/Susan_Balenger/publication/275968599_Plumage_color_and_pathogen-induced_gene_expression_in_a_wild_bird/links/555b469008ae8f66f3ad52b3.pdf}, author = {Balenger, Susan L. and Bonneaud, Camille and Sefick, Stephen A. and Edwards, Scott V. and Hill, Geoffrey E.} } @article {905766, title = {Comparative genomics reveals insights into avian genome evolution and adaptation}, journal = {Science}, volume = {346}, number = {6215}, year = {2014}, note = {

Aw3maTimes Cited:9Cited References Count:90

}, month = {Dec 12}, pages = {1311-1320}, abstract = {

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

}, keywords = {Birds, diversity, functional diversification, Gene Duplication, intron size, Mammals, mutation-rate, rapid evolution, transposable elements, vertebrate}, isbn = {0036-8075}, author = {Zhang, G. J. and Li, C. and Li, Q. Y. and Li, B. and Larkin, D. M. and Lee, C. and Storz, J. F. and Antunes, A. and Greenwold, M. J. and Meredith, R. W. and Odeen, A. and Cui, J. and Zhou, Q. and Xu, L. H. and Pan, H. L. and Wang, Z. J. and Jin, L. J. and Zhang, P. and Hu, H. F. and Yang, W. and Hu, J. and Xiao, J. and Yang, Z. K. and Liu, Y. and Xie, Q. L. and Yu, H. and Lian, J. M. and Wen, P. and Zhang, F. and Li, H. and Zeng, Y. L. and Xiong, Z. J. and Liu, S. P. and Zhou, L. and Huang, Z. Y. and An, N. and J. Wang and Zheng, Q. M. and Xiong, Y. Q. and Wang, G. B. and Wang, B. and Wang, J. J. and Fan, Y. and da Fonseca, R. R. and Alfaro-Nunez, A. and Schubert, M. and Orlando, L. and Mourier, T. and Howard, J. T. and Ganapathy, G. and Pfenning, A. and Whitney, O. and Rivas, M. V. and Hara, E. and Smith, J. and Farre, M. and Narayan, J. and Slavov, G. and Romanov, M. N. and Borges, R. and Machado, J. P. and Khan, I. and Springer, M. S. and Gatesy, J. and Hoffmann, F. G. and Opazo, J. C. and Hastad, O. and Sawyer, R. H. and Kim, H. and Kim, K. W. and Kim, H. J. and Cho, S. and Li, N. and Huang, Y. H. and Bruford, M. W. and Zhan, X. J. and Dixon, A. and Bertelsen, M. F. and Derryberry, E. and Warren, W. and Wilson, R. K. and Li, S. B. and Ray, D. A. and Green, R. E. and O{\textquoteright}Brien, S. J. and Griffin, D. and Johnson, W. E. and Haussler, D. and Ryder, O. A. and Willerslev, E. and Graves, G. R. and Alstrom, P. and Fjeldsa, J. and Mindell, D. P. and Edwards, S. V. and Braun, E. L. and Rahbek, C. and Burt, D. W. and Houde, P. and Zhang, Y. and Yang, H. M. and J. Wang and Jarvis, E. D. and Gilbert, M. T. P. and J. Wang and Avian Genome Consortium} } @article {905771, title = {The Evolution of Bipedalism in Jerboas (Rodentia: Dipodoidea): Origin in Humid and Forested Environments}, journal = {Evolution}, volume = {68}, number = {7}, year = {2014}, note = {

Al3tkTimes Cited:0Cited References Count:67

}, month = {Jul}, pages = {2108-2118}, abstract = {

Mammalian bipedalism has long been thought to have arisen in response to arid and open environments. Here, we tested whether bipedalism coevolved with environmental changes using molecular and paleontological data from the rodent superfamily Dipodoidea and statistical methods for reconstructing ancestral characteristics and past climates. Our results show that the post-Late Miocene aridification exerted selective pressures on tooth shape, but not on leg length of bipedal jerboas. Cheek tooth crown height has increased since the Late Miocene, but the hind limb/head-body length ratios remained stable and high despite the environmental change from humid and forested to arid and open conditions, rather than increasing from low to high as predicted by the arid-bipedalism hypothesis. The decoupling of locomotor and dental character evolution indicates that bipedalism evolved under selective pressure different from that of dental hypsodonty in jerboas. We reconstructed the habitats of early jerboas using floral and faunal data, and the results show that the environments in which bipedalism evolved were forested. Our results suggest that bipedalism evolved as an adaptation to humid woodlands or forests for vertical jumping. Running at high speeds is likely a by-product of selection for jumping, which became advantageous in open environments later on.

}, keywords = {adaptation, aridification, bipedalism, Climate, convergent function, decoupled evolution, humid environments, late neogene, locomotion, Mammals, Miocene, north china, patterns, plant fossils, quantitative reconstructions}, isbn = {0014-3820}, author = {Wu, S. Y. and Zhang, F. C. and Edwards, S. V. and Wu, W. Y. and Ye, J. and Bi, S. D. and Ni, X. J. and Quan, C. and Meng, J. and Organ, C. L.} } @article {905781, title = {Feather development genes and associated regulatory innovation predate the origin of Dinosauria}, journal = {Molecular Biology and Evolution}, volume = {32}, number = {1}, year = {2014}, pages = {23-28}, abstract = {
The evolution of avian feathers has recently been illumin
ated by fossils and the identification of genes involved in
feather patterning and morphogenesis. However, molecula
r studies have focused mainly on protein-coding genes.
Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86\% of such regulatory elements and 100\% of the nonkeratin feather gene set were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near insulin-like growth factor binding protein (IGFBP) 2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.
}, keywords = {2003, 2011, 2012, Body Size, comparative genomics, dermis and epidermis, dinosaur, enhancer, feathers constitute complex-branched structures, gene regulation, Integument, li et al, mou et al, ng et al, that arise, through interactions between the, widelitz et al}, author = {Lowe, Craig B. and Clarke, Julia A. and Baker, Allan J. and Haussler, David and Edwards, Scott V.} } @article {905761, title = {A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines}, journal = {Bmc Genomics}, volume = {15}, number = {1}, year = {2014}, pages = {305-305}, abstract = {

BACKGROUND: With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions. As part of our ongoing efforts to make available genomic resources for this species, here we report a transcriptome assembly derived from genes expressed in spleen. RESULTS: We characterize transcriptomes from two populations with different histories of demography and disease exposure: a recently founded population in the eastern US that has been exposed to MG for over a decade and a native population from the western range that has never been exposed to MG. We utilize this resource to quantify conservation in gene expression in passerine birds over approximately 50 MY by comparing splenic expression profiles for 9,646 house finch transcripts and those from zebra finch and find that less than half of all genes expressed in spleen in either species are expressed in both species. Comparative gene annotations from several vertebrate species suggest that the house finch transcriptomes contain ~15 genes not yet found in previously sequenced vertebrate genomes. The house finch transcriptomes harbour ~85,000 SNPs, ~20,000 of which are non-synonymous. Although not yet validated by biological or technical replication, we identify a set of genes exhibiting differences between populations in gene expression (n = 182; 2\% of all transcripts), allele frequencies (76 FST ouliers) and alternative splicing as well as genes with several fixed non-synonymous substitutions; this set includes genes with functions related to double-strand break repair and immune response. CONCLUSIONS: The two house finch spleen transcriptome profiles will add to the increasing data on genome and transcriptome sequence information from natural populations. Differences in splenic expression between house finch and zebra finch imply either significant evolutionary turnover of splenic expression patterns or different physiological states of the individuals examined. The transcriptome resource will enhance the potential to annotate an eventual house finch genome, and the set of gene-based high-quality SNPs will help clarify the genetic underpinnings of host-pathogen interactions and sexual selection.

}, author = {Zhang, Qu and Hill, Geoffrey E. and Edwards, Scott V. and Backstr{\"o}m, Niclas} } @article {905791, title = {Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia}, journal = {Biology Letters}, volume = {10}, number = {12}, year = {2014}, note = {

Janes, Daniel EOrgan, Christopher LStiglec, RamiO{\textquoteright}Meally, DenisSarre, Stephen DGeorges, ArthurGraves, Jennifer A MValenzuela, NicoleLiterman, Robert ARutherford, KimGemmell, NeilIverson, John BTamplin, Jeffrey WEdwards, Scott VEzaz, TariqengEngland2014/12/30 06:00Biol Lett. 2014 Dec;10(12). pii: 20140809. doi: 10.1098/rsbl.2014.0809.

}, month = {Dec}, abstract = {

In reptiles, sex-determining mechanisms have evolved repeatedly and reversibly between genotypic and temperature-dependent sex determination. The gene Dmrt1 directs male determination in chicken (and presumably other birds), and regulates sex differentiation in animals as distantly related as fruit flies, nematodes and humans. Here, we show a consistent molecular difference in Dmrt1 between reptiles with genotypic and temperature-dependent sex determination. Among 34 non-avian reptiles, a convergently evolved pair of amino acids encoded by sequence within exon 2 near the DM-binding domain of Dmrt1 distinguishes species with either type of sex determination. We suggest that this amino acid shift accompanied the evolution of genotypic sex determination from an ancestral condition of temperature-dependent sex determination at least three times among reptiles, as evident in turtles, birds and squamates. This novel hypothesis describes the evolution of sex-determining mechanisms as turnover events accompanied by one or two small mutations.

}, isbn = {1744-957X (Electronic)1744-9561 (Linking)}, author = {Janes, D. E. and Organ, C. L. and Stiglec, R. and O{\textquoteright}Meally, D. and Sarre, S. D. and Georges, A. and Graves, J. A. and Valenzuela, N. and Literman, R. A. and Rutherford, K. and Gemmell, N. and Iverson, J. B. and Tamplin, J. W. and Edwards, S. V. and Ezaz, T.} } @article {905801, title = {Natural History Collections as Emerging Resources for Innovative Education}, journal = {Bioscience}, volume = {64}, number = {8}, year = {2014}, note = {

Cook, Joseph A. Edwards, Scott V. Lacey, Eileen A. Guralnick, Robert P. Soltis, Pamela S. Soltis, Douglas E. Welch, Corey K. Bell, Kayce C. Galbreath, Kurt E. Himes, Christopher Allen, Julie M. Heath, Tracy A. Carnaval, Ana C. Cooper, Kimberly L. Liu, Mark Hanken, James Ickert-Bond, Stefanie

}, month = {Aug}, pages = {725-734}, abstract = {

There is an emerging consensus that undergraduate biology education in the United States is at a crucial juncture, especially as we acknowledge the need to train a new generation of scientists to meet looming environmental and health crises. Digital resources for biology now available online provide an opportunity to transform biology curricula to include more authentic and inquiry-driven educational experiences. Digitized natural history collections have become tremendous assets for research in environmental and health sciences, but, to date, these data remain largely untapped by educators. Natural history collections have the potential to help transform undergraduate science education from passive learning into an active exploration of the natural world, including the exploration of the complex relationships among environmental conditions, biodiversity, and human well-being. By incorporating natural history specimens and their associated data into undergraduate curricula, educators can promote participatory learning and foster an understanding of essential interactions between organisms and their environments.

}, isbn = {0006-3568}, author = {Cook, J. A. and Edwards, S. V. and Lacey, E. A. and Guralnick, R. P. and Soltis, P. S. and Soltis, D. E. and Welch, C. K. and Bell, K. C. and Galbreath, K. E. and Himes, C. and Allen, J. M. and Heath, T. A. and Carnaval, A. C. and Cooper, K. L. and Liu, M. and Hanken, J. and Ickert-Bond, S.} } @article {905776, title = {Parallel Evolution of Tetrodotoxin Resistance in Three Voltage-Gated Sodium Channel Genes in the Garter Snake Thamnophis sirtalis}, journal = {Molecular Biology and Evolution}, year = {2014}, month = {August 18, 2014}, abstract = {

Members of a gene family expressed in a single species often experience common selection pressures. Consequently, the molecular basis of complex adaptations may be expected to involve parallel evolutionary changes in multiple paralogs. Here, we use bacterial artificial chromosome library scans to investigate the evolution of the voltage-gated sodium channel (Nav) family in the garter snake Thamnophis sirtalis, a predator of highly toxic Taricha newts. Newts possess tetrodotoxin (TTX), which blocks Nav{\textquoteright}s, arresting action potentials in nerves and muscle. Some Thamnophis populations have evolved resistance to extremely high levels of TTX. Previous work has identified amino acid sites in the skeletal muscle sodium channel Nav1.4 that confer resistance to TTX and vary across populations. We identify parallel evolution of TTX resistance in two additional Nav paralogs, Nav1.6 and 1.7, which are known to be expressed in the peripheral nervous system and should thus be exposed to ingested TTX. Each paralog contains at least one TTX-resistant substitution identical to a substitution previously identified in Nav1.4. These sites are fixed across populations, suggesting that the resistant peripheral nerves antedate resistant muscle. In contrast, three sodium channels expressed solely in the central nervous system (Nav1.1{\textendash}1.3) showed no evidence of TTX resistance, consistent with protection from toxins by the blood{\textendash}brain barrier. We also report the exon{\textendash}intron structure of six Nav paralogs, the first such analysis for snake genes. Our results demonstrate that the molecular basis of adaptation may be both repeatable across members of a gene family and predictable based on functional considerations.

}, author = {McGlothlin, Joel W. and Chuckalovcak, John P. and Janes, Daniel E. and Edwards, Scott V. and Feldman, Chris R. and Brodie, Edmund D. and Pfrender, Michael E. and Brodie, Edmund D.} } @article {905806, title = {Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor}, journal = {Science (New York, N.Y.)}, volume = {345}, number = {6199}, year = {2014}, pages = {929-33}, abstract = {

Sensory systems define an animal{\textquoteright}s capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies revealed that the ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in hummingbirds to function as a carbohydrate receptor. Furthermore, the molecular recognition properties of T1R1-T1R3 guided taste behavior in captive and wild hummingbirds. We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar, facilitating the massive radiation of hummingbird species.

}, author = {Baldwin, Maude W. and Toda, Yasuka and Nakagita, Tomoya and O{\textquoteright}Connell, Mary J. and Klasing, Kirk C. and Misaka, Takumi and Edwards, Scott V. and Liberles, Stephen D.} } @article {905796, title = {Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs}, journal = {Science}, volume = {346}, number = {6215}, year = {2014}, note = {

Aw3maTimes Cited:2Cited References Count:82

}, month = {Dec 12}, pages = {1335-+}, abstract = {

To provide context for the diversification of archosaurs-the group that includes crocodilians, dinosaurs, and birds-we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

}, keywords = {alignment, Birds, body-size, divergence times, maximum-likelihood, molecular clock, scale phylogenetic analyses, sister group, species-tree, ultraconserved elements}, isbn = {0036-8075}, author = {Green, R. E. and Braun, E. L. and Armstrong, J. and Earl, D. and Nguyen, N. and Hickey, G. and Vandewege, M. W. and St John, J. A. and Capella-Gutierrez, S. and Castoe, T. A. and Kern, C. and Fujita, M. K. and Opazo, J. C. and Jurka, J. and Kojima, K. K. and Caballero, J. and Hubley, R. M. and Smit, A. F. and Platt, R. N. and Lavoie, C. A. and Ramakodi, M. P. and Finger, J. W. and Suh, A. and Isberg, S. R. and Miles, L. and Chong, A. Y. and Jaratlerdsiri, W. and Gongora, J. and Moran, C. and Iriarte, A. and McCormack, J. and Burgess, S. C. and Edwards, S. V. and Lyons, E. and Williams, C. and Breen, M. and Howard, J. T. and Gresham, C. R. and Peterson, D. G. and Schmitz, J. and Pollock, D.D. and Haussler, D. and Triplett, E. W. and Zhang, G. and Irie, N. and Jarvis, E. D. and Brochu, C. A. and Schmidt, C. J. and McCarthy, F. M. and Faircloth, B. C. and Hoffmann, F. G. and Glenn, T. C. and Gabaldoon, T. and Paten, B. and Ray, D. A.} } @article {905786, title = {Whole-genome analyses resolve early branches in the tree of life of modern birds}, journal = {Science}, volume = {346}, number = {6215}, year = {2014}, note = {

Aw3maTimes Cited:11Cited References Count:101

}, month = {Dec 12}, pages = {1320-1331}, abstract = {

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

}, keywords = {biased gene conversion, coalescent model, cretaceous origin, fossil record, mass extinction, parallel radiations, passerine birds, phylogenetic trees, sequence alignments, species trees}, isbn = {0036-8075}, author = {Jarvis, E. D. and Mirarab, S. and Aberer, A. J. and Li, B. and Houde, P. and Li, C. and Ho, S. Y. W. and Faircloth, B. C. and Nabholz, B. and Howard, J. T. and Suh, A. and Weber, C. C. and da Fonseca, R. R. and Li, J. W. and Zhang, F. and Li, H. and Zhou, L. and Narula, N. and Liu, L. and Ganapathy, G. and Boussau, B. and Bayzid, M. S. and Zavidovych, V. and Subramanian, S. and Gabaldon, T. and Capella-Gutierrez, S. and Huerta-Cepas, J. and Rekepalli, B. and Munch, K. and Schierup, M. and Lindow, B. and Warren, W. C. and Ray, D. and Green, R. E. and Bruford, M. W. and Zhan, X. J. and Dixon, A. and Li, S. B. and Li, N. and Huang, Y. H. and Derryberry, E. P. and Bertelsen, M. F. and Sheldon, F. H. and Brumfield, R. T. and Mello, C. V. and Lovell, P. V. and Wirthlin, M. and Schneider, M. P. C. and Prosdocimi, F. and Samaniego, J. A. and Velazquez, A. M. V. and Alfaro-Nunez, A. and Campos, P. F. and Petersen, B. and Sicheritz-Ponten, T. and Pas, A. and Bailey, T. and Scofield, P. and Bunce, M. and Lambert, D. M. and Zhou, Q. and Perelman, P. and Driskell, A. C. and Shapiro, B. and Xiong, Z. J. and Zeng, Y. L. and Liu, S. P. and Li, Z. Y. and Liu, B. H. and Wu, K. and Xiao, J. and Yinqi, X. and Zheng, Q. M. and Zhang, Y. and Yang, H. M. and J. Wang and Smeds, L. and Rheindt, F. E. and Braun, M. and Fjeldsa, J. and Orlando, L. and Barker, F. K. and Jonsson, K. A. and Johnson, W. and Koepfli, K. P. and O{\textquoteright}Brien, S. and Haussler, D. and Ryder, O. A. and Rahbek, C. and Willerslev, E. and Graves, G. R. and Glenn, T. C. and McCormack, J. and Burt, D. and Ellegren, H. and Alstrom, P. and Edwards, S. V. and Stamatakis, A. and Mindell, D. P. and Cracraft, J. and Braun, E. L. and Warnow, T. and Jun, W. and Gilbert, M. T. P. and Zhang, G. J.} } @article {905841, title = {Frequent Coinfection Reduces RNA Virus Population Genetic Diversity}, journal = {Journal of Heredity}, volume = {104}, number = {5}, year = {2013}, pages = {704-712}, abstract = {
The masking of deleterious mutations by complementation and the reassortment of virus segments (virus sex) are expected
to increase population genetic diversity among coinfecting viruses. Conversely, clonally reproducing or noncoinfecting virus
populations may experience clonal interference where viral clones compete with one another, preventing selective sweeps.
This dynamic reduces the efficiency of selection and increases the genetic diversity. To determine the relative influences of
these forces on population genetic diversity, we evolved 6 populations of bacteriophage φ6 under conditions promoting
or preventing coinfection. Following 300 generations, we isolated and partially sequenced 10 clones from each population.
We found greater diversity among asexual populations than sexual populations. Moreover, sexual populations did not show greater relative fitnesses than asexual populations, implying that reduced genetic variation did not result from purifying selection. However, sexual populations were less genetically robust than asexual populations and likely more prone to the deleterious epistatic effects of mutations. As such, a neutral mutation on the asexually evolved (robust) background could be profoundly deleterious on the sexually evolved (brittle) background. This could facilitate sexual populations undergoing greater purifying selection to remove deleterious mutations, but this selection is not reflected by increases in average population fitness. Our results bolster a growing literature suggesting that RNA virus segmentation is probably not a mechanism that evolved because it provides a generalized benefit of sex.
}, isbn = {0022-1503}, author = {Dennehy, John J and Duffy, Siobain and O{\textquoteright}Keefe, Kara J and Edwards, Scott V. and Turner, Paul E} } @article {905816, title = {New Frontiers for Organismal Biology}, journal = {Bioscience}, volume = {63}, number = {6}, year = {2013}, note = {

168YDTimes Cited:0Cited References Count:68

}, month = {Jun}, pages = {464-471}, abstract = {

Understanding how complex organisms function as integrated units that constantly interact with their environment is a long-standing challenge in biology. To address this challenge, organismal biology reveals general organizing principles of physiological systems and behavior-in particular, in complex multicellular animals. Organismal biology also focuses on the role of individual variability in the evolutionary maintenance of diversity. To broadly advance these frontiers, cross-compatibility of experimental designs, methodological approaches, and data interpretation pipelines represents a key prerequisite. It is now possible to rapidly and systematically analyze complete genomes to elucidate genetic variation associated with traits and conditions that define individuals, populations, and species. However, genetic variation alone does not explain the varied individual physiology and behavior of complex organisms. We propose that such emergent properties of complex organisms can best be explained through a renewed emphasis on the context and life-history dependence of individual phenotypes to complement genetic data.

}, keywords = {Behavior, climate-change, developmental plasticity, Ecology, Environment, Evolution, Gene-Environment Interaction, individuality, integrative-biology, life history, molecular-biology, Phenotype, proteomics, Systems Biology}, isbn = {0006-3568}, author = {Kultz, D. and Clayton, D. F. and Robinson, G. E. and Albertson, C. and Carey, H. V. and Cummings, M. E. and Dewar, K. and Edwards, S. V. and Hofmann, H. A. and Gross, L. J. and Kingsolver, J. G. and Meaney, M. J. and Schlinger, B. A. and Shingleton, A. W. and Sokolowski, M. B. and Somero, G. N. and Stanzione, D. C. and Todgham, A. E.} } @article {905831, title = {Next-generation QTL mapping: crowdsourcing SNPs, without pedigrees}, journal = {Molecular Ecology}, volume = {22}, number = {15}, year = {2013}, pages = {3885-3887}, abstract = {

For many molecular ecologists, the mantra and mission
of the field of ecological genomics could be encapsulated
by the phrase {\textquoteleft}to find the genes that matter{\textquoteright} (Mitchell-
Olds 2001; Rockman 2012). This phrase of course refers to
the early hope and current increasing success in the
search for genes whose variation underlies phenotypic
variation and fitness in natural populations. In the years
since the modern incarnation of the field of ecological
genomics, many would agree that the low-hanging fruit
has, at least in principle, been plucked: we now have several
elegant examples of genes whose variation influences
key adaptive traits in natural populations, and these
examples have revealed important insights into the architecture
of adaptive variation (Hoekstra et al. 2006; Shapiro
et al. 2009; Chan et al. 2010). But how well will these
early examples, often involving single genes of large
effect on discrete or near-discrete phenotypes, represent
the dynamics of adaptive change for the totality of
phenotypes in nature? Will traits exhibiting continuous
rather than discrete variation in natural populations have
as simple a genetic basis as these early examples suggest
(Prasad et al. 2012; Rockman 2012)? Two papers in this
issue (Robinson et al. 2013; Santure et al. 2013) not only
suggest answers to these questions but also provide
useful extensions of statistical approaches for ecological
geneticists to study the genetics of continuous variation
in nature. Together these papers, by the same research
groups studying evolution in a natural population of
Great Tits (Parus major), provide a glimpse of what we
should expect as the field begins to dissect the genetic
basis of what is arguably the most common type of
variation in nature, and how genome-wide surveys of
variation can be applied to natural populations without
pedigrees.

}, author = {Edwards, Scott V.} } @article {905811, title = {Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {13}, year = {2013}, note = {

Wu, ShaoyuanSong, SenLiu, LiangEdwards, Scott VProc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1180.

}, month = {Mar 26}, pages = {E1180}, type = {CommentLetterResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.}, edition = {2013/05/08}, keywords = {*Evolution, Molecular, *Models, Genetic, *Phylogeny, Animals, Classification/*methods, Mammals/*genetics}, isbn = {1091-6490 (Electronic)0027-8424 (Linking)}, author = {Wu, S. and Song, S. and Liu, L. and Edwards, S. V.} } @article {905826, title = {Sequence and gene content of a large fragment of a lizard sex chromosome and evaluation of candidate sex differentiating gene R-spondin 1}, journal = {Bmc Genomics}, volume = {14}, number = {1}, year = {2013}, pages = {899-899}, abstract = {

BACKGROUND: Scant genomic information from non-avian reptile sex chromosomes is available, and for only a few lizards, several snakes and one turtle species, and it represents only a small fraction of the total sex chromosome sequences in these species. RESULTS: We report a 352\ kb of contiguous sequence from the sex chromosome of a squamate reptile, Pogona vitticeps, with a ZZ/ZW sex microchromosome system. This contig contains five protein coding genes (oprd1, rcc1, znf91, znf131, znf180), and major families of repetitive sequences with a high number of copies of LTR and non-LTR retrotransposons, including the CR1 and Bov-B LINEs. The two genes, oprd1 and rcc1 are part of a homologous syntenic block, which is conserved among amniotes. While oprd1 and rcc1 have no known function in sex determination or differentiation in amniotes, this homologous syntenic block in mammals and chicken also contains R-spondin 1 (rspo1), the ovarian differentiating gene in mammals. In order to explore the probability that rspo1 is sex determining in dragon lizards, genomic BAC and cDNA clones were mapped using fluorescence in situ hybridisation. Their location on an autosomal microchromosome pair, not on the ZW sex microchromosomes, eliminates rspo1 as a candidate sex determining gene in P. vitticeps. CONCLUSION: Our study has characterized the largest contiguous stretch of physically mapped sex chromosome sequence (352\ kb) from a ZZ/ZW lizard species. Although this region represents only a small fraction of the sex chromosomes of P. vitticeps, it has revealed several features typically associated with sex chromosomes including the accumulation of large blocks of repetitive sequences.

}, author = {Ezaz, Tariq and Azad, Bhumika and O{\textquoteright}Meally, Denis and Young, Matthew J. and Matsubara, Kazumi and Edwards, Melanie J. and Zhang, Xiuwen and Holleley, Clare E. and Deakin, Janine E. and Marshall Graves, Jennifer A. and Georges, Arthur and Edwards, Scott V. and Sarre, Stephen D.} } @article {905821, title = {Sex-Biased Expression of Sex-Differentiating Genes FOXL2 and FGF9 in American Alligators, Alligator mississippiensis}, journal = {Sexual Development}, year = {2013}, abstract = {

Across amniotes, sex-determining mechanisms exhibit great variation, yet the genes that govern sexual differentiation are largely conserved. Studies of evolution of sex-determining and sex-differentiating genes require an exhaustive characterization of functions of those genes such as FOXL2 and FGF9. FOXL2 is associated with ovarian development, and FGF9 is known to play a role in testicular organogenesis in mammals and other amniotes. As a step toward characterization of the evolutionary history of sexual development, we measured expression of FOXL2 and FGF9 across 3 developmental stages and 8 juvenile tissue types in male and female American alligators, Alligator mississippiensis. We report surprisingly high expression of FOXL2 before the stage of embryonic development when sex is determined in response to temperature, and sustained and variable expression of FGF9 in juvenile male, but not female tissue types. Novel characterization of gene expression in reptiles with temperature-dependent sex determination such as American alligators may inform the evolution of sex-determining and sex-differentiating gene networks, as they suggest alternative functions from which the genes may have been exapted. Future functional profiling of sex-differentiating genes should similarly follow other genes and other species to enable a broad comparison across sex-determining mechanisms.

}, isbn = {1661-5433}, author = {Janes, D. E. and Elsey, R. M. and Langan, EM and Valenzuela, N and SV Edwards} } @article {905846, title = {The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage}, journal = {Genome Biology}, volume = {14}, number = {3}, year = {2013}, pages = {R28}, abstract = {

BACKGROUND:We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species{\textquoteright} physiological capacities to withstand extreme anoxia and tissue freezing.RESULTS:Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented.CONCLUSIONS:Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle{\textquoteright}s extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

}, isbn = {1465-6906}, author = {Bradley Shaffer, H and Minx, Patrick and Warren, Daniel and Shedlock, Andrew and Thomson, Robert and Valenzuela, Nicole and Abramyan, John and Amemiya, Chris and Badenhorst, Daleen and Biggar, Kyle and Borchert, Glen and Botka, Christopher and Bowden, Rachel and Braun, Edward and Bronikowski, Anne and Bruneau, Benoit and Buck, Leslie and Capel, Blanche and Castoe, Todd and Czerwinski, Mike and Delehaunty, Kim and Edwards, Scott and Fronick, Catrina and Fujita, Matthew and Fulton, Lucinda and Graves, Tina and Green, Richard and Haerty, Wilfried and Hariharan, Ramkumar and Hernandez, Omar} } @article {RN131, title = {Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus)}, journal = {Ecology and Evolution}, volume = {3}, year = {2013}, pages = {655-666}, type = {Journal Article}, abstract = {
Characterization of the genetic basis of fitness traits in natural populations is
important for understanding how organisms adapt to the changing environ-
ment and to novel events, such as epizootics. However, candidate fitness-
influencing loci, such as regulatory regions, are usually unavailable in nonmodel
species. Here, we analyze sequence data from targeted resequencing of the cis-
regulatory regions of three candidate genes for disease resistance (CD74,
HSP90a, and LCP1) in populations of the house finch (Carpodacus mexicanus)
historically exposed (Alabama) and na
{\texteuro}
{\i}ve (Arizona) to Mycoplasma gallisepti-
cum. Our study, the first to quantify variation in regulatory regions in wild
birds, reveals that the upstream regions of CD74 and HSP90a are GC-rich, with
the former exhibiting unusually low sequence variation for this species. We
identified two SNPs, located in a GC-rich region immediately upstream of an
inferred promoter site in the gene HSP90a, that were significantly associated
with Mycoplasma pathogen load in the two populations. The SNPs are closely
linked and situated in potential regulatory sequences: one in a binding site for
the transcription factor nuclear NFYa and the other in a dinucleotide microsat-
ellite ((GC)
6
). The genotype associated with pathogen load in the putative
NFYa binding site was significantly overrepresented in the Alabama birds.
However, we did not see strong effects of selection at this SNP, perhaps because
selection has acted on standing genetic variation over an extremely short time
in a highly recombining region. Our study is a useful starting point to explore
functional relationships between sequence polymorphisms, gene expression, and
phenotypic traits, such as pathogen resistance that affect fitness in the wild.
}, issn = {2045-7758}, doi = {10.1002/ece3.484}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.484/epdf}, author = {Backstroem, Niclas and Shipilina, Daria and Blom, Mozes P. K. and Edwards, Scott V.} } @article {RN130, title = {Evidence from a House Finch (Haemorhous mexicanus) Spleen Transcriptome for Adaptive Evolution and Biased Gene Conversion in Passerine Birds}, journal = {Molecular Biology and Evolution}, volume = {30}, year = {2013}, pages = {1046-1050}, type = {Journal Article}, abstract = {
Identifying genes influenced by natural selection can provid
e information about lineage-specific adaptations, and tran-
scriptomes generated by next-generation sequencing are a us
eful resource for identifying such genes. Here, we utilize a
spleen transcriptome for the house finch (
Haemorhous mexicanus
), an emerging model for sexual selection and disease
ecology, together with previously sequenced avian geno
mes (chicken, turkey, and zebra finch), to investigate
lineage-specific adaptations within birds. An analysis of 4,
398 orthologous genes revealed a significantly higher ratio
of nonsynonymous to synonymous substit
utions and significantly higher GC content in passerines than in galliforms, an
observation deviating from strictly neutral expectations b
ut consistent with an effect of biased gene conversion on the
evolutionary rate in passerines. These data also showed that ge
nes exhibiting signs of positive selection and fast evolution
in passerines have functional roles related to fat m
etabolism, neurodevelopment, and ion binding.
}, issn = {0737-4038}, doi = {10.1093/molbev/mst033}, url = {http://mbe.oxfordjournals.org/content/30/5/1046.full.pdf+html}, author = {Backstroem, Niclas and Zhang, Qu and Edwards, Scott V.} } @article {RN129, title = {Multilocus tests of Pleistocene refugia and ancient divergence in a pair of Atlantic Forest antbirds (Myrmeciza)}, journal = {Molecular Ecology}, volume = {22}, year = {2013}, pages = {3996-4013}, type = {Journal Article}, abstract = {
The Atlantic Forest (AF) harbours one of the most diverse vertebrate faunas of the
world, including 199 endemic species of birds. Understanding the evolutionary pro-
cesses behind such diversity has become the focus of many recent, primarily single
locus, phylogeographic studies. These studies suggest that isolation in forest refugia
may have been a major mechanism promoting diversification, although there is also
support for a role of riverine and geotectonic barriers, two sets of hypotheses that can
best be tested with multilocus data. Here we combined multilocus data (one mtDNA
marker and eight anonymous nuclear loci) from two species of parapatric antbirds,
Myrmeciza loricata
and
M. squamosa
, and Approximate Bayesian Computation to
determine whether isolation in refugia explains current patterns of genetic variation
and their status as independent evolutionary units. Patterns of population structure,
differences in intraspecific levels of divergence and coalescent estimates of historical
demography fit the predictions of a recently proposed model of refuge isolation in
which climatic stability in the northern AF sustains higher diversity and demographic
stability than in the southern AF. However, a pre-Pleistocene divergence associated
with their abutting range limits in a region of past tectonic activity also suggests a role
for rivers or geotectonic barriers. Little or no gene flow between these species suggests
the development of reproductive barriers or competitive exclusion. Our results sug-
gests that limited marker sampling in recent AF studies may compromise estimates of
divergence times and historical demography, and we discuss the effects of such sam-
pling on this and other studies.
}, issn = {0962-1083}, doi = {10.1111/mec.12361}, url = {https://www.researchgate.net/profile/Fabio_Amaral2/publication/240307775_Multilocus_tests_of_Pleistocene_refugia_and_ancient_divergence_in_a_pair_of_Atlantic_Forest_antbirds_Myrmeciza/links/0c96051ccf12c518ba000000.pdf}, author = {do Amaral, Fabio Raposo and Albers, Patrick K. and Edwards, Scott V. and Miyaki, Cristina Y.} } @article {RN128, title = {Sex-Biased Expression of Sex-Differentiating Genes FOXL2 and FGF9 in American Alligators, Alligator mississippiensis}, journal = {Sexual Development}, volume = {7}, year = {2013}, pages = {253-260}, type = {Journal Article}, issn = {1661-5425}, doi = {10.1159/000350787}, url = {http://www.karger.com/Article/FullText/350787}, author = {Janes, D. E. and Elsey, R. M. and Langan, E. M. and Valenzuela, N. and Edwards, S. V.} } @article { ISI:000312449300016, title = {Out of Florida: mtDNA reveals patterns of migration and Pleistocene range expansion of the Green Anole lizard (Anolis carolinensis)}, journal = {Ecology and Evolution}, volume = {2}, year = {2012}, month = {SEP}, pages = {2274-2284}, abstract = {Anolis carolinensis is an emerging model species and the sole member of its genus native to the United States. Considerable morphological and physiological variation has been described in the species, and the recent sequencing of its genome makes it an attractive system for studies of genome variation. To inform future studies of molecular and phenotypic variation within A. carolinensis, a rigorous account of intraspecific population structure and relatedness is needed. Here, we present the most extensive phylogeographic study of this species to date. Phylogenetic analyses of mitochondrial DNA sequence data support the previous hypothesis of a western Cuban origin of the species. We found five well-supported, geographically distinct mitochondrial haplotype clades throughout the southeastern United States. Most Florida populations fall into one of three divergent clades, whereas the vast majority of populations outside Florida belong to a single, shallowly diverged clade. Genetic boundaries do not correspond to major rivers, but may reflect effects of Pleistocene glaciation events and the Appalachian Mountains on migration and expansion of the species. Phylogeographic signal should be examined using nuclear loci to complement these findings.}, issn = {2045-7758}, doi = {10.1002/ece3.324}, author = {Campbell-Staton, Shane C. and Goodman, Rachel M. and Backstroem, Niclas and Edwards, Scott V. and Jonathan B. Losos and Kolbe, Jason J.} } @inbook {905906, title = {Tangled Trees: The challenge of inferring species trees from coalescent and non-coalescent genes}, booktitle = {Evolutionary Genomics: Statistical and Computational Methods, volume 2}, year = {2012}, pages = {3-28}, publisher = {Springer}, organization = {Springer}, address = {New York}, author = {Anderson, C. and Liu, L. and Pearl, D. and Edwards, S. V,}, editor = {Anisimova, M.} } @article {905856, title = {The evolution of intron size in amniotes: a role for powered flight?}, journal = {Genome Biology and Evolution}, year = {2012}, month = {August 28, 2012}, abstract = {

Intronic DNA is a major component of eukaryotic genes and genomes and can be subject to selective constraint and have functions in gene regulation. Intron size is of particular interest given that it is thought to be the target of a variety of evolutionary forces and has been suggested to be linked ultimately to various phenotypic traits, such as powered flight. Using whole-genome analyses and comparative approaches that account for phylogenetic nonindependence, we examined interspecific variation in intron size variation in three data sets encompassing from 12 to 30 amniotes genomes and allowing for different levels of genome coverage. In addition to confirming that intron size is negatively associated with intron position and correlates with genome size, we found that on average mammals have longer introns than birds and nonavian reptiles, a trend that is correlated with the proliferation of repetitive elements in mammals. Two independent comparisons between flying and nonflying sister groups both showed a reduction of intron size in volant species, supporting an association between powered flight, or possibly the high metabolic rates associated with flight, and reduced intron/genome size. Small intron size in volant lineages is less easily explained as a neutral consequence of large effective population size. In conclusion, we found that the evolution of intron size in amniotes appears to be non-neutral, is correlated with genome size, and is likely influenced by powered flight and associated high metabolic rates.

}, author = {Q. Zhang and Edwards, Scott V.} } @article {905901, title = {Innate immunity and the evolution of resistance to an emerging infectious disease in a wild bird}, journal = {Molecular Ecology}, volume = {21}, number = {11}, year = {2012}, month = {May 19}, pages = {2628-2639}, abstract = {

Innate immunity is expected to play a primary role in conferring resistance to novel infectious diseases, but few studies have attempted to examine its role in the evolution of resistance to emerging pathogens in wild vertebrate populations. Here, we used experimental infections and cDNA microarrays to examine whether changes in the innate and/or acquired immune responses likely accompanied the emergence of resistance in house finches (Carpodacus mexicanus) in the eastern United States subject to a recent outbreak of conjunctivitis-causing bacterium (Mycoplasma gallisepticum{\textemdash}MG). Three days following experimental infection with MG, we observed differences in the splenic transcriptional responses between house finches from eastern U.S. populations, with a 12-year history of MG exposure, versus western U.S. populations, with no history of exposure to MG. In particular, western birds down-regulated gene expression, while eastern finches showed no expression change relative to controls. Studies involving poultry have shown that MG can manipulate host immunity, and our observations suggest that pathogen manipulation occurred only in finches from the western populations, outside the range of MG. Fourteen days after infection, eastern finches, but not western finches, up-regulated genes associated with acquired immunity (cell-mediated immunity) relative to controls. These observations suggest population differences in the temporal course of the response to infection with MG and imply that innate immune processes were targets of selection in response to MG in the eastern U.S. population.

}, author = {Bonneaud, Camille and Balenger, Susan L and Zhang, Jiangwen and Edwards, Scott V. and Hill, Geoffrey E} } @article {905861, title = {Molecular and Paleontological Evidence for a Post-Cretaceous Origin of Rodents}, journal = {Plos One}, volume = {7}, number = {10}, year = {2012}, pages = {e46445}, abstract = {
The timing of the origin and diversification of rodents remains controversial, due to conflicting results from molecular clocks
and paleontological data. The fossil record tends to support an early Cenozoic origin of crown-group rodents. In contrast,
most molecular studies place the origin and initial diversification of crown-Rodentia deep in the Cretaceous, although some
molecular analyses have recovered estimated divergence times that are more compatible with the fossil record. Here we attempt to resolve this conflict by carrying out a molecular clock investigation based on a nine-gene sequence dataset and a novel set of seven fossil constraints, including two new rodent records (the earliest known representatives of Cardiocraniinae and Dipodinae). Our results indicate that rodents originated around 61.7{\textendash}62.4 Ma, shortly after the Cretaceous/Paleogene (K/Pg) boundary, and diversified at the intraordinal level around 57.7{\textendash}58.9 Ma. These estimates are broadly consistent with the paleontological record, but challenge previous molecular studies that place the origin and early diversification of rodents in the Cretaceous. This study demonstrates that, with reliable fossil constraints, the\  incompatibility between paleontological and molecular estimates of rodent divergence times can be eliminated using currently available tools and genetic markers. Similar conflicts between molecular and paleontological evidence bedevil attempts to establish the origination times of other placental groups. The example of the present study suggests that more reliable fossil calibration points may represent the key to resolving these controversies.
}, isbn = {1932-6203}, author = {Shaoyuan Wu and Wu, Wenyu and Zhang, Fuchun and Ye, Jie and Ni, Xijun and Sun, Jimin and Edwards, Scott V. and Meng, Jin and Organ, Chris L} } @article {905876, title = {Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {37}, year = {2012}, note = {

012APTimes Cited:0Cited References Count:46

}, month = {Sep 11}, pages = {14942-14947}, abstract = {

The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both Bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.

}, keywords = {bayesian phylogenetics, data sets, diversification, estimating species trees, gene tree heterogeneity, genomic data, incomplete lineage sorting, inference, mixed models, multispecies coalescent model, phylogenetic incongruence, placental mammals, sequence data, Systematics}, isbn = {0027-8424}, author = {Song, S. and Liu, L. and Edwards, S. V. and Wu, S. Y.} } @article {905871, title = {Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes}, journal = {Genome Biology}, volume = {13}, number = {1}, year = {2012}, pages = {415}, abstract = {

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

}, isbn = {1465-6906}, author = {St John, John and Braun, Edward and Isberg, Sally and Miles, Lee and Chong, Amanda and Gongora, Jaime and Dalzell, Pauline and Moran, Christopher and Bed{\textquoteright}Hom, Bertrand and Abzhanov, Arkhat and Burgess, Shane and Cooksey, Amanda and Castoe, Todd and Crawford, Nicholas and Densmore, Llewellyn and Drew, Jennifer and Edwards, Scott and Faircloth, Brant and Fujita, Matthew and Greenwold, Matthew and Hoffmann, Federico and Howard, Jonathan and Iguchi, Taisen and Janes, Daniel and Khan, Shahid and Kohno, Satomi and de Koning, AP Jason and Lance, Stacey and McCarthy, Fiona and McCormack, John} } @article {905881, title = {A Species Tree for the Australo-Papuan Fairy-wrens and Allies (Aves: Maluridae)}, journal = {Systematic Biology}, volume = {61}, number = {2}, year = {2012}, month = {March 1, 2012}, pages = {253-271}, abstract = {

We explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that incomplete lineage sorting (ILS) of neutrally evolving loci could be substantial, a situation that could compromise traditional methods of combining loci in phylogenetic analysis. Using 18 molecular markers (5 anonymous loci, 7 exons, 5 introns, and 1 mitochondrial DNA locus), we show that gene tree monophyly across species could be rejected for 16 of 18 loci, suggesting substantial ILS at the family level in these birds. Using the software Concaterpillar, we also detect three statistically distinct clusters of gene trees among the 18 loci. Despite substantial variation in gene trees, species trees constructed using four different species tree estimation methods (BEST, BUCKy, and STAR) were generally well supported and similar to each other and to the concatenation tree, with a few mild discordances at nodes that could be explained by rapid and recent speciation events. By contrast, minimizing deep coalescences produced a species tree that was topologically more divergent from those of the other methods as measured by multidimensional scaling of trees. Additionally, gene and species trees were topologically more similar in the BEST analysis, presumably because of the species tree prior employed in BEST which appropriately assumes that gene trees are correlated with each other and with the species tree. Among the 18 loci, we also discovered 102 independent indel markers, which also proved phylogenetically informative, primarily among genera, and displayed a {\quotesinglbase}{\`a}{\textordmasculine}4-fold bias towards deletions. As suggested in earlier work, the grasswrens (Amytornis) are sister to the rest of the family and the emu-wrens (Stipiturus) are sister to fairy-wrens (Malurus, Clytomyias). Our study shows that ILS is common at the family level in birds yet, despite this, species tree methods converge on broadly similar results for this family.

}, author = {Lee, June Y. and Joseph, Leo and Edwards, Scott V.} } @article {905886, title = {Triploid plover female provides support for a role of the W chromosome in avian sex determination}, journal = {Biology Letters}, volume = {8}, number = {5}, year = {2012}, month = {October 23, 2012}, pages = {787-789}, abstract = {

Two models, Z Dosage and Dominant W, have been proposed to explain sex determination in birds, in which males are characterized by the presence of two Z chromosomes, and females are hemizygous with a Z and a W chromosome. According to the Z Dosage model, high dosage of a Z-linked gene triggers male development, whereas the Dominant W model postulates that a still unknown W-linked gene triggers female development. Using 33 polymorphic microsatellite markers, we describe a female triploid Kentish plover Charadrius alexandrinus identified by characteristic triallelic genotypes at 14 autosomal markers that produced viable diploid offspring. Chromatogram analysis showed that the sex chromosome composition of this female was ZZW. Together with two previously described ZZW female birds, our results suggest a prominent role for a female determining gene on the W chromosome. These results imply that avian sex determination is more dynamic and complex than currently envisioned.

}, author = {K{\"u}pper, Clemens and Augustin, Jakob and Edwards, Scott and Sz{\'e}kely, Tam{\'a}s and Kosztol{\'a}nyi, Andr{\'a}s and Burke, Terry and Janes, Daniel E.} } @article {905891, title = {Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum}, journal = {PLoS Genetics}, volume = {8}, number = {2}, year = {2012}, pages = {e1002511}, publisher = {Public Library of Science}, type = {doi:10.1371/journal.pgen.1002511}, abstract = {

Author Summary

Documenting the evolutionary changes occurring in pathogens when they switch hosts is important for understanding mechanisms of adaptation and rates of evolution. We took advantage of a novel host{\quotesinglbase}{\"A}{\`\i}pathogen system involving a bacterial pathogen (Mycoplasma gallisepticum, or MG) and a songbird host, the House Finch, to study genome-wide changes during a host-shift. Around 1994, biologists noticed that House Finches were contracting conjunctivitis and MG from poultry was discovered to be the cause. The resulting epizootic was one of the best documented for a wildlife species, partly as a result of thousands of citizen science observers. We sequenced the genomes of 12 House Finch MG strains sampled throughout the epizootic, from 1994{\quotesinglbase}{\"A}{\`\i}2007, as well as four additional putatively ancestral poultry MG strains. Using this serial sample, we estimate a remarkably high rate of substitution, consistent with past implications that mycoplasmas are among the fastest evolving bacteria. We also find that an array of likely phage-derived sequences known as CRISPRs has degraded and ceased to recruit new repeats in the House Finch MG strains, as compared to the poultry strains in which it is diverse and rapidly evolving. This suggests that phage dynamics might be important in the dynamics of MG infection.

}, author = {Delaney, Nigel F. and Balenger, Susan and Bonneaud, Camille and Marx, Christopher J. and Hill, Geoffrey E. and Ferguson-Noel, Naola and Tsai, Peter and Rodrigo, Allen and Edwards, Scott V.} } @article {RN133, title = {Ventromedial prefrontal cortex modulates social pressure effects on decision-making while driving}, journal = {Society for Neuroscience Abstract Viewer and Itinerary Planner}, volume = {42}, year = {2012}, type = {Journal Article}, url = {://BCI:BCI201200730261}, author = {Chen, K. H. and Rusch, M. and Edwards, S. V. and Rizzo, M. and Anderson, S. W.} } @article {RN134, title = {Innate immunity and the evolution of resistance to an emerging infectious disease in a wild bird}, journal = {Molecular Ecology}, volume = {21}, year = {2012}, pages = {2628-2639}, type = {Journal Article}, abstract = {

Innate immunity is expected to play a primary role in conferring resistance to novel infectious diseases, but few studies have attempted to examine its role in the evolution of resistance to emerging pathogens in wild vertebrate populations. Here, we used experimental infections and cDNA microarrays to examine whether changes in the innate and/or acquired immune responses likely accompanied the emergence of resistance in house finches (Carpodacus mexicanus) in the eastern United States subject to a recent outbreak of conjunctivitis-causing bacterium (Mycoplasma gallisepticum{\textemdash}MG). Three days following experimental infection with MG, we observed differences in the splenic transcriptional responses between house finches from eastern U.S. populations, with a 12-year history of MG exposure, versus western U.S. populations, with no history of exposure to MG. In particular, western birds down-regulated gene expression, while eastern finches showed no expression change relative to controls. Studies involving poultry have shown that MG can manipulate host immunity, and our observations suggest that pathogen manipulation occurred only in finches from the western populations, outside the range of MG. Fourteen days after infection, eastern finches, but not western finches, up-regulated genes associated with acquired immunity (cell-mediated immunity) relative to controls. These observations suggest population differences in the temporal course of the response to infection with MG and imply that innate immune processes were targets of selection in response to MG in the eastern U.S. population.

}, issn = {0962-1083}, doi = {10.1111/j.1365-294X.2012.05551.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2012.05551.x/full}, author = {Bonneaud, Camille and Balenger, Susan L. and Zhang, Jiangwen and Edwards, Scott V. and Hill, Geoffrey E.} } @article {RN132, title = {Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum}, journal = {Plos Genetics}, volume = {8}, year = {2012}, type = {Journal Article}, abstract = {
Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial
pathogens in the wild, particularly during and after host switches.
Mycoplasma gallisepticum
(MG) is a pathogenic bacterium
that has evolved predominantly in poultry and recently jumped to wild house finches (
Carpodacus mexicanus
), a common
North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House
Finch isolates of MG, as well as in poultry outgroups. Using whole-genome sequences of 12 House Finch isolates across a
13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House
Finch isolates of only
,
2\% of ancestral poultry strains and a nucleotide substitution rate of 0.8
2
1.2
6
10
2
5
per site per year
both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for
bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to
the House Finch host, but after the invasion of House Finches there is progressive loss of CRISPR repeat diversity, and
recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only
,
50\% of the CRISPR
repertoire founding (1994{\textendash}95) strains and have lost the CRISPR{\textendash}associated genes required for CRISPR function. Our results
suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied

by apparent functional loss of CRISPRs

}, issn = {1553-7390}, doi = {10.1371/journal.pgen.1002511}, url = {http://journals.plos.org/plosgenetics/article/asset?id=10.1371\%2Fjournal.pgen.1002511.PDF}, author = {Delaney, Nigel F. and Balenger, Susan and Bonneaud, Camille and Marx, Christopher J. and Hill, Geoffrey E. and Ferguson-Noel, Naola and Tsai, Peter and Rodrigo, Allen and Edwards, Scott V.} } @inbook {905926, title = {Major events in genome evolution}, booktitle = {Living Dinosaurs: The Evolutionary History of Modern Birds}, year = {2011}, pages = {325-337}, publisher = {John Wiley \& Sons, Ltd.}, organization = {John Wiley \& Sons, Ltd.}, address = {Hoboken, NJ}, author = {Organ, C. L. and Edwards, S. V.}, editor = {Dyke, Gareth and Kaiser, Gary} } @article {905916, title = {Conflict between Genetic and PhenotypicDifferentiation: The Evolutionary History of a {\textquoteleft}Lost and Rediscovered{\textquoteright} Shorebird}, journal = {Plos One}, volume = {6}, number = {11}, year = {2011}, pages = {e26995}, publisher = {Public Library of Science}, type = {doi:10.1371/journal.pone.0026995}, abstract = {

Understanding and resolving conflicts between phenotypic and genetic differentiation is central to evolutionary research. While phenotypically monomorphic species may exhibit deep genetic divergences, some morphologically distinct taxa lack notable genetic differentiation. Here we conduct a molecular investigation of an enigmatic shorebird with a convoluted taxonomic history, the White-faced Plover (Charadrius alexandrinus dealbatus), widely regarded as a subspecies of the Kentish Plover (C. alexandrinus). Described as distinct in 1863, its name was consistently misapplied in subsequent decades until taxonomic clarification ensued in 2008. Using a recently proposed test of species delimitation, we reconfirm the phenotypic distinctness of dealbatus. We then compare three mitochondrial and seven nuclear DNA markers among 278 samples of dealbatus and alexandrinus from across their breeding range and four other closely related plovers. We fail to find any population genetic differentiation between dealbatus and alexandrinus, whereas the other species are deeply diverged at the study loci. Kentish Plovers join a small but growing list of species for which low levels of genetic differentiation are accompanied by the presence of strong phenotypic divergence, suggesting that diagnostic phenotypic characters may be encoded by few genes that are difficult to detect. Alternatively, gene expression differences may be crucial in producing different phenotypes whereas neutral differentiation may be lagging behind.

}, author = {Rheindt, Frank E. and Sz{\'e}kely, Tamas and Edwards, Scott V. and Lee, Patricia L. M. and Burke, Terry and Kennerley, Peter R. and Bakewell, David N. and Alrashidi, Monif and Kosztol{\'a}nyi, Andr{\'a}s and Weston, Michael A. and Liu, Wei-Ting and Lei, Wei-Pan and Shigeta, Yoshimitsu and Javed, S{\'a}lim and Zefania, Sama and K{\"u}pper, Clemens} } @article {905921, title = {Genetic introgression: an integral but neglected component of speciation in birds}, journal = {The Auk}, volume = {128}, number = {4}, year = {2011}, pages = {620-632}, isbn = {0004-8038}, author = {Rheindt, Frank E and Edwards, Scott V.} } @article {905951, title = {The genome of the green anole lizard and a comparative analysis with birds and mammals}, journal = {Nature}, volume = {477}, number = {7366}, year = {2011}, note = {

825ZMTimes Cited:1Cited References Count:26

}, month = {Sep 29}, pages = {587-591}, abstract = {

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

}, keywords = {chicken, Evolution, Fish, microchromosomes, Proteome, reptiles, sauropsida}, isbn = {0028-0836}, author = {Alfoldi, J. and Di Palma, F. and Grabherr, M. and Williams, C. and Kong, L. S. and Mauceli, E. and Russell, P. and Lowe, C. B. and R.E. Glor and Jaffe, J. D. and Ray, D. A. and Boissinot, S. and Shedlock, A. M. and Botka, C. and Castoe, T. A. and Colbourne, J. K. and Fujita, M. K. and Moreno, R. G. and ten Hallers, B. F. and Haussler, D. and Heger, A. and Heiman, D. and Janes, D. E. and Johnson, J. and de Jong, P. J. and Koriabine, M. Y. and Lara, M. and Novick, P. A. and Organ, C. L. and Peach, S. E. and S. Poe and Pollock, D.D. and de Queiroz, K. and Sanger, T. and Searle, S. and Smith, J. D. and Smith, Z. and Swofford, R. and Turner-Maier, J. and Wade, J. and Young, S. and Zadissa, A. and Edwards, S. V. and Glenn, T. C. and Schneider, C. J. and Losos, J. B. and Lander, E. S. and Breen, M. and Ponting, C. P. and Lindblad-Toh, K.} } @article {905936, title = {Near complete erosion of isochores in the Anolis lizard genome}, journal = {Genome Biology and Evolution}, volume = {3}, year = {2011}, pages = {974-984}, abstract = {
Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date. The newly sequenced genome of Anolis carolinensis provides the first opportunity to quantify isochore structure in a nonavian reptile. We find Anolis to have the most compositionally homogeneous genome of all amniotes sequenced thus far, a homogeneity exceeding that for the frog Xenopus. Based on a Bayesian algorithm, Anolis has smaller and less GC-richisochores compared with human and chicken. Correlates generally associated with GC-rich isochores, including shorter introns and higher gene density, have all but disappeared from the Anolis genome. Using genic GC as a proxy for isochore structure so as to compare with other vertebrates, we found that GC content has substantially decreased in the lineage leading to Anolis since diverging from the common ancestor of Reptilia; 275 Ma, perhaps reflecting weakened or reversed GC-biased gene conversion, a nonadaptive substitution process that is thought to be important in the maintenance and trajectory of isochore evolution. Our results demonstrate that GC composition in Anolis is not associated with important features of genome structure, including gene density and intron size, in contrast to patterns seen in mammal and bird genomes.
}, author = {Fujita, M. K. and Edwards, S. V. and Ponting, C. P.} } @article {905941, title = {A proposal to sequence the genome of a garter snake (Thamnophis sirtalis)}, journal = {Standards in genomic sciences}, volume = {4}, number = {2}, year = {2011}, pages = {257}, abstract = {
Here we develop an argument in support of sequencing a garter snake (Thamnophis sirtalis) genome, and outline a plan to accomplish this. This snake is a common, widespread, nonve-nomous North American species that has served as a model for diverse studies in evolutio-nary biology, physiology, genomics, behavior and coevolution. The anole lizard is currently the only genome sequence available for a non-avian reptile. Thus, the garter snake at this time would be the first available snake genome sequence and as such would provide much needed comparative representation of non-avian reptilian genomes, and would also allow critical new in sights for vertebrate comparative genomic studies. We outline the major areas of discovery that the availability of the garter snake genome would enable, and describe a plan for whole-genome sequencing.
}, author = {Castoe, Todd A and Bronikowski, Anne M and Brodie III, Edmund D and Edwards, Scott V. and Pfrender, Michael E and Shapiro, Michael D and Pollock, David D and Warren, Wesley C} } @article {905946, title = {Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {19}, year = {2011}, note = {

761YNTimes Cited:4Cited References Count:46

}, month = {May 10}, pages = {7866-7871}, abstract = {

Wild organisms are under increasing pressure to adapt rapidly to environmental changes. Predicting the impact of these changes on natural populations requires an understanding of the speed with which adaptive phenotypes can arise and spread, as well as of the underlying mechanisms. However, our understanding of these parameters is poor in natural populations. Here we use experimental and molecular approaches to investigate the recent emergence of resistance in eastern populations of North American house finches (Carpodacus mexicanus) to Mycoplasma galliseptum (MG), a severe conjunctivitis-causing bacterium. Two weeks following an experimental infection that took place in 2007, finches from eastern US populations with a 12-y history of exposure to MG harbored 33\% lower MG loads in their conjunctivae than finches from western US populations with no prior exposure to MG. Using a cDNA microarray, we show that this phenotypic difference in resistance was associated with differences in splenic gene expression, with finches from the exposed populations up-regulating immune genes postinfection and those from the unexposed populations generally down-regulating them. The expression response of western US birds to experimental infection in 2007 was more similar to that of the eastern US birds studied in 2000, 7 y earlier in the epizootic, than to that of eastern birds in 2007. These results support the hypothesis that resistance has evolved by natural selection in the exposed populations over the 12 y of the epizootic. We hypothesize that host resistance arose and spread from standing genetic variation in the eastern US and highlight that natural selection can lead to rapid phenotypic evolution in populations when acting on such variation.

}, keywords = {Chickens, conjunctivitis, darwins finches, dynamics, emerging disease, finches carpodacus-mexicanus, genetic basis of resistance, host, host-parasite co-evolution, house finches, Immunosuppression, mycoplasma-gallisepticum infection, natural-selection, quantitative rt-pcr, responses}, isbn = {0027-8424}, author = {Bonneaud, C. and Balenger, S. L. and Russell, A. F. and Zhang, J. W. and Hill, G. E. and Edwards, S. V.} } @article {RN135, title = {Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. (vol 19, pg 266, 2010)}, journal = {Molecular Ecology}, volume = {20}, year = {2011}, pages = {2871-2871}, type = {Journal Article}, abstract = {
Next-generation sequencing technology provides an attractive means to obtain large-scale sequence
data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation
and selection intensity across the avian genome, we performed brain transcriptome sequencing using
Roche 454 technology of 10 different non-model avian species. Contigs from
de novo
assemblies
were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we
identified 6499 different genes across all 10 species, with ~1000 genes found in each full run per
species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-
biased mutation) and a negative correlation between the neutral substitution rate (
d
S
) and
chromosome size. Analyses of the mean
d
N
/
d
S
ratio (
ω
) of genes across chromosomes supported the
Hill{\textendash}Robertson effect (the effect of selection at linked loci) and point at stochastic problems with
ω
as an independent measure of selection. Overall, this study demonstrates the usefulness of next-
generation sequencing for obtaining genomic resources for comparative genomic analysis of non-

model organisms

}, issn = {0962-1083}, doi = {10.1111/j.1365-294X.2011.05169.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904817/}, author = {Kuenstner, A. and Wolf, J. B. W. and Backstroem, N. and Whitney, O. and Balakrishnan, C. N. and Day, L. and Edwards, S. V. and Janes, D. E. and Schlinger, B. A. and Wilson, R. K. and Jarvis, E. D. and Warren, W. C. and Ellegren, H.} } @article {RN137, title = {Molecular Evolution of the Toll-Like Receptor Multigene Family in Birds}, journal = {Molecular Biology and Evolution}, volume = {28}, year = {2011}, pages = {1703-1715}, type = {Journal Article}, abstract = {
Toll-like receptors (TLR) are membrane-bound sensors of the innate immune system that recognize invariant and
distinctive molecular features of invading microbes and are also essential for initiating adaptive immunity in vertebrates.
The genetic variation at TLR genes has been directly related to differential pathogen outcomes in humans and livestock.
Nonetheless, new insights about the impact of TLRs polymorphism on the evolutionary ecology of infectious diseases can
be gained through the investigation of additional vertebrate groups not yet investigated in detail. In this study, we have
conducted the first characterization of the entire TLR multigene family (
N
5
10 genes) in non-model avian species. Using
primers targeting conserved coding regions, we aimed at amplifying large segments of the extracellular domains (275{\textendash}435
aa) involved in pathogen recognition across seven phylogenetically diverse bird species. Our analyses suggest avian TLRs
are dominated by stabilizing selection, suggesting that slow rates of nonsynonymous substitution help preserve biological
function. Overall, mean values of
x
(
5
d
n
/d
s
) at each TLR locus ranged from 0.196 to 0.517. However, we also found
patterns of positive selection acting on specific amino acid sites that could be linked to species-specific differences in
pathogen-associated molecular pattern recognition. Only 39 of 2,875 (
;
1.35\%) of the codons analyzed exhibited
significant patterns of positive selection. At least one half of these positively selected codons can be mapped to putative
ligand-binding regions, as suggested by crystallographic structures of TLRs and their ligands and mutagenic analyses. We
also surveyed TLR polymorphism in wild populations of two bird species, the Lesser Kestrel
Falco naumanni
and the House
Finch
Carpodacus mexicanus
. In general, avian TLRs displayed low to moderate single nucleotide polymorphism levels and
an excess of silent nucleotide substitutions, but also conspicuous instances of positive directional selection. In particular,
TLR5 and TLR15 exhibited the highest degree of genetic polymorphism and the highest occurrence of nonconservative
amino acid substitutions. This study provides critical primers and a first look at the evolutionary patterns and implications
of TLR polymorphism in non-model avian species and extends the list of candidate loci for avian eco-immunogenetics
beyond the widely employed genes of the Major Histocompatibility Complex (MHC).
}, issn = {0737-4038}, doi = {10.1093/molbev/msq351}, url = {http://mbe.oxfordjournals.org/content/28/5/1703.full}, author = {Alcaide, Miguel and Edwards, Scott V.} } @article {RN139, title = {Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, pages = {7866-7871}, type = {Journal Article}, abstract = {
Wild organisms are under increasing pressure to adapt rapidly to
environmental changes. Predicting the impact of these changes on
natural populations requires an understanding of the speed with
which adaptive phenotypes can arise and spread, as well as of
the underlying mechanisms. However, our understanding of these
parameters is poor in natural populations. Here we use experimen-
tal and molecular approaches to investigate the recent emergence
of resistance in eastern populations of North American house
fi
nches (
Carpodacus mexicanus
)to
Mycoplasma galliseptum
(MG),
a severe conjunctivitis-causing bacterium. Two weeks following an
experimentalinfectionthattookplacein2007,
fi
nchesfromeastern
US populations with a 12-y history of exposure to MG harbored
33\% lower MG loads in their conjunctivae than
fi
nches from west-
ern US populations with no prior exposure to MG. Using a cDNA
microarray, we show that this phenotypic difference in resistance
was associated with differences in splenic gene expression, with
fi
nchesfromthe exposedpopulations up-regulatingimmunegenes
postinfection and those from the unexposed populations generally
down-regulating them. The expression response of western US
birds to experimental infection in 2007 was more similar to that
of the eastern US birds studied in 2000, 7 y earlier in the epizootic,
than to that of eastern birds in 2007. These results support the
hypothesis that resistance has evolved by natural selection in the
exposedpopulationsoverthe12yoftheepizootic.Wehypothesize
that host resistance arose and spread from standing genetic varia-
tion in the eastern US and highlight that natural selection can lead
to rapid phenotypic evolution in populations when acting on

such variation

}, issn = {0027-8424}, doi = {10.1073/pnas.1018580108}, url = {http://www.pnas.org/content/108/19/7866.full}, author = {Bonneaud, Camille and Balenger, Susan L. and Russell, Andrew F. and Zhang, Jiangwen and Hill, Geoffrey E. and Edwards, Scott V.} } @article {RN136, title = {Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor}, journal = {Genome Biology and Evolution}, volume = {3}, year = {2011}, pages = {102-113}, type = {Journal Article}, abstract = {
Many noncoding regions of genomes appear to be essential to genome function. Conservation of large numbers of
noncoding sequences has been reported repeatedly among mammals but not thus far among birds and reptiles. By searching
genomes of chicken (
Gallus gallus
), zebra finch (
Taeniopygia guttata
), and green anole (
Anolis carolinensis
), we quantified
the conservation among birds and reptiles and across amniotes of long, conserved noncoding sequences (LCNS), which we
define as sequences
500 bp in length and exhibiting
95\% similarity between species. We found 4,294 LCNS shared
between chicken and zebra finch and 574 LCNS shared by the two birds and
Anolis
. The percent of genomes comprised by
LCNS in the two birds (0.0024\%) is notably higher than the percent in mammals (
,
0.0003\% to
,
0.001\%), differences that
we show may be explained in part by differences in genome-wide substitution rates. We reconstruct a large number of LCNS
for the amniote ancestor (ca. 8,630) and hypothesize differential loss and substantial turnover of these sites in descendent
lineages. By contrast, we estimated a small role for recruitment of LCNS via acquisition of novel functions over time. Across
amniotes, LCNS are significantly enriched with transcription factor binding sites for many developmental genes, and 2.9\% of
LCNS shared between the two birds show evidence of expression in brain expressed sequence tag databases. These results
show that the rate of retention of LCNS from the amniote ancestor differs between mammals and Reptilia (including birds)

and that this may reflect differing roles and constraints in gene regulation

}, issn = {1759-6653}, doi = {10.1093/gbe/evq087}, url = {http://gbe.oxfordjournals.org/content/3/102.long}, author = {Janes, D. E. and Chapus, C. and Gondo, Y. and Clayton, D. F. and Sinha, S. and Blatti, C. A. and Organ, C. L. and Fujita, M. K. and Balakrishnan, C. N. and Edwards, S. V.} } @article {RN138, title = {Temporal increase in organic mercury in an endangered pelagic seabird assessed by century-old museum specimens}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, pages = {7466-7471}, type = {Journal Article}, abstract = {

Methylmercury cycling in the Pacific Ocean has garnered significant attention in recent years, especially with regard to rising mercury emissions from Asia. Uncertainty exists concerning whether increases in anthropogenic emissions over time may have caused increased mercury bioaccumulation in the biota. To address this, we measured total mercury and, for a subset of samples, methylmercury (the bioaccumulated form of mercury) in museum feathers from an endangered seabird, the black-footed albatross (Phoebastria nigripes), spanning a 120-y period. We analyzed stable isotopes of nitrogen (δ15N) and carbon (δ13C) to control for temporal changes in trophic structure and diet. In post-1940 and -1990 feathers, we detected significantly higher mean methylmercury concentrations and higher proportions of samples exhibiting above deleterious threshold levels (\~{}40,000 ng{\textperiodcentered}g-1) of methylmercury relative to prior time points, suggesting that mercury toxicity may undermine reproductive effort in the species. We also found higher levels of (presumably curator-mediated) inorganic mercury in older specimens of albatross as well as two nonpelagic species lacking historical exposure to bioavailable mercury, patterns suggesting that studies on bioaccumulation should measure methylmercury rather than total mercury when using museum collections. δ15N contributed substantially to models explaining the observed methylmercury variation. After simultaneously controlling for significant trends in δ13C over time and δ15N with methylmercury exposure, year remained a significant independent covariate with feather methylmercury levels among the albatrosses. These data show that remote seabird colonies in the Pacific basin exhibit temporal changes in methylmercury levels consistent with historical global and recent regional increases in anthropogenic emissions.

}, issn = {0027-8424}, doi = {10.1073/pnas.1013865108}, url = {http://www.pnas.org/content/108/18/7466.full.pdf}, author = {Vo, Anh-Thu E. and Bank, Michael S. and Shine, James P. and Edwards, Scott V.} } @inbook {906001, title = {Bayesian estimation of species trees: a practical guide to optimal sampling and analysis}, booktitle = {Estimating Species Trees: Practical and Theoretical Aspects}, year = {2010}, pages = {15-33}, publisher = {Wiley-Blackwell}, organization = {Wiley-Blackwell}, address = {New Jersey}, author = {Castillo-Ram{\'\i}rez, S. and Liu, L. and Pearl, D. and Edwardsm S. V,}, editor = {Knowles, L. L. and Kubatko, L. S.} } @inbook {906006, title = {Phylogeography and phylogenetics in the nuclear age}, booktitle = {Searching for the Causes of Evolution: From Field Observations to Mechanisms}, year = {2010}, pages = {65-88}, publisher = {Princeton University Press}, organization = {Princeton University Press}, address = {Princeton, NJ}, author = {Balakrishnan, C. N. and Lee J. Y. and Edwards, S. V.}, editor = {Peter Grant and Rosemary Grant} } @inbook {905966, title = {Phylogenomic approach to the evolutionary dynamics of gene duplication in birds}, booktitle = {Evolution After Gene Duplication}, year = {2010}, pages = {253-267}, publisher = {Wiley \& Sons}, organization = {Wiley \& Sons}, address = {New York}, author = {Organ, C. L. and Rasmussen, M. and Baldwin, M. W. and Kellis, M. and Edwards, S. V.}, editor = {Dittmar, K. and Liberles, D.} } @article {905981, title = {Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species}, journal = {Molecular Ecology}, volume = {19}, year = {2010}, note = {

Suppl. 1570BDTimes Cited:24Cited References Count:60

}, month = {Mar}, pages = {266-276}, abstract = {

Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with similar to 1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.

}, keywords = {454, avian genomics, chicken genome, differentiation, Drosophila, effective population-size, gene-expression, hill-robertson effect, male-biased mutation, male-mutation bias, molecular evolution, natural-selection, next generation sequencing, nucleotide divergence, recombination, selection}, isbn = {0962-1083}, author = {Kunstner, A. and Wolf, J. B. W. and Backstrom, N. and Whitney, O. and Balakrishnan, C. N. and Day, L. and Edwards, S. V. and Janes, D. E. and Schlinger, B. A. and Wilson, R. K. and Jarvis, E. D. and Warren, W. C. and Ellegren, H.} } @article {905986, title = {Expansion of the miRNA Pathway in the Hemipteran Insect Acyrthosiphon pisum}, journal = {Molecular Biology and Evolution}, volume = {27}, number = {5}, year = {2010}, note = {

587LUTimes Cited:1Cited References Count:40

}, month = {May}, pages = {979-987}, abstract = {

The pathways that allow short noncoding RNAs such as the microRNAs (miRNAs) to mediate gene regulation and control critical cellular and developmental processes involve a limited number of key protein components. These proteins are the Dicer-like RNases, double-stranded RNA (dsRNA)-binding proteins, and the Argonaute (AGO) proteins that process stem-loop hairpin transcripts of endogenous genes to generate miRNAs or long dsRNA precursors (either exogenous or endogenous). Comparative genomics studies of metazoans have shown the pathways to be highly conserved overall; the major difference observed is that the vertebrate pathways overlap in sharing a single Dicer (DCR) and AGO proteins, whereas those of insects appear to be parallel, with distinct Dicers and AGOs required for each pathway. The genome of the pea aphid is the first available for a hemipteran insect and discloses an unexpected expansion of the miRNA pathway. It has two copies of the miRNA-specific dicr-1 and ago1 genes and four copies of pasha a cofactor of drosha involved in miRNA biosynthesis. For three of these expansions, we showed that one copy of the genes diverged rapidly and in one case (ago1b) shows signs of positive selection. These expansions occurred concomitantly within a brief evolutionary period. The pea aphid, which reproduces by viviparous parthenogenesis, is able to produce several adapted phenotypes from one single genotype. We show by reverse transcriptase-polymerase chain reaction that all the duplicated copies of the miRNA machinery genes are expressed in the different morphs. Investigating the function of these novel genes offers an exciting new challenge in aphid biology.

}, keywords = {aphids, biogenesis, Drosophila, Evolution, Genes, genome, maximum-likelihood, parthenogenesis, pea aphid, Phenotypic plasticity, positive selection, primary micrornas, rna pathway, Sequence Alignment}, isbn = {0737-4038}, author = {Jaubert-Possamai, S. and Rispe, C. and Tanguy, S. and Gordon, K. and Walsh, T. and Edwards, O. and Tagu, D.} } @article {905996, title = {Genome evolution in Reptilia, the sister group of mammals}, journal = {Annual Review of Genomics and Human Genetics}, volume = {11}, year = {2010}, note = {

Janes, Daniel EOrgan, Christopher LFujita, Matthew KShedlock, Andrew MEdwards, Scott Veng5F32GM072494/GM/NIGMS NIH HHS/5F32GM075490/GM/NIGMS NIH HHS/Research Support, N.I.H., ExtramuralResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.Review2010/07/02 06:00Annu Rev Genomics Hum Genet. 2010;11:239-64. doi: 10.1146/annurev-genom-082509-141646.

}, pages = {239-64}, abstract = {

The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.

}, keywords = {*Biological Evolution, *Genome, Animals, Birds/genetics, Chromosomes, Chromosomes, Mammalian, Mammals/*genetics, Phylogeny, Reptiles/*genetics}, isbn = {1545-293X (Electronic)1527-8204 (Linking)}, author = {Janes, D. E. and Organ, C. L. and Fujita, M. K. and Shedlock, A. M. and Edwards, S. V.} } @article {905961, title = {The genome of a songbird}, journal = {Nature}, volume = {464}, number = {7289}, year = {2010}, note = {

577EOTimes Cited:27Cited References Count:35

}, month = {Apr 1}, pages = {757-762}, abstract = {

The zebra finch is an important model organism in several fields(1,2) with unique relevance to human neuroscience(3,4). Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken(5)-the only bird with a sequenced genome until now(6). Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes(7). We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.

}, keywords = {Brain, chicken, dosage compensation, Evolution, gene-expression, learned birdsong, mechanisms, Nucleus, reveals, RNA}, isbn = {0028-0836}, author = {Warren, W. C. and Clayton, D. F. and Ellegren, H. and Arnold, A. P. and Hillier, L. W. and Kunstner, A. and Searle, S. and White, S. and Vilella, A. J. and Fairley, S. and Heger, A. and Kong, L. S. and Ponting, C. P. and Jarvis, E. D. and Mello, C. V. and Minx, P. and Lovell, P. and Velho, T. A. F. and Ferris, M. and Balakrishnan, C. N. and Sinha, S. and Blatti, C. and London, S. E. and Li, Y. and Lin, Y. C. and George, J. and Sweedler, J. and Southey, B. and Gunaratne, P. and Watson, M. and Nam, K. and Backstrom, N. and Smeds, L. and Nabholz, B. and Itoh, Y. and Whitney, O. and Pfenning, A. R. and Howard, J. and Voelker, M. and Skinner, B. M. and Griffin, D. K. and Ye, L. and McLaren, W. M. and Flicek, P. and Quesada, V. and Velasco, G. and Lopez-Otin, C. and Puente, X. S. and Olender, T. and Lancet, D. and Smit, A. F. A. and Hubley, R. and Konkel, M. K. and Walker, J. A. and Batzer, M. A. and Gu, W. J. and Pollock, D.D. and Chen, L. and Cheng, Z. and Eichler, E. E. and Stapley, J. and Slate, J. and Ekblom, R. and Birkhead, T. and Burke, T. and Burt, D. and Scharff, C. and Adam, I. and Richard, H. and Sultan, M. and Soldatov, A. and Lehrach, H. and Edwards, S. V. and Yang, S. P. and Li, X. C. and Graves, T. and Fulton, L. and Nelson, J. and Chinwalla, A. and Hou, S. F. and Mardis, E. R. and Wilson, R. K.} } @article {905971, title = {Geographic differences in sexual reassortment in an RNA phage}, journal = {Evolution}, volume = {64}, number = {10}, year = {2010}, note = {

Times Cited: 1O{\textquoteright}Keefe, Kara J. Silander, Olin K. McCreery, Helen Weinreich, Daniel M. Wright, Kevin M. Chao, Lin Edwards, Scott V. Remold, Susanna K. Turner, Paul E.

}, month = {Oct}, pages = {3010-3023}, abstract = {
The genetic structure of natural bacteriophage populations is poorly understood. Recent metagenomic studies suggest that phage biogeography is characterized by frequent migration. Using virus samples mostly isolated in Southern California, we recently showed that very little population structure exists in segmented RNA phage of the Cystoviridae family due to frequent segment reassortment (sexual genetic mixis) between unrelated virus individuals. Here we use a larger genetic dataset to examine the structure of Cystoviridae phage isolated from three geographic locations in Southern New England. We document extensive natural variation in the physical sizes of RNA genome segments for these viruses. In addition, consistent with earlier findings, our phylogenetic analyses and calculations of linkage disequilibrium (LD) show no evidence of within-segment recombination in wild populations. However, in contrast to the prior study, our analysis finds that reassortment of segments between individual phage plays a lesser role among cystoviruses sampled in New England, suggesting that the evolutionary importance of genetic mixis in Cystoviridae phage may vary according to geography. We discuss possible explanations for these conflicting results across the studies, such as differing local ecology and its impact on phage growth, and geographic differences in selection against hybrid phage genotypes.
}, isbn = {0014-3820}, author = {O{\textquoteright}Keefe, K. J. and Silander, O. K. and McCreery, H. and Weinreich, D. M. and Wright, K. M. and Chao, L. and Edwards, S. V. and Remold, S. K. and Turner, P. E.} } @article {905976, title = {A maximum pseudo-likelihood approach for estimating species trees under the coalescent model}, journal = {BMC Evolutionary Biology}, volume = {10}, number = {1}, year = {2010}, pages = {302}, abstract = {

BACKGROUND:Several phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE) of the species tree (topology, branch lengths, and population sizes) from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE) of species trees, with branch lengths of the species tree in coalescent units.RESULTS:We show that the MPE of the species tree is statistically consistent as the number M of genes goes to infinity. In addition, the probability that the MPE of the species tree matches the true species tree converges to 1 at rate O(M -1). The simulation results confirm that the maximum pseudo-likelihood approach is statistically consistent even when the species tree is in the anomaly zone. We applied our method, Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST) to a mammal dataset. The four major clades found in the MP-EST tree are consistent with those in the Bayesian concatenation tree. The bootstrap supports for the species tree estimated by the MP-EST method are more reasonable than the posterior probability supports given by the Bayesian concatenation method in reflecting the level of uncertainty in gene trees and controversies over the relationship of four major groups of placental mammals.CONCLUSIONS:MP-EST can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species.

}, isbn = {1471-2148}, author = {Liu, Liang and Yu, Lili and Edwards, Scott} } @booklet {905991, title = {Sex chromosome evolution in amniotes: applications for bacterial artificial chromosome libraries}, howpublished = {Journal of Biomedicine and Biotechnology}, volume = {2011}, year = {2010}, publisher = {Hindawi Publishing Corporation}, address = {Cairo Free Zone, Egypt}, abstract = {

Variability among sex chromosome pairs in amniotes denotes a dynamic history. Since amniotes diverged from a common
ancestor, their sex chromosome pairs and, more broadly, sex-determining mechanisms have changed reversibly and frequently.
These changes have been studied and characterized through the use of many tools and experimental approaches but perhaps
most effectively through applications for bacterial artificial chromosome (BAC) libraries. Individual BAC clones carry 100{\textendash}200 kb
of sequence from one individual of a target species that can be isolated by screening, mapped onto karyotypes, and sequenced.
With these techniques, researchers have identified differences and similarities in sex chromosome content and organization across
amniotes and have addressed hypotheses regarding the frequency and direction of past changes. Here, we review studies of sex
chromosome evolution in amniotes and the ways in which the field of research has been affected by the advent of BAC libraries.

}, author = {Janes, Daniel E. and Valenzuela, Nicole and Ezaz, Tariq, and Amemiya, Chris, and Edwards, Scott V.} } @article {906016, title = {The Zebra Finch genome and avian genomics in the wild}, journal = {Emu}, volume = {110}, number = {3}, year = {2010}, note = {

640DZTimes Cited:4Cited References Count:74

}, pages = {233-241}, abstract = {

The Zebra Finch (Taeniopygia guttata) is the first species of passerine bird with a complete genome sequence, making it an exciting time for avian evolutionary biology. Native to Australia and the Lesser Sunda Islands, this species has long played an important role in the study of ecology, behaviour and neuroscience. With the sequencing of its genome, the Zebra Finch now also represents an important model system for evolutionary and population genomics. The production of a genome sequence for the Zebra Finch will have far-reaching impacts on the study of avian biology. Here we discuss the genomic resources available for the Zebra Finch, including the genome sequence itself, and some of the ways in which they will facilitate the study of avian diversity. We also highlight recent examples from the literature that have already begun to leverage Zebra Finch genomic tools towards the study of birds in nature.

}, keywords = {bird populations, chromosomal-polymorphism, class iib genes, genetic-linkage map, Major Histocompatibility Complex, passerine bird, song system, taeniopygia-guttata, white-throated sparrow, zonotrichia-albicollis gmelin}, isbn = {0158-4197}, author = {Balakrishnan, C. N. and Edwards, S. V. and Clayton, D. F.} } @article {RN140, title = {Gene duplication and fragmentation in the zebra finch major histocompatibility complex}, journal = {BMC Biology}, volume = {8}, year = {2010}, pages = {(1 April 2010)-(1 April 2010)}, type = {Journal Article}, abstract = {
Background:
Due to its high polymorphism and importance for disease resistance, the major histocompatibility
complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of
particular interest because the chicken
Gallus gallus
, the avian species with the best characterized MHC, possesses a
highly streamlined
minimal essential
MHC, which is linked to resistance against specific pathogens. It remains
unclear the extent to which this organization describes the situation in other birds and whether it represents a
derived or ancestral condition. The sequencing of the zebra finch
Taeniopygia guttata
genome, in combination
with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a
highly divergent and diverse avian lineage, the passerines.
Results:
The zebra finch MHC exhibits a complex structure and history involving gene duplication and
fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be
pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the
presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome
assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to
different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content.
Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes.
Conclusion:
The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a
complete genome sequence. The apparent lack of synteny between
TAP
and the expressed MHC Class I locus is in
fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our
analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and
translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and

organization among avian lineages

}, issn = {1741-7007}, url = {http://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-8-29}, author = {Balakrishnan, C. N. and Ekblom, R. and Volker, M. and Westerdahl, H. and Godinez, R. and Kotkiewicz, H. and Burt, D. W. and Graves, T. and Griffin, D. K. and Warren, W. C. and Edwards, S. V.} } @article {921326, title = {Amniotes (Amniota)}, journal = {The timetree of life}, year = {2009}, pages = {375-379}, author = {Shedlock, Andrew M and Edwards, Scott V.} } @article {921311, title = {Coalescent methods for estimating phylogenetic trees}, journal = {Mol Phylogenet Evol}, volume = {53}, number = {1}, year = {2009}, note = {

Liu, LiangYu, LiliKubatko, LauraPearl, Dennis KEdwards, Scott VResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.ReviewUnited StatesMolecular phylogenetics and evolutionMol Phylogenet Evol. 2009 Oct;53(1):320-8. Epub 2009 Jun 6.

}, month = {Oct}, pages = {320-8}, abstract = {

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.

}, keywords = {*Models, Genetic, *Phylogeny, Bayes Theorem, Evolution, Molecular, Genetic Speciation, Likelihood Functions, Sequence Analysis, DNA/*methods, Statistics, Nonparametric}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Liu, L. and Yu, L. and Kubatko, L. and Pearl, D. K. and Edwards, S. V.} } @article {921321, title = {Estimating species phylogenies using coalescence times among sequences}, journal = {Systematic Biology}, volume = {58}, number = {5}, year = {2009}, note = {

520FGTimes Cited:39Cited References Count:44

}, month = {Oct}, pages = {468-477}, abstract = {

The estimation of species trees (phylogenies) is one of the most important problems in evolutionary biology, and recently, there has been greater appreciation of the need to estimate species trees directly rather than using gene trees as a surrogate. A Bayesian method constructed under the multispecies coalescent model can consistently estimate species trees but involves intensive computation, which can hinder its application to the phylogenetic analysis of large-scale genomic data. Many summary statistics-based approaches, such as shallowest coalescences (SC) and Global LAteSt Split (GLASS), have been developed to infer species phylogenies for multilocus data sets. In this paper, we propose 2 methods, species tree estimation using average ranks of coalescences (STAR) and species tree estimation using average coalescence times (STEAC), based on the summary statistics of coalescence times. It can be shown that the 2 methods are statistically consistent under the multispecies coalescent model. STAR uses the ranks of coalescences and is thus resistant to variable substitution rates along the branches in gene trees. A simulation study suggests that STAR consistently outperforms STEAC, SC, and GLASS when the substitution rates among lineages are highly variable. Two real genomic data sets were analyzed by the 2 methods and produced species trees that are consistent with previous results.

}, keywords = {bootstrap, coalescent model, consensus, divergence, DNA-sequences, gene tree, gene tree distributions, maximum-likelihood, Probability, reconstruction, species tree}, isbn = {1063-5157}, author = {Liu, L. and Yu, L. L. and Pearl, D. K. and Edwards, S. V.} } @article {921316, title = {Estimating species phylogenies using coalescence times among sequences}, journal = {Systematic Biology}, volume = {58}, number = {5}, year = {2009}, pages = {468-477}, isbn = {1063-5157}, author = {Liu, Liang and Yu, Lili and Pearl, Dennis K and Edwards, Scott V.} } @article {921291, title = {Genome 10K: A proposal to obtain whole-genome sequence for 10 000 Vertebrate Species}, journal = {Journal of Heredity}, volume = {100}, number = {6}, year = {2009}, note = {

520CNTimes Cited:18Cited References Count:94

}, month = {Nov-Dec}, pages = {659-674}, abstract = {

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

}, keywords = {ancestral state reconstruction, antimicrobial peptides, comparative genomics, Conservation, divergence times, Evolution, g10k, generation, Genetics, molecular evolution, molecules, origins, pluripotent stem-cells, poison frogs, species conservation, vertebrate biology}, isbn = {0022-1503}, author = {Haussler, D. and O{\textquoteright}Brien, S. J. and Ryder, O. A. and Barker, F. K. and Clamp, M. and Crawford, A. J. and Hanner, R. and Hanotte, O. and Johnson, W. E. and McGuire, J. A. and Miller, W. and Murphy, R. W. and Murphy, W. J. and Sheldon, F. H. and Sinervo, B. and Venkatesh, B. and Wiley, E. O. and Allendorf, F. W. and Amato, G. and Baker, C. S. and Bauer, A. and Beja-Pereira, A. and Bermingham, E. and Bernardi, G. and Bonvicino, C. R. and Brenner, S. and Burke, T. and Cracraft, J. and Diekhans, M. and Edwards, S. and Ericson, P. G. P. and Estes, J. and Fjelsda, J. and Flesness, N. and Gamble, T. and Gaubert, P. and Graphodatsky, A. S. and Graves, J. A. M. and Green, E. D. and Green, R. E. and Hackett, S. and Hebert, P. and Helgen, K. M. and Joseph, L. and Kessing, B. and Kingsley, D. M. and Lewin, H. A. and Luikart, G. and Martelli, P. and Moreira, M. A. M. and Nguyen, N. and Orti, G. and Pike, B. L. and Rawson, D. M. and Schuster, S. C. and Seuanez, H. N. and Shaffer, H. B. and Springer, M. S. and Stuart, J. M. and Sumner, J. and Teeling, E. and Vrijenhoek, R. C. and Ward, R. D. and Warren, W. C. and Wayne, R. and Williams, T. M. and Wolfe, N. D. and Zhang, Y. P. and Graph-Odatsky, A. and Johnson, W. E. and Felsenfeld, A. and Turner, S. and Genome 10K Community Scientists and Mammals Grp and Birds Grp and Amphibians Reptiles Grp and Fishes Grp and General Policy Grp and Anal Grp} } @article {921301, title = {Inferring the phylogeography and evolutionary history of the splendid fairy-wren Malurus splendens from mitochondrial DNA and spectrophotometry}, journal = {Journal of Avian Biology}, volume = {40}, number = {1}, year = {2009}, pages = {7-17}, isbn = {1600-048X}, author = {Kearns, Anna M and Joseph, Leo and Edwards, Scott V. and Double, Michael C} } @article {921276, title = {Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008}, journal = {Molecular Ecology}, volume = {18}, number = {14}, year = {2009}, note = {

464WKTimes Cited:86Cited References Count:25

}, month = {Jul}, pages = {2930-2933}, keywords = {distance, divergence, diversity, Evolution, Geography, mitochondrial-DNA, population-structure, sequences, Speciation, warblers}, isbn = {0962-1083}, author = {Edwards, S. and Bensch, S.} } @article {921271, title = {Multilocus phylogeography and phylogenetics using sequence-based markers}, journal = {Genetica}, volume = {135}, number = {3}, year = {2009}, pages = {439-455}, isbn = {0016-6707}, author = {Brito, Patr{\'\i}cia H and Edwards, Scott V.} } @article {921286, title = {Natural selection and phylogenetic analysis}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {22}, year = {2009}, note = {

452ZUTimes Cited:6Cited References Count:19

}, month = {Jun 2}, pages = {8799-8800}, keywords = {Evolution, heterotachy, long-branch attraction, parsimony}, isbn = {0027-8424}, author = {Edwards, S. V.} } @article {921281, title = {Is a new and general theory of molecular systematics emerging?}, journal = {Evolution}, volume = {63}, number = {1}, year = {2009}, pages = {1-19}, isbn = {1558-5646}, author = {Edwards, Scott V.} } @article {921266, title = {Nucleotide Variation, Linkage Disequilibrium and Founder-Facilitated Speciation in Wild Populations of the Zebra Finch (Taeniopygia guttata)}, journal = {Genetics}, volume = {181}, number = {2}, year = {2009}, note = {

499ITTimes Cited:12Cited References Count:100

}, month = {Feb}, pages = {645-660}, abstract = {

The zebra finch has long been an important model system for the study of vocal learning, vocal production, and behavior. With the imminent sequencing of its genome, the zebra finch is now poised to become a model system for population genetics. Using a panel of 30 noncoding loci, we characterized patterns of polymorphism and divergence among wild zebra finch populations. Continental Australian populations displayed little population structure, exceptionally high levels of nucleotide diversity (pi = 0.010), a rapid decay of linkage disequilibrium (LD), and a high population recombination rate (rho approximate to 0.05), all of which suggest an open and fluid genomic background that could facilitate adaptive variation. By contrast, Substantial divergence between the Australian and Lesser Sunda Island populations (K-ST = 0.193), reduced genetic diversity (pi = 0.002), and higher levels of LD in the island Population suggest a strong but relatively recent founder event, which may have contributed to speciation between these populations as envisioned under founder-effect speciation models. Consistent with this hypothesis, we find that tinder a simple quantitative genetic model both drift and selection could have contributed to the observed divergence in six quantitative traits. In both Australian and Lesser Sundas populations, diversity in Z-linked loci was significantly lower than in autosomal loci. Our analysis provides a quantitative framework for studying the role of selection and drift in shaping patterns of molecular evolution in the zebra finch genome.

}, keywords = {adaptive evolution, bird population, foxp2 expression, genetic-variation, genome evolution, multilocus genotype data, natural-selection, passerine bird, recombination rate, sexual selection}, isbn = {0016-6731}, author = {Balakrishnan, C. N. and Edwards, S. V.} } @article {921306, title = {Phylogenetic analysis in the anomaly zone}, journal = {Syst Biol}, volume = {58}, number = {4}, year = {2009}, note = {

Liu, LiangEdwards, Scott VResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.EnglandSystematic biologySyst Biol. 2009 Aug 1;58(4):452-60. Epub 2009 Jul 9.

}, month = {Aug 1}, pages = {452-60}, isbn = {1076-836X (Electronic)1063-5157 (Linking)}, author = {Liu, L. and Edwards, S. V.} } @article {921296, title = {Recombination and nucleotide diversity in the sex chromosomal pseudoautosomal region of the Emu, Dromaius novaehollandiae}, journal = {Journal of Heredity}, volume = {100}, number = {2}, year = {2009}, note = {

408FDTimes Cited:8Cited References Count:74

}, month = {Mar-Apr}, pages = {125-136}, abstract = {

Pseudoautosomal regions (PARs) shared by avian Z and W sex chromosomes are typically small homologous regions within which recombination still occurs and are hypothesized to share the properties of autosomes. We capitalized on the unusual structure of the sex chromosomes of emus, Dromaius novaehollandiae, which consist almost entirely of PAR shared by both sex chromosomes, to test this hypothesis. We compared recombination, linkage disequilibrium (LD), GC content, and nucleotide diversity between pseudoautosomal and autosomal loci derived from 11 emu bacterial artificial chromosome (BAC) clones that were mapped to chromosomes by fluorescent in situ hybridization. Nucleotide diversity (pi = 4N(e)mu) was not significantly lower in pseudoautosomal loci (14 loci, 1.9 +/- 2.4 x 10(-3)) than autosomal loci (8 loci, 4.2 +/- 6.1 x 10(-3)). By contrast, recombination per site within BAC-end sequences (rho = 4Nc) (pseudoautosomal, 3.9 +/- 6.9 x 10(-2); autosomal, 2.3 +/- 3.7 x 10(-2)) was higher and average LD (D{\textquoteright}) (pseudoautosomal, 4.2 +/- 0.2 x 10(-1); autosomal, 4.7 +/- 0.5 x 10(-1)) slightly lower in pseudoautosomal sequences. We also report evidence of deviation from a simple neutral model in the PAR and in autosomal loci, possibly caused by departures from demographic equilibrium, such as population growth. This study provides a snapshot of the population genetics of avian sex chromosomes at an early stage of differentiation.

}, keywords = {bacterial artificial chromosomes, Birds, DNA polymorphism, drosophila-miranda, fluorescent in situ hybridization, human genome, Linkage Disequilibrium, maximum-likelihood-estimation, molecular evolution, neo-y chromosome, nucleotide diversity, population-structure, pseudoautosomal region, recombination, Sex Chromosomes, statistical-method}, isbn = {0022-1503}, author = {Janes, D. E. and Ezaz, T. and Graves, J. A. M. and Edwards, S. V.} } @article {RN141, title = {Aves 3D: A new online resource for avian skeletal anatomy}, journal = {Integrative and Comparative Biology}, volume = {49}, year = {2009}, pages = {E213-E213}, type = {Journal Article}, abstract = {
P2.108
CLAESSENS, L.P.*; EDWARDS, S.V.; MARTINEZ, R.; KRZYZAK,
M.; ECKARDT, M.; LESLIE, G.; MARCUCCI, M.; NEABORE, S.; VRCEK, I.;
MOSS, S.; GRASSI, K.; College of the Holy Cross, Worcester, MA, Harvard
University, Cambridge, MA;
lclaesse@holycross.edu
Aves 3D: A new online resource for avian skeletal anatomy
Here we report the launch of a new National Science Foundation funded
online resource for avian skeletal anatomy, www.Aves3D.org, which will offer
three-dimensional models of a wide selection of skeletal elements of extant
and extinct birds. The Aves 3D database is produced through non-contact
laser scanning of skeletal material from, amongst others, the Harvard
Museum of Comparative Zoology and the Yale Peabody Museum of Natural
History. Database growth is fueled by undergraduate student research
projects, which involve a variety of functional and phylogenetic studies
supervised by both affiliated and external post-graduate students and
researchers. The online database will also serve as a digital archive for the
collections of contributing museums and allows for rapid global dissemination
of 3D digital data on common as well as rare and potentially fragile
specimens, in a format ready for a wide range of two and three-dimensional
computational analyses. The size of the database is currently limited, and
opportunities exist for initiating new student-based projects that will

contribute to database growth

}, issn = {1540-7063}, url = {https://icb.oxfordjournals.org/content/49/suppl_1/e191.full.pdf+html?sid=95c38d68-4642-4025-b836-0e70333fee73}, author = {Claessens, L. P. and Edwards, S. V. and Martinez, R. and Krzyzak, M. and Eckardt, M. and Leslie, G. and Marcucci, M. and Neabore, S. and Vrcek, I. and Moss, S. and Grassi, K.} } @article {RN143, title = {Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird}, journal = {Bmc Genomics}, volume = {10}, year = {2009}, type = {Journal Article}, abstract = {

Background

With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken.

Results

From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2\%), 24 (turtle, 1.3\%) and 479 (emu, 16.3\%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes.

Conclusion

Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50\% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.

}, issn = {1471-2164}, doi = {10.1186/1471-2164-10-s2-s8}, url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-10-S2-S8}, author = {Chapus, Charles and Edwards, Scott V.} } @article {RN142, title = {Variability in Sex-Determining Mechanisms Influences Genome Complexity in Reptilia}, journal = {Cytogenetic and Genome Research}, volume = {127}, year = {2009}, pages = {242-248}, type = {Journal Article}, abstract = {

In this review, we describe the history of amniote sex determination as a classic example of Darwinian evolution. We suggest that evolutionary changes in sex determination provide a foundation for understanding important aspects of chromosome and genome organization that otherwise appear haphazard in their origins and contents. Species with genotypic sex determination often possess heteromorphic sex chromosomes, whereas species with environmental sex determination lack them. Through a series of mutations followed by selection at key genes, sex-determining mechanisms have turned over many times throughout the amniote lineage. As a consequence, amniote genomes have undergone gains or losses of sex chromosomes. We review the genomic and ecological contexts in which either temperature-dependent or genotypic sex determination has evolved. Once genotypic sex determination emerges in a lineage, viviparity and heteromorphic sex chromosomes become more likely to evolve. For example, in extinct marine reptiles, genotypic sex determination apparently led to viviparity, which in turn facilitated their pelagic radiation. Sex chromosomes comprise genome regions that differ from autosomes in recombination rate, mutation rate, levels of polymorphism, and the presence of sex-determining and sexually antagonistic genes. In short, many aspects of amniote genome complexity, life history, and adaptive radiation appear contingent on evolutionary changes in sex-determining mechanisms.

}, issn = {1424-8581}, doi = {10.1159/000293283}, url = {http://www.karger.com/Article/Abstract/293283}, author = {Janes, D. E. and Organ, C. L. and Edwards, S. V.} } @article {921246, title = {Characterization, chromosomal location, and genomic neighborhood of a ratite ortholog of a gene with gonadal expression in mammals}, journal = {Integrative and Comparative Biology}, volume = {48}, number = {4}, year = {2008}, note = {

356GXTimes Cited:2Cited References Count:24

}, month = {Oct}, pages = {505-511}, abstract = {

A locus that we name SubA was discovered during large-scale sequencing and characterization of a bacterial artificial chromosome library from an emu, Dromaius novaehollandiae. This locus yields a significantly negative Tajimas D in emus and is conserved across emu, chicken, mouse, and human. Expression of SubA orthologs has been reported in human ovaries and in mouse testes, but remains unknown in emus. The locus was physically mapped onto a pair of microchromosomes in emus by fluorescent in situ hybridization and also in chicken as previously reported. By characterizing emu SubA in this article, we aim to improve current descriptions of the cascade of genes associated with avian sex differentiation. Future experimentation will report the expression of SubA in ratites, other birds, and nonavian reptiles.

}, keywords = {chicken, database, DNA polymorphism, Evolution, sequence, sex determination, statistical-method, tool}, isbn = {1540-7063}, author = {Janes, D. E. and Ezaz, T. and Graves, J. A. M. and Edwards, S. V.} } @article {921241, title = {Comparison of Species Tree Methods for Reconstructing the Phylogeny of Bearded Manakins (Aves: Pipridae, Manacus) from Multilocus Sequence Data}, journal = {Systematic Biology}, volume = {57}, number = {5}, year = {2008}, note = {

359OATimes Cited:17Cited References Count:100

}, pages = {719-731}, abstract = {

Although the power of multi-locus data in estimating species trees is apparent, it is also clear that the analytical methodologies for doing so are still maturing. For example, of the methods currently available for estimating species trees from multiocus data, the Bayesian method introduced by Liu and Pearl (2007; BEST) is the only one that provides nodal support values. Using gene sequences from five nuclear loci, we explored two analytical methods (deep coalescence and BEST) to reconstruct the species tree of the five primary Manacus OTUs: M. aurantiacus, M. candei, M. vitellinus, populations of M. manacus from west of the Andes (M. manacus (w)), and populations of M. manacus from east of the Andes (M. manacus (e)). Both BEST and deep coalescence supported a sister relationship between M. vitellinus and M. manacus (w). A lower probability tree from the BEST analysis and one of the most parsimonious deep coalescence trees also supported a sister relationship between M. candei and M. aurantiacus. Because hybrid zones connect the distributions of most Manacus species, we examined the potential influence of post-divergence gene flow on the sister relationship of parapatrically distributed M. vitellinus and M. manacus (w). An isolation-with-migration (IM) analysis found relatively high levels of gene flow between M. vitellinus and M. manacus (w). Whether the gene flow is obscuring a true sister relationship between M. manacus (w) and M. manacus (e) remained unclear, pointing to the need for more detailed models accommodating multispecies, multilocus DNA sequence data.

}, keywords = {bayesian-inference, divergence, DNA-sequences, gene trees, haplotype reconstruction, History, hybrid zone, incomplete lineage sorting, manakin, migration rates, Phylogeny, population parameters, single-nucleotide polymorphisms, species tree}, isbn = {1063-5157}, author = {Brumfield, R. T. and Liu, L. and Lum, D. E. and Edwards, S. V.} } @article {921261, title = {Developing markers for multilocus phylogenetics in non-model organisms: a test case with turtles}, journal = {Molecular Phylogenetics and Evolution}, volume = {49}, year = {2008}, pages = {514-525.}, author = {Thomson, R. C. and Shedlock, A. M. and Edwards, S. V. and Shaffer, H. B.} } @article {921251, title = {Divergence across Australia{\textquoteright}s Carpentarian Barrier: Statistical Phylogeography of the Red-Backed Fairy Wren(Malurus Melanocephalus)}, journal = {Evolution}, volume = {62}, number = {12}, year = {2008}, note = {

380CITimes Cited:37Cited References Count:98

}, month = {Dec}, pages = {3117-3134}, abstract = {

Multilocus analysis of phylogeography and population history is a powerful tool for understanding the origin, dispersal, and geographic structure of species over time and space. Using 36 genetic markers (29 newly developed anonymous nuclear loci, six introns and one from mitochondrial DNA, amounting to over 15 kb per individual), we studied population structure and demographic history of the red-backed fairy wren Malurus melanocephalus, a small passerine distributed in the northern and eastern part of Australia across the Carpentarian barrier. Analysis of anonymous loci markers revealed large amounts of genetic diversity (pi = 0.016 +/- 0.01; average number of SNPs per locus = 48; total number of SNPs = 1395), and neither nuclear nor mitochondrial gene trees showed evidence of reciprocal monophyly among Cape York (CY), Eastern Forest (EF), and Top End (TE) populations. Despite traditional taxonomy linking TE and CY populations to the exclusion of EF, we found that the CY population is genetically closer to the EF population, consistent with predicted area cladograms in this region. Multilocus coalescent analysis suggests that the CY population was separated from the other two regions approximately 0.27 million years ago, and that significant gene flow between the ER and the CY populations (similar to 2 migrants per generation) suggests geographic continuity in eastern Australia. By contrast, gene flow between the CY and the TE populations has been dampened by divergence across the Carpentarian barrier.

}, keywords = {ancestral population sizes, anonymous loci, carpentarian barrier, eastern australia, gene trees, historical demography, hybrid zones, intraspecific phylogeography, malurus melanocephalus, mitochondrial-DNA, phylogeography, plumage morphs, recombination rates, single-nucleotide polymorphisms, species divergence}, isbn = {0014-3820}, author = {Lee, J. Y. and Edwards, S. V.} } @article {921236, title = {High-speed developments in avian genomics}, journal = {Bioscience}, volume = {58}, number = {7}, year = {2008}, month = {Jul-Aug}, pages = {587-595}, author = {Bonneaud, C. and Burnside, J. and Edwards, S. V.} } @article {921256, title = {Three tiers of genome evolution in reptiles}, journal = {Integrative and Comparative Biology}, volume = {48}, number = {4}, year = {2008}, note = {

356GXTimes Cited:10Cited References Count:68

}, month = {Oct}, pages = {494-504}, abstract = {

Characterization of reptilian genomes is essential for understanding the overall diversity and evolution of amniote genomes, because reptiles, which include birds, constitute a major fraction of the amniote evolutionary tree. To better understand the evolution and diversity of genomic characteristics in Reptilia, we conducted comparative analyses of online sequence data from Alligator mississippiensis (alligator) and Sphenodon punctatus (tuatara) as well as genome size and karyological data from a wide range of reptilian species. At the whole-genome and chromosomal tiers of organization, we find that reptilian genome size distribution is consistent with a model of continuous gradual evolution while genomic compartmentalization, as manifested in the number of microchromosomes and macrochromosomes, appears to have undergone early rapid change. At the sequence level, the third genomic tier, we find that exon size in Alligator is distributed in a pattern matching that of exons in Gallus (chicken), especially in the 101200 bp size class. A small spike in the fraction of exons in the 301 bp1 kb size class is also observed for Alligator, but more so for Sphenodon. For introns, we find that members of Reptilia have a larger fraction of introns within the 101 bp2 kb size class and a lower fraction of introns within the 530 kb size class than do mammals. These findings suggest that the mode of reptilian genome evolution varies across three hierarchical levels of the genome, a pattern consistent with a mosaic model of genomic evolution.

}, keywords = {chicken genome, chromosomal evolution, DNA Methylation, family estrildidae aves, gallus-gallus-domesticus, lambrush chromosomes, mitochondrial, Phylogeny, protein-coding genes, squamate reptiles}, isbn = {1540-7063}, author = {Organ, C. L. and Moreno, R. G. and Edwards, S. V.} } @article {RN146, title = {Ecology of avian influenza virus in birds}, journal = {Journal of Infectious Diseases}, volume = {197}, year = {2008}, pages = {S29-S33}, type = {Journal Article}, abstract = {

Avian influenza A virus (an orthomyxovirus) is a zoonotic pathogen with a natural reservoir entirely in birds. The influenza virus genome is an 8-segment single-stranded RNA with high potential for in situ recombination. Two segments code for the hemagglutinin (H) and neuraminidase (N) antigens used for host-cell entry. At present, 16 H and 9 N subtypes are known, for a total of 144 possible different influenza subtypes, each with potentially different host susceptibility. With \>10,000 species of birds found in nearly every terrestrial and aquatic habitat, there are few places on earth where birds cannot be found. The avian immune system differs from that of humans in several important features, including asynchronous B and T lymphocyte systems and a polymorphic multigene immune complex, but little is known about the immunogenetics of pathogenic response. Postbreeding dispersal and migration and a naturally high degree of environmental vagility mean that wild birds have the potential to be vectors that transmit highly pathogenic variants great distances from the original sources of infection.

}, issn = {0022-1899}, doi = {10.1086/524991}, url = {http://jid.oxfordjournals.org/content/197/Supplement_1/S29.full7}, author = {Causey, Douglas and Edwards, Scott V.} } @article {RN144, title = {Estimating species trees using multiple-allele DNA sequence data}, journal = {Evolution}, volume = {62}, year = {2008}, pages = {2080-2091}, type = {Journal Article}, abstract = {
Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce
a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it becomes
more challenging to estimate relationships at the level of species, either because concatenation becomes inappropriate due to
conflicts among individual gene trees, or because the species from which multiple alleles have been sampled may not form
monophyletic groups in the estimated tree. We propose a Bayesian hierarchical model to reconstruct species trees from multiple-
allele, multilocus sequence data, building on a recently proposed method for estimating species trees from single allele multilocus
data. A two-step Markov Chain Monte Carlo (MCMC) algorithm is adopted to estimate the posterior distribution of the species tree.
The model is applied to estimate the posterior distribution of species trees for two multiple-allele datasets{\textemdash}yeast (
Saccharomyces
)
and birds (
Manacus
{\textemdash}manakins). The estimates of the species trees using our method are consistent with those inferred from other
methods and genetic markers, but in contrast to other species tree methods, it provides credible regions for the species tree. The
Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics
and phylogenetics.
}, issn = {0014-3820}, doi = {10.1111/j.1558-5646.2008.00414.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2008.00414.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Liu, Liang and Pearl, Dennis K. and Brumfield, Robb T. and Edwards, Scott V.} } @article {RN145, title = {Prevalence and evolutionary origins of autoimmune susceptibility alleles in natural mouse populations}, journal = {Genes and Immunity}, volume = {9}, year = {2008}, pages = {61-68}, type = {Journal Article}, abstract = {
The evolutionary origin of genetic diversity in the SLAM/CD2 gene cluster, implicated in autoimmune lupus susceptibility in
mice, was investigated by sequence analysis of exons from six members of the cluster in 48 wild mouse samples derived from
the global mouse population. A total of 80 coding region SNPs were identified among the six genes analyzed, indicating that
this gene cluster is highly polymorphic in natural mouse populations. Phylogenetic analyses of these allelic sequences revealed
clustering of alleles derived from multiple Mus species and subspecies, indicating alleles at several SLAM/CD2 loci were
present in ancestral Mus populations prior to speciation and have persisted as polymorphisms for more than 1 million years.
Analyses of nonsynonymous/synonymous ratios using likelihood codon substitution models identified several segments in
Cd229, Cd48 and Cd84 that were impacted by positive diversifying selective pressures. These findings support
the interpretation that selection favoring the generation and retention of functional polymorphisms has played a role in the
evolutionary origin of genetic polymorphisms that are predisposing to autoimmunity.
}, issn = {1466-4879}, doi = {10.1038/sj.gene.6364446}, url = {http://www.nature.com/gene/journal/v9/n1/full/6364446a.html}, author = {Limaye, N. and Belobrajdic, K. A. and Wandstrat, A. E. and Bonhomme, F. and Edwards, S. V. and Wakeland, E. K.} } @article {921221, title = {High-resolution species trees without concatenation}, journal = {Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {14}, year = {2007}, note = {0027-8424 (Print)Comparative StudyJournal ArticleResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.}, month = {Apr 3}, pages = {5936-41}, abstract = {The vast majority of phylogenetic models focus on resolution of gene trees, despite the fact that phylogenies of species in which gene trees are embedded are of primary interest. We analyze a Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process. Application of the model to a 106-gene data set from yeast shows that the set of gene trees recovered by statistically acknowledging the shared but unknown species tree from which gene trees are sampled is much reduced compared with treating the history of each locus independently of an overarching species tree. The analysis also yields a concentrated posterior distribution of the yeast species tree whose mode is congruent with the concatenated gene tree but can do so with less than half the loci required by the concatenation method. Using simulations, we show that, with large numbers of loci, highly resolved species trees can be estimated under conditions in which concatenation of sequence data will positively mislead phylogeny, and when the proportion of gene trees matching the species tree is <10\%. However, when gene tree/species tree congruence is high, species trees can be resolved with just two or three loci. These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories.}, keywords = {*DNA, Concatenated, *Models, Genetic, *Models, Statistical, Alleles, Base Composition, Base Sequence, Bayes Theorem, DNA, Fungal/genetics, Genomics, Likelihood Functions, Markov Chains, Molecular Sequence Data, Monte Carlo Method, Phylogeny, Saccharomyces cerevisiae/genetics, Sequence Analysis, DNA, Species Specificity, Stochastic Processes}, author = {Edwards, S. V. and Liu, L. and Pearl, D. K.} } @article {921216, title = {Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes}, journal = {Evolution Int J Org Evolution}, volume = {61}, number = {2}, year = {2007}, note = {

0014-3820 (Print)Journal ArticleResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.

}, month = {Feb}, pages = {346-67}, abstract = {

The Andean uplift played important roles in the historical diversification of Neotropical organisms, both by producing new high-elevation habitats that could be colonized and by isolating organisms on either side of the mountains. Here, we present a molecular phylogeny of Thamnophlius antshrikes, a clade of 30 species whose collective distribution spans nearly the entirety of lowland habitats in tropical South America, the eastern slope foothills of the Andes, and the tepuis of northern South America. Our goal was to examine the role of the Andes in the diversification of lowland and foothill species. Using parsimony and Bayesian ancestral state reconstructions of a three-state distribution character (lowland-restricted, lowland-to-highland, highland-restricted), we found that the Andes were colonized twice independently and the tepuis once from lowland-restricted ancestors. Over the entire evolutionary history of Thamnophilus, the highest transition rates were between highland-restricted and lowland-to-highland distributions, with extremely low rates into and out of lowland-restricted distributions. This pattern suggests lowland-restricted distributions are limited not by physiological constraints, but by other forces, such as competition. These results highlight the need for additional comparative studies in elucidating processes associated with the colonization of high-elevation habitats and the differentiation of populations within them.

}, keywords = {*Ecosystem, *Evolution, *Geography, Animals, Bayes Theorem, demography, Passeriformes/classification/*genetics/*physiology, South America, Variation (Genetics)}, author = {Brumfield, R. T. and Edwards, S. V.} } @article {921226, title = {Origin of avian genome size and structure in non-avian dinosaurs}, journal = {Nature}, volume = {446}, number = {7132}, year = {2007}, note = {

143JSTimes Cited:45Cited References Count:30

}, month = {Mar 8}, pages = {180-184}, abstract = {

Avian genomes are small and streamlined compared with those of other amniotes by virtue of having fewer repetitive elements and less non-coding DNA(1,2). This condition has been suggested to represent a key adaptation for flight in birds, by reducing the metabolic costs associated with having large genome and cell sizes(3,4). However, the evolution of genome architecture in birds, or any other lineage, is difficult to study because genomic information is often absent for long-extinct relatives. Here we use a novel bayesian comparative method to show that bone-cell size correlates well with genome size in extant vertebrates, and hence use this relationship to estimate the genome sizes of 31 species of extinct dinosaur, including several species of extinct birds. Our results indicate that the small genomes typically associated with avian flight evolved in the saurischian dinosaur lineage between 230 and 250 million years ago, long before this lineage gave rise to the first birds. By comparison, ornithischian dinosaurs are inferred to have had much larger genomes, which were probably typical for ancestral Dinosauria. Using comparative genomic data, we estimate that genome-wide interspersed mobile elements, a class of repetitive DNA, comprised 5 - 12\% of the total genome size in the saurischian dinosaur lineage, but was 7 - 19\% of total genome size in ornithischian dinosaurs, suggesting that repetitive elements became less active in the saurischian lineage. These genomic characteristics should be added to the list of attributes previously considered avian but now thought to have arisen in non-avian dinosaurs, such as feathers(5), pulmonary innovations 6, and parental care and nesting

}, keywords = {c-value, cell-size, DNA-content, Evolution, growth, patterns, strategies}, isbn = {0028-0836}, author = {Organ, C. L. and Shedlock, A. M. and Meade, A. and Pagel, M. and Edwards, S. V.} } @article {921231, title = {Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {8}, year = {2007}, note = {

Shedlock, Andrew MBotka, Christopher WZhao, ShayingShetty, JyotiZhang, TingtingLiu, Jun SDeschavanne, Patrick JEdwards, Scott VengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2007/02/20 09:00Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2767-72. Epub 2007 Feb 16.

}, month = {Feb 20}, pages = {2767-72}, abstract = {

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of approximately 65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome. The sequences reported in this paper have been deposited in the GenBank database (accession nos. CZ 250707-CZ 257443 and DX 390731-DX 389174).

}, keywords = {*Genomics, *Phylogeny, Animals, Base Composition/genetics, Birds/*genetics, Genetic Variation, Genome/*genetics, Mammals/genetics, Molecular Sequence Data, Reptiles/*genetics, Retroelements/genetics, Tandem Repeat Sequences/genetics}, isbn = {0027-8424 (Print)0027-8424 (Linking)}, author = {Shedlock, A. M. and Botka, C. W. and Zhao, S. and Shetty, J. and T. Zhang and Liu, J. S. and Deschavanne, P. J. and Edwards, S. V.} } @article {RN147, title = {Evolutionary genetics of Carpodacus mexicanus, a recently colonized host of a bacterial pathogen, Mycoplasma gallisepticum}, journal = {Genetica}, volume = {129}, year = {2007}, pages = {217-225}, type = {Journal Article}, abstract = {
Abstract
We present molecular data documenting
how introduction to the eastern United States and an
epizootic involving a bacterial pathogen has affected
the genetic diversity of house finches, a cardueline
songbird. Population bottlenecks during introduction
can cause loss of genetic variation and may negatively
affect a population{\textquoteright}s ability to adapt to novel stressors
such as disease. Although a genome-wide survey using
Amplified Fragment Length Polymorphism (AFLP)
markers suggests little loss of genetic diversity in
introduced populations, an epizootic of bacterial
Mycoplasma
has nonetheless caused dramatic declines
in the eastern US population. Sequence analysis of a
candidate gene for pathogen resistance in the Major
Histocompatibity Complex (MHC) in pre- and post-
epizootic population samples reveals allele frequency
shifts since introduction of the pathogen, but similar
shifts are also observed in control populations not ex-
posed to the bacteria, and in a neutral non-coding lo-
cus. Expression studies using a novel subtractive
hybridization approach indicate decreased expression
of the class II MHC locus upon exposure to
Myco-
plasma
, a pattern also seen in MHC class I loci in mice
infected with cytomegalovirus and consistent with
manipulation of the finch immune system by
Myco-
plasma
. These results will be further expanded using
experimental studies as well as examination of evolu-
tion of the pathogen genome itself.
}, issn = {0016-6707}, doi = {10.1007/s10709-006-9016-6}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.377.6221\&rep=rep1\&type=pdf}, author = {Hess, Christopher M. and Wang, Zhenshan and Edwards, Scott V.} } @article {921206, title = {Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers}, journal = {Biol Lett}, volume = {2}, number = {3}, year = {2006}, note = {

1744-9561 (Print)Journal ArticleResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.

}, month = {Sep 22}, pages = {466-9}, abstract = {

We used ancient DNA analysis of seven museum specimens of the endangered North American ivory-billed woodpecker (Campephilus principalis) and three specimens of the species from Cuba to document their degree of differentiation and their relationships to other Campephilus woodpeckers. Analysis of these mtDNA sequences reveals that the Cuban and North American ivory bills, along with the imperial woodpecker (Campephilus imperialis) of Mexico, are a monophyletic group and are roughly equidistant genetically, suggesting each lineage may be a separate species. Application of both internal and external rate calibrations indicates that the three lineages split more than one million years ago, in the Mid-Pleistocene. We thus can exclude the hypothesis that Native Americans introduced North American ivory-billed woodpeckers to Cuba. Our sequences of all three woodpeckers also provide an important DNA barcoding resource for identification of non-invasive samples or remains of these critically endangered and charismatic woodpeckers.

}, keywords = {*Evolution, Animals, Bayes Theorem, Birds/*genetics/*physiology, Conservation of Natural Resources, Cuba, DNA, Mitochondrial/metabolism, Ecology, Likelihood Functions, Models, Biological, North America, Phylogeny, Polymerase Chain Reaction}, author = {Fleischer, R. C. and Kirchman, J. J. and Dumbacher, J. P. and Bevier, L. and Dove, C. and Rotzel, N. C. and Edwards, S. V. and Lammertink, M. and Miglia, K. J. and Moore, W. S.} } @article {921211, title = {Tuatara (Sphenodon) genomics: BAC library construction, sequence survey, and application to the DMRT gene family}, journal = {J Hered}, volume = {97}, number = {6}, year = {2006}, note = {

0022-1503 (Print)Journal ArticleResearch Support, N.I.H., ExtramuralResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.

}, month = {Nov-Dec}, pages = {541-8}, abstract = {

The tuatara (Sphenodon punctatus) is of "extraordinary biological interest" as the most distinctive surviving reptilian lineage (Rhyncocephalia) in the world. To provide a genomic resource for an understanding of genome evolution in reptiles, and as part of a larger project to produce genomic resources for various reptiles (evogen.jgi.doe.gov/second_levels/BACs/our_libraries.html), a large-insert bacterial artificial chromosome (BAC) library from a male tuatara was constructed. The library consists of 215 424 individual clones whose average insert size was empirically determined to be 145 kb, yielding a genomic coverage of approximately 6.3x. A BAC-end sequencing analysis of 121 420 bp of sequence revealed a genomic GC content of 46.8\%, among the highest observed thus far for vertebrates, and identified several short interspersed repetitive elements (mammalian interspersed repeat-type repeats) and long interspersed repetitive elements, including chicken repeat 1 element. Finally, as a quality control measure the arrayed library was screened with probes corresponding to 2 conserved noncoding regions of the candidate sex-determining gene DMRT1 and the DM domain of the related DMRT2 gene. A deep coverage contig spanning nearly 300 kb was generated, supporting the deep coverage and utility of the library for exploring tuatara genomics.

}, keywords = {*Chromosomes, Artificial, Bacterial, *Multigene Family, Animals, Bayes Theorem, Gene Library, genome, Genomics/methods, Male, Phylogeny, Reptiles/*genetics, Transcription Factors/classification/*genetics}, author = {Wang, Z. and Miyake, T. and Edwards, S. V. and Amemiya, C. T.} } @article {RN148, title = {A cDNA macroarray approach to parasite-induced gene expression changes in a songbird host: genetic response of house finches to experimental infection by Mycoplasma gallisepticum}, journal = {Molecular Ecology}, volume = {15}, year = {2006}, pages = {1263-1273}, type = {Journal Article}, abstract = {
In 1994, the bacterial parasite
Mycoplasma gallisepticum
expanded its host range and
swept through populations of a novel host {\textemdash} eastern US populations of the house finch
(
Carpodacus mexicanus
). This epizootic caused a dramatic decline in finch population
numbers, has been shown to have caused strong selection on house finch morphology, and
presumably caused evolutionary change at the molecular level as finches evolved enhanced
resistance. As a first step toward identifying finch genes that respond to infection by
Mycoplasma
and which may have experienced natural selection by this parasite, we used
suppression subtractive hybridization (SSH) and cDNA macroarray approaches to identify
differentially expressed genes regulated by the
Mycoplasma
parasite. Two subtractive cDNA
libraries consisting of 16 512 clones were developed from spleen using an experimentally
uninfected bird as the {\textquoteleft}tester{\textquoteright} and an infected bird as {\textquoteleft}driver{\textquoteright}, and vice versa. Two hundred
and twenty cDNA clones corresponding 34 genes with known vertebrate homologues and a
large number of novel transcripts were found to be qualitatively up- or down-regulated
genes by high-density filter hybridization. These gene expression changes were further
confirmed by a high throughout reverse Northern blot approach and in specific cases by
targeted Northern analysis.
BLAST
searches show that heat shock protein (HSP) 90, MHC
II-associated invariant chain (CD74), T-cell immunoglobulin mucin 1 (TIM1), as well as
numerous novel expressed genes not found in the databases were up- or down-regulated
by the host in response to this parasite. Our results and macroarray resources provide a
foundation for molecular co-evolutionary studies of the
Mycoplasma
parasite and its
recently colonized avian host.
}, issn = {0962-1083}, doi = {10.1111/j.1365-294X.2005.02753.x}, url = {http://www.auburn.edu/cosam/faculty/biology/hill/lab/documents/138.pdf}, author = {Wang, Z. S. and Farmer, K. and Hill, G. E. and Edwards, S. V.} } @article {507536, title = {Avian Genetic Resources Collections: Archives of Evolutionary and Environmental History}, journal = {Auk}, volume = {122}, year = {2005}, pages = {979-984}, url = {http://www.aoucospubs.org/doi/full/10.1642/0004-8038\%282005\%29122\%5B0979\%3AFOAGRC\%5D2.0.CO\%3B2}, author = {SV Edwards and Birks, S and RT Brumfield and R Hanner} } @article {507541, title = {Conservation genetics and Pacific fisheries bycatch: mitochondrial differentiation and population assignment in black-footed albatrosses ( Phoebastria nigripes )}, journal = {Conservation Genetics}, volume = {6}, year = {2005}, pages = {289-295}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.377.1447\&rep=rep1\&type=pdf}, author = {Walsh, HE and SV Edwards} } @article {507551, title = {Exploration of phylogenetic data using a global sequence analysis method}, journal = {BMC Evolutionary Biology}, volume = {5}, year = {2005}, pages = {63}, abstract = {

Background

Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.

Results

Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses {\textendash} in particular explicit statements of homology inherent in character matrices {\textendash} the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 γ-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers.

Conclusion

The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis.

}, url = {http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-5-63}, author = {Chapus, C and C Dufraigne and S Edwards and Giron, A and Fertil, B and P Deschavanna} } @article {507521, title = {Phylogenetics of modern birds in the era of genomics}, journal = {Proceeding of the Royal Society of London series}, volume = {272}, year = {2005}, pages = {979-992}, abstract = {
In the 14 years since the first higher-level bird phylogenies based on DNA sequence data, avian
phylogenetics has witnessed the advent and maturation of the genomics era, the completion of the chicken
genome and a suite of technologies that promise to add considerably to the agenda of avian phylogenetics.
In this review, we summarize current approaches and data characteristics of recent higher-level bird studies
and suggest a number of as yet untested molecular and analytical approaches for the unfolding tree of life
for birds. A variety of comparative genomics strategies, including adoption of objective quality scores for
sequence data, analysis of contiguous DNA sequences provided by large-insert genomic libraries, and the
systematic use of retroposon insertions and other rare genomic changes all promise an integrated
phylogenetics that is solidly grounded in genome evolution. The avian genome is an excellent testing
ground for such approaches because of the more balanced representation of single-copy and repetitive
DNA regions than in mammals. Although comparative genomics has a number of obvious uses in avian
phylogenetics, its application to large numbers of taxa poses a number of methodological and
infrastructural challenges, and can be greatly facilitated by a {\textquoteleft}community genomics{\textquoteright} approach in which
the modest sequencing throughputs of single PI laboratories are pooled to produce larger, complementary
datasets. Although the polymerase chain reaction era of avian phylogenetics is far from complete, the
comparative genomics era{\textemdash}with its ability to vastly increase the number and type of molecular characters
and to provide a genomic context for these characters{\textemdash}will usher in a host of new perspectives and
opportunities for integrating genome evolution and avian phylogenetics.
}, url = {https://www.researchgate.net/profile/Andrew_Shedlock/publication/7721156_Phylogenetics_of_modern_birds_in_the_era_of_genomics._Proc_R_Soc_Lond_B_Biol_Sci/links/53dbcc5c0cf2cfac9928fa2b.pdf}, author = {SV Edwards and Jennings, WB and Shedlock, AM} } @inbook {507506, title = {Gene and Genome Evolution}, booktitle = {Evolution}, year = {2005}, publisher = {Sinauer Associates}, organization = {Sinauer Associates}, address = {Sunderland}, author = {SV Edwards} } @article {507516, title = {Speciation in birds: genes, geography and sexual selection}, journal = {Proc. Natl. Acad. Sci. (USA)}, volume = {102}, year = {2005}, pages = {6550-6557}, abstract = {
Molecular studies of speciation in birds over the last three decades
have been dominated by a focus on the geography, ecology, and
timing of speciation, a tradition traceable to Mayr{\textquoteright}s
Systematics
and the Origin of Species
. However, in the recent years, interest in
the behavioral and molecular mechanisms of speciation in birds has
increased, building in part on the older traditions and observations
from domesticated species. The result is that many of the same
mechanisms proffered for model lineages such as
Drosophila
{\textemdash}
mechanisms such as genetic incompatibilities, reinforcement, and
sexual selection{\textemdash}are now being seriously entertained for birds,
albeit with much lower resolution. The recent completion of a draft
sequence of the chicken genome, and an abundance of single-
nucleotide polymorphisms on the autosomes and sex chromo-
somes, will dramatically accelerate research on the molecular
mechanisms of avian speciation over the next few years. The
challenge for ornithologists is now to inform well studied exam-
ples of speciation in nature with increased molecular resolu-
tion{\textemdash}to clone speciation genes if they exist{\textemdash}and thereby evaluate
the relative roles of extrinsic, intrinsic, deterministic, and stochastic
causes for avian diversification.
}, url = {http://www.pnas.org/content/102/suppl_1/6550.full}, author = {SV Edwards and Kingan, SB and Calkins, JD and Balakrishnan, CN and W Bryan Jennings and Swanson, WJ and Sorenson, MD} } @article {507531, title = {Speciational history of Australian grass finches ( Poephila ) inferred from 30 gene trees}, journal = {Evolution}, volume = {59}, year = {2005}, pages = {2033-2047}, abstract = {

Multilocus genealogical approaches are still uncommon in phylogeography and historical demography, fields which have been dominated by microsatellite markers and mitochondrial DNA, particularly for vertebrates. Using 30 newly developed anonymous nuclear loci, we estimated population divergence times and ancestral population sizes of three closely related species of Australian grass finches (Poephila) distributed across two barriers in northern Australia. We verified that substitution rates were generally constant both among lineages and among loci, and that intralocus recombination was uncommon in our dataset, thereby satisfying two assumptions of our multilocus analysis. The reconstructed gene trees exhibited all three possible tree topologies and displayed considerable variation in coalescent times, yet this information provided the raw data for maximum likelihood and Bayesian estimation of population divergence times and ancestral population sizes. Estimates of these parameters were in close agreement with each other regardless of statistical approach and our Bayesian estimates were robust to prior assumptions. Our results suggest that black-throated finches (Poephila cincta) diverged from long-tailed finches (P. acuticauda and P. hecki) across the Carpentarian Barrier in northeastern Australia around 0.6 million years ago (mya), and that P. acuticauda diverged from P. hecki across the Kimberley Plateau{\textendash}Arnhem Land Barrier in northwestern Australia approximately 0.3 mya. Bayesian 95\% credibility intervals around these estimates strongly support Pleistocene timing for both speciation events, despite the fact that many gene divergences across the Carpentarian region clearly predated the Pleistocene. Estimates of ancestral effective population sizes for the basal ancestor and long-tailed finch ancestor were large (about 521,000 and about 384,000, respectively). Although the errors around the population size parameter estimates are considerable, they are the first for birds taking into account multiple sources of variance.

}, url = {http://www.bioone.org/doi/abs/10.1554/05-280.1}, author = {Jennings, WB and SV Edwards} } @article {507501, title = {Hitchhiking and recombination in birds: evidence from Mhc-linked and unlinked loci in red-winged blackbirds (Agelaius phoeniceus)}, journal = {Genetical Research}, volume = {84}, year = {2004}, pages = {175-192}, abstract = {
Hitchhiking phenomena and genetic recombination have important consequences for a variety of fields for which birds are model species, yet we know virtually nothing about naturally occurringrates of recombination or the extent of linkage disequilibrium in birds. We took advantage of apreviously sequenced cosmid clone from Red-winged Blackbirds (Agelaius phoeniceus) bearing a highly polymorphic Mhc class II gene, Agph-DAB1, to measure the extent of linkage disequilibrium acrossy 40 kb of genomic DNA and to determine whether non-coding nucleotide diversity was elevated as a result of physical proximity to a target of balancing selection. Application of coalescent theory predicts that the hitchhiking effect is enhanced by the larger effective population size of blackbirds compared with humans, despite the presumably higher rates of recombination in birds. We surveyed sequence polymorphism at three Mhc-linked loci occurring 1. 5{\textendash}40 kb away from Agph-DAB1 and found that nucleotide diversity was indistinguishable from that found at three presumably unlinked, non-coding introns (b -actin intron 2, b-fibrinogen intron 7 and rhodopsin intron 2). Linkage disequilibrium as measured by Lewontin{\textquoteright}s D{\textquoteright} was found only across a few hundred base pairs within any given locus, and was not detectable among any Mhc-linked loci. Estimated rates of the per site recombination rater derived from three different analytical methods suggest that the amounts of recombination in blackbirds are up to two orders of magnitude higher than in humans, a discrepancy that cannot be explained entirely by the higher effective population size of blackbirds relative to humans. In addition, the ratio of the number of estimated recombination events per mutation frequently exceeds 1, as in Drosophila, again much higher than estimates in humans. Although the confidence limits of the blackbird estimates themselves span an order of magnitude, these data suggest that in blackbirds the hitchhiking effect for this region is negligible and may imply that the per site per individual recombination rate is high, resembling those of Drosophila more than those of humans.
}, author = {SV Edwards and Smith, M} } @article {507496, title = {Reconciling actual and inferred population histories in the House FInch (Carpodacus mexicanus) by AFLP analysis}, journal = {Evolution}, volume = {57}, year = {2003}, pages = {2852-2864}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.133.7999\&rep=rep1\&type=pdf}, author = {Wang, Z and Hill, GE and Baker, AJ and SV Edwards} } @article {507486, title = {Australo-Papuan Babblers}, journal = {Encyclopedia of Birds}, year = {2003}, author = {SV Edwards} } @article {507481, title = {The utility of single nucleotide polymorphisms in inferences of population history}, journal = {Trends in Ecology and Evolution}, volume = {18}, year = {2003}, pages = {249-256}, abstract = {

Single nucleotide polymorphisms (SNPs) represent the most widespread type of sequence variation in genomes, yet they have only emerged recently as valuable genetic markers for revealing the evolutionary history of populations. Their occurrence throughout the genome also makes them ideal for analyses of speciation and historical demography, especially in light of recent theory suggesting that many unlinked nuclear loci are needed to estimate population genetic parameters with statistical confidence. In spite of having lower variation compared with microsatellites, SNPs should make the comparison of genomic diversities and histories of different species (the core goal of comparative biogeography) more straightforward than has been possible with microsatellites. The most pervasive, but correctable, complication to SNP analysis is a bias towards analyzing only the most variable loci, an artifact that is usually introduced by the limited number of individuals used to screen initially for polymorphisms. Although the use of SNPs as markers in population studies is still new, innovative methods for SNP identification, automated screening, haplotype inference and statistical analysis might quickly make SNPs the marker of choice.

}, url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347\%2803\%2900018-1?_returnURL=http\%3A\%2F\%2Flinkinghub.elsevier.com\%2Fretrieve\%2Fpii\%2FS0169534703000181\%3Fshowall\%3Dtrue\&cc=y=}, author = {Brumfield, RD and D Nickerson and P Beerli and SV Edwards} } @article {507471, title = {Estimating divergence times from molecular data on population genetic and phylogenetic time scales}, journal = {Annual Review of Ecology and Systematics}, volume = {33}, year = {2002}, pages = {707-740}, abstract = {

Molecular clocks have profoundly influenced modern views on the
timing of important events in evolutionary history. We review recent advances in estimating divergence times from molecular data, emphasizing the continuum between processes at the phylogenetic and population genetic scales. On the phylogenetic scale, we address the complexities of DNA sequence evolution as they relate to estimating divergences, focusing on models of nucleotide substitution and problems associated with among-site and among-lineage rate variation. On the population genetic scale, we review advances in the incorporation of ancestral population processes into the estimation of divergence times between recently separated species. Throughout the review we emphasize new statistical methods and the importance of model testing during the process of divergence time estimation.

}, url = {http://www.jstor.org/stable/3069277?seq=1$\#$page_scan_tab_contents}, author = {Arbogast, Brian S. and Edwards, Scott V. and Wakeley, J.} } @article {507446, title = {The evolution of major histocompatibility genes in birds}, journal = {Bioscience }, volume = {52}, year = {2002}, pages = {431}, abstract = {
SCALING UP AND TAKING A GENOMIC
APPROACH TO THE MAJOR HISTO-COMPATIBILTY COMPLEX (MHC)
OF BIRDS REVEALS SURPRISING DEPARTURES FROM GENERALITIES FOUND IN MAMMALS IN BOTH LARGE - SCALE STRUCTURE AND THE MECHANISMS SHAPING THE EVOLUTION
OF THE MHC
}, url = {https://bioscience.oxfordjournals.org/content/52/5/423.full.pdf+html}, author = {Hess, CM and SV Edwards} } @article {507461, title = {The evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs}, journal = {American Naturalist}, volume = {106}, year = {2002}, pages = {539-552}, abstract = {
It has been proposed that intron and genome sizes in birds
are reduced in comparison with mammals because of the metabolic
demands of flight. To test this hypothesis, we examined the sizes of
14 introns in a nonflying relative of birds, the American alligator (
Al-
ligator mississippiensis
), and in 19 flighted and flightless birds in 12
taxonomic orders. Our results indicate that a substantial fraction (66\%)
of the reduction in intron size as well as in genome size had already
occurred in nonflying archosaurs. Using phylogenetically independent
contrasts, we found that the proposed inverse correlation of genome
size and basal metabolic rate (BMR) is significant among amniotes
and archosaurs, whereas intron and genome size variation within birds
showed no significant correlation with BMR. We show statistically that
the distribution of genome sizes in birds and mammals is underdis-
persed compared with the Brownian motion model and consistent
with strong stabilizing selection; that genome size differences between
vertebrate clades are overdispersed and punctuational; and that evo-
lution of BMR and avian intron size is consistent with Brownian mo-
tion. These results suggest that the contrast between genome size/BMR
and intron size/BMR correlations may be a consequence of different
intensities of selection for these traits and that we should not expect
changes in intron size to be significantly associated with metabolically
costly behaviors such as flight.
}, url = {http://www.jstor.org/stable/10.1086/342079}, author = {Waltari, E and SV Edwards} } @article {507416, title = {A genomic schism in birds revealed by phylogenetic analysis of DNA strings}, journal = {Systematic Biology}, volume = {51}, year = {2002}, pages = {599-613}, abstract = {

The molecular systematics of vertebrates has been based entirely on alignments of primary structures of macromolecules; however, higher order features of DNA sequences not used in traditional studies also contain valuable phylogenetic information. Recent molecular data sets conflict over the phylogenetic placement of flightless birds (ratites - paleognaths), but placement of this clade critically influences interpretation of character change in birds. To help resolve this issue, we applied a new bioinformatics approach to the largest molecular data set currently available. We distilled nearly one megabase (1 million base pairs) of heterogeneous avian genomic DNA from 20 birds and an alligator into genomic signatures, defined as the complete set of frequencies of short sequence motifs (strings), thereby providing a way to directly compare higher order features of nonhomologous DNA sequences. Phylogenetic analysis and principal component analysis of the signatures strongly support the traditional hypothesis of basal ratites and monophyly of the nonratite birds (neognaths) and imply that ratite genomes are linguistically primitive within birds, despite their base compositional similarity to neognath genomes. Our analyses show further that the phylogenetic signal of genomic signatures are strongest among deep splits within vertebrates. Despite clear problems with phylogenetic analysis of genomic signatures, our study raises intriguing issues about the biological and genomic differences that fundamentally differentiate paleognaths and neognaths. [Bioinformatics; CpG island; genomics; isochore; ratite.]

}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.377.6288\&rep=rep1\&type=pdf}, author = {SV Edwards and Fertil, B and Giron, A and Deschavanne, PJ} } @article {507476, title = {An Mhc component to kin recognition and mate choice in birds: predictions, progress, and prospects}, journal = {American Naturalist}, volume = {106}, year = {2002}, pages = {225-237}, abstract = {
The major histocompatibility complex (Mhc) has been identified as a locus influencing disease resistance, mate choice, and kin recognition in mammals and fish. However, it is unclear whether the mechanisms by which Mhc genes influence behavior in mammals are applicable to other nonmammalian vertebrates such as birds. We review the biology of Mhc genes with particular reference to their relevance to avian mating and social systems. New genomics ap-proaches recently have been applied to the Mhcs of chickens, quail, and several icons of avian behavioral ecology, including red-winged blackbirds (Agelaius phoeniceus) and house finches (Carpodacus mex-icanus). The predominance of concerted evolution at avian Mhc loci makes such methods attractive for providing access to this compli-cated multigene family. Although some biological processes influ-enced by Mhc in mammals are physiologically implausible for birds, Mhc could influence cues that form well-known bases for mate choice in birds by influencing the health and vigor of individuals. The tight associations of Mhc variation and disease resistance in chickens raise hope that finding associations of Mhc genes, disease, and mate choice in natural populations of birds will be as fruitful as in mammalian systems.
}, url = {http://www.jstor.org/stable/10.1086/342897?seq=1$\#$page_scan_tab_contents}, author = {Zelano, B and SV Edwards} } @article {507451, title = {Out of Gondwana: the origin of passerine birds}, journal = {Trends in Ecology and Evolution}, volume = {17}, year = {2002}, pages = {347-349}, abstract = {
Two recent papers analysing nuclear DNA sequence data shed new light on the origin of perching birds (Passeriformes) and the structure of their radiation. Both papers find that the New Zealand wrens Acanthisitta fall at the base of the passerine radiation, implying an origin of this clade in Gondwana. Additionally, among oscine passerines (songbirds), both papers fail to support a sister group relationship between the largely Australo{\textendash}Papuan Corvida and the Afro{\textendash}Eurasian Passerida, as outlined in Sibley and Ahlquist{\textquoteright}s tapestry. Rather, they converge on a phylogeny in which the Passerida is nested within the Corvida, suggesting an origin of songbirds in eastern Gondwana (Australia plus New Guinea). Finally, a Cretaceous origin of passerine birds is supported by the new data, albeit more on grounds of biogeography than of molecular clocks. The new papers solidify a synthesis of paleontological, phylogenetic and molecular data that has been growing over the past decade, and pave the way for a new generation of comparative studies of passerines.
}, url = {https://www.researchgate.net/profile/Walter_Boles/publication/222659063_Out_of_Gondwana_the_origin_of_passerine_birds/links/0f3175351d5decab69000000.pdf}, author = {SV Edwards and WE Boles} } @article {507456, title = {A phylogeny of megapodes (Aves: Megapodidae) based on nuclear and mitochondrial DNA sequences}, journal = {Molecular Phylogenetics and Evolution}, volume = {23}, year = {2002}, pages = {408-421}, abstract = {
DNA sequences from the first intron of the nuclear gene rhodopsin (RDP1) and from the mitochondrial gene ND2 were used to construct a phylogeny of the avian family Megapodiidae. RDP1 sequences evolved about six times more slowly than ND2 and showed less homoplasy, substitution bias, and rate heterogeneity across sites. Analysis of RDP1 produced a phylogeny that was well resolved at the genus level, but RDP1 did not evolve rapidly enough for intrageneric comparisons. The ND2 phylogeny resolved intrageneric relationships and was congruent with the RDP1 phylogeny except for a single node: this node was the only aspect of tree topology sensitive to weighting in parsimony analyses. Despite differences in sequence evolution, RDP1 and ND2 contained congruent phylogenetic signal and were combined to produce a phylogeny that reflects the resolving power of both genes. This phylogeny shows an early split within the megapodes, leading to two major clades: (1) Macrocephalon and the mound-building genera Talegalla, Leipoa, Aepypodius, and Alectura, and (2) Eulipoa and Megapodius. It differs significantly from previous hy-potheses based on morphology but is consistent with affiliations suggested by a recent study of parasitic chewing lice.
}, url = {https://www.researchgate.net/profile/Sharon_Birks/publication/11276031_A_phylogeny_of_the_megapodes_\%28Aves_Megapodiidae\%29_based_on_nuclear_and_mitochondrial_DNA_sequences/links/0a85e537138e926b22000000.pdf}, author = {Birks, S and SV Edwards} } @book {921196, title = {Molecular genetic markers in the analysis of seabird bycatch populations}, series = {Seabird Bycatch: Trends,Roadblocks and Solutions}, volume = {2001}, number = {1}, year = {2001}, note = {Times Cited: 6Edwards, SV Silva, MC Burg, T Friesen, V Warheit, KI26th Annual Meeting of the Pacific-Seabird-GroupFeb 26-27, 1999Blaine, wa}, pages = {115-140}, isbn = {1-56612-066-7}, author = {Edwards, S. V. and Silva, M. C. and Burg, T. and Friesen, V. and Warheit, K. I.}, editor = {Melvin, E. F. and Parrish, J. K.} } @article {921201, title = {Cryptic differentiation and geographic variation in genetic diversity of Hall{\textquoteright}s Babbler (Pomatostomus halli)}, journal = {Journal of Avian Biology}, volume = {32}, year = {2001}, pages = {102-110}, author = {Miura, G. and Edwards, S. V.} } @article {507411, title = {Songbird genomics: analysis of 45-kb upstream of a polymorphic Mhc class II gene in Red-winged Blackbird (Agelaius phoeniceus)}, journal = {Genomics}, volume = {75}, year = {2001}, pages = {26-34}, abstract = {
Here we present the sequence of a 45 kb cosmid containing a previously characterized poly-morphic Mhc class II B gene (Agph-DAB1) from the red-winged blackbird (Agelaius phoeniceus). We compared it with a previously sequenced cosmid from this species, revealing two regions of 7.5 kb and 13.0 kb that averaged greater than 97\% similarity to each another, indicating a very recent shared duplication. We found 12 retroelements, including two chicken repeat 1 (CR1) elements, constituting 6.4\% of the sequence and indicating a lower frequency of retroelements than that found in mammalian genomic DNA. Agph-DAB3, a new class II B gene discovered in the cosmid, showed a low rate of polymorphism and may be functional. In addi-tion, we found a Mhc class II B gene fragment and three genes likely to be functional (encod-ing activin receptor type II, a zinc finger, and a putativeγ-filamin). Phylogenetic analysis of exon 2 alleles of all three known blackbird Mhc genes indicated strong clustering of alleles by locus, implying that large amounts of interlocus gene conversion have not occurred since these genes have been diverging. Despite this, interspecific comparisons indicate that all three black-bird Mhc genes diverged from one another less than 35 million years ago and are subject to con-certed evolution in the long term. Comparison of blackbird and chicken Mhc promoter regions revealed songbird promoter elements for the first time. The high gene density of this cosmid confirms similar findings for the chicken Mhc, but the segment duplications and diversity of retroelements resembles mammalian sequences.
}, url = {http://www.sciencedirect.com/science/article/pii/S0888754301965966}, author = {Gasper, J and Shiina, T and Inoko, H and SV Edwards} } @article {921191, title = {Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies}, journal = {Evolution}, volume = {54}, year = {2000}, pages = {1839-1854}, author = {Edwards, S. V. and P. Beerli} } @article {507376, title = {A 39-kb sequence around a blackbird Mhc class II B gene: ghost of selection past and songbird genome architecture}, journal = {Molecular Biology and Evolution}, volume = {17}, year = {2000}, pages = {1384-1395}, url = {https://mbe.oxfordjournals.org/content/17/9/1384.full}, author = {SV Edwards and Gasper, J and D Garrigan and Martindale, DA and Koop, BF} } @inbook {507391, title = {Characterization and evolution of Mhc genes from non-model organisms, with examples from birds}, booktitle = {Molecular Methods in Ecology}, year = {2000}, pages = {168-207}, url = {https://books.google.com/books?hl=en\&lr=\&id=nODnsP5Orc0C\&oi=fnd\&pg=PA168\&dq=Characterization+and+evolution+of+Mhc+genes+from+non-model+organisms,+with+examples+from+birds\&ots=rvvu6f5ZCK\&sig=hmIjJwQjaG96GlLowX0nWIr6Hg0$\#$v=onepage\&q=Characterization\%20and\%20}, author = {SV Edwards and Nusser, J and Gasper, J} } @article {507401, title = {Dynamics and phylogenetic implications of mtDNA control region in New World Jays (Aves: Corvidae)}, journal = {Journal of Molecular Evolution}, volume = {51}, year = {2000}, pages = {97-109}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.377.5370\&rep=rep1\&type=pdf}, author = {Saunders, M and SV Edwards} } @article {507361, title = {MHC class II pseudogene and genomic signature of a 32-kb cosmid in the House Finch (Carpodacus mexicanus)}, journal = {Genome Research}, volume = {10}, year = {2000}, pages = {13-23}, url = {http://genome.cshlp.org/content/10/5/613.long}, author = {Hess, CM and Gasper, J and Hoekstra, H and Hill, C and SV Edwards} } @article {507386, title = {Molecular genetic markers in the analysis of seabird bycatch populations}, journal = {Seabird Bycatch: Trends, Roadblocks and Solutions}, year = {2000}, pages = {115-140}, url = {http://nsgl.gso.uri.edu/aku/akuw99002.pdf$\#$page=123}, author = {SV Edwards and MC Silva and T Burg and V Friesen and KI Warheit} } @article {507396, title = {Multiple origins of XY female mice (genus Akodon): phylogenetic and chromosomal evidence}, journal = {Proceedings of the Royal Society of London Series B Biological Sciences}, volume = {267}, year = {2000}, pages = {182-1831}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1690748/pdf/11052532.pdf}, author = {Hoekstra, HE and SV Edwards} } @article {507356, title = {Polymorphism across an exon-intron boundary in an avian Mhc class II B gene}, journal = {Molecular Biology and Evolution}, volume = {16}, year = {1999}, pages = {1599-1606}, url = {http://mbe.oxfordjournals.org/content/16/11/1599.full.pdf}, author = {D Garrigan and SV Edwards} } @article {507341, title = {Toward an evolutionary genomics of the avian Mhc}, journal = {Immunological Reviews}, volume = {167}, year = {1999}, pages = {119-132}, url = {https://www.researchgate.net/profile/Daniel_Garrigan/publication/12979911_Toward_an_evolutionary_genomics_of_the_avian_Mhc/links/02e7e523b313f27c47000000.pdf}, author = {SV Edwards and C Hess and Gasper, J and D Garrigan} } @article {507326, title = {Can weighting improve bushy trees?: models of cytochrome b evolution and the molecular systematics of pipits and wagtails (Motacillidae)}, journal = {Systematic Biology}, volume = {47}, year = {1998}, pages = {589-603}, url = {https://www.researchgate.net/profile/Gary_Voelker/publication/11308860_Can_Weighting_Improve_Bushy_Trees_Models_of_Cytochrome_b_Evolution_and_the_Molecular_Systematics_of_Pipits_and_Wagtails_\%28Aves_Motacillidae\%29/links/0912f50c1f9a0bf1d4000000.pdf}, author = {Voelker, G and SV Edwards} } @article {507316, title = {Evolution and ecology of MHC molecules: from genomics to sexual selection}, journal = {Trends in Ecology and Evolution}, volume = {13}, year = {1998}, pages = {305-311}, url = {http://nature.berkeley.edu/genomicswg/EE_seven.pdf}, author = {SV Edwards and P Hedrick} } @article {507311, title = {Genomics and polymorphism of Agph-DAB1, and Mhc class II B gene in Red-winged Blackbirds (Agelaius phoeniceus)}, journal = {Molecular Biology and Evolution}, volume = {15}, year = {1998}, pages = {236-250}, url = {http://mbe.oxfordjournals.org/content/15/3/236.full.pdf}, author = {SV Edwards and Gasper, J and March, M} } @article {507336, title = {Molecular Evolution and Adaptive Radiation}, journal = {American Zoologist}, volume = {38}, year = {1998}, pages = {986-988}, author = {SV Edwards} } @inbook {507321, title = {Diversity of Birds}, booktitle = {Encyclopedia of Reproduction}, year = {1998}, pages = {358-369}, publisher = {Academic Press}, organization = {Academic Press}, address = {San Diego}, author = {Edwads, SV} } @article {921186, title = {Passeriformes}, journal = {Tree of Life Web PageTree of Life Web Page}, volume = {http://phylogeny.arizona.edu/tree/eukaryotes/animals/chordata/dinosauria/aves/passeriformes/passeriformes.html}, year = {1997}, author = {Edwards, S. V.} } @article {507301, title = {Congruence and phylogenetic re-analysis of perching bird cytochrome b sequences}, journal = {Molecular Phylogenetics and Evolution}, volume = {7}, year = {1997}, pages = {266-271}, author = {SV Edwards and P Arctander} } @article {507291, title = {Ancestral polymorphism of Mhc class II genes in mice: implications for balancing selection and the mammalian molecular clock}, journal = {Genetics}, volume = {148}, year = {1997}, pages = {655-668}, author = {SV Edwards and K Chesnut and Y Satta and EK Wakeland} } @article {507306, title = {Relevance of microevolutionary processes to higher level molecular systematics}, journal = {Avian Molecular Systematics and Evolution}, year = {1997}, pages = {251-278}, author = {SV Edwards} } @article {507296, title = {Short- and long-term evolution of Mhc class II B genes in birds: first glimpses}, journal = {Current Topics in Molecular Evolution}, year = {1996}, pages = {169-178}, author = {SV Edwards} } @article {507286, title = {Polymorphism of Mhc genes: implications for conservation genetics of vertebrates}, journal = {Molecular Genetic Approaches to Conservation}, year = {1996}, pages = {214-237}, author = {SV Edwards and WK Potts} } @article {507271, title = {Comparative methods at the species level: geographic variation in morphology and group size in grey-crowned babblers (Pomatostomus temporalis)}, journal = {Evolution}, volume = {49}, year = {1995}, pages = {1134-1146}, author = {SV Edwards and M Kot} } @article {507276, title = {Dynamics of Mhc evolution in birds and crocodilians: amplification with degenerate primers}, journal = {Molecular Ecology}, volume = {4}, year = {1995}, pages = {719-729}, url = {http://www.oeb.harvard.edu/faculty/edwards/research/publications_files/Edwards_et_al_Mhc_Mol_Ecol_1995.pdf}, author = {SV Edwards and M Grahn and WK Potts} } @article {507281, title = {Contrasting histories of avian and mammalian MHC genes revealed by class II B genes of songbirds}, journal = {Proceedings of the National Academy of Sciences}, volume = {92}, year = {1995}, pages = {12200-12204}, author = {SV Edwards and EK Wakeland and WK Potts} } @article {507261, title = {Homology and comparative methods in the study of avian cooperative breeding}, journal = {The American Naturalist}, volume = {143}, year = {1994}, pages = {723-733}, author = {SV Edwards and Naeem, S} } @article {507256, title = {Mitochondrial gene genealogy and gene flow among island and mainland populations of a sedentary songbird, the grey-crowned babbler (Pomatostomus temporalis)}, journal = {Evolution}, volume = {47}, year = {1993}, pages = {1118-1137}, author = {SV Edwards} } @article {507246, title = {The phylogenetic component of cooperative breeding in perching birds}, journal = {The American Naturalist}, volume = {141}, year = {1993}, pages = {754-789}, author = {SV Edwards and Naeem, S} } @article {507251, title = {Long-distance gene flow in a cooperative breeder detected in genealogies of mitochondrial DNA sequences}, journal = {Proceedings of the Royal Society of London series}, volume = {252}, year = {1993}, pages = {177-185}, author = {SV Edwards} } @article {507236, title = {Mitochondrial resolution of a deep branch in the genealogical tree for perching birds}, journal = {Proceedings of the Royal Society of London series}, volume = {243}, year = {1991}, pages = {99-107}, author = {SV Edwards and P Arctander and AC Wilson} } @article {507241, title = {Systematics and evolution of the family Bathyergidae}, journal = {The Biology of the Naked Mole-Rat}, year = {1991}, pages = {45-65}, author = {Honeycutt, RL and MW Allard and SV Edwards and DA Schlitter} } @article {921181, title = {Phylogenetically informative length polymorphism and sequence variability in mitochondrial DNA of Australian songbirds (Pomatostomus)}, journal = {Genetics}, volume = {126}, year = {1990}, pages = {695-711}, author = {Edwards, S. V. and Wilson, A. C.} } @article {507231, title = {Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers}, journal = {Proceedings of the National Academy of Sciences (USA)}, volume = {86}, year = {1989}, pages = {6196-6200}, author = {Kocher, TD and WK Thomas and A Meyer and SV Edwards and S Paabo and FX Villablanca and AC Wilson} } @article {507226, title = {Mitochondrial DNA variation and the phylogeny of African mole-rats (Rodentia: Bathyergidae)}, journal = {Systematic Zoology}, volume = {36}, year = {1987}, pages = {280-292}, author = {Honeycutt, S and V Edwards and K Nelson and E Nevo} }