Publications

2017
Liu L, Zhang J, Rheindt FE, Lei F, Qu Y, Wang Y, Zhang Y, Sullivan C, Nie W, Wang J, et al. Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary. PNAS [Internet]. 2017;114 (35) :E7282-E7290. Open Access Download
Termignoni-Garcia F, Jaramillo-Correa JP, Chable-Santos J, Liu M, Shultz AJ, Edwards SV, Escalante-Pliego P. Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient. Molecular Ecology. 2017;26 (17) :4483-4496. PDF
Tigano A, Shultz AJ, Edwards SV, Robertson GJ, Friesen VL. Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird. Ecology and Evolution [Internet]. 2017;7 (7) :2370-2381. Open Access Download
Edwards SV, Cloutier AC, Baker AJ. Conserved Nonexonic Elements : A Novel Class of Marker for Phylogenomics. Systematic Biology [Internet]. 2017;66 (October) :1028–1044. Open Access DownloadAbstract
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–∼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.
Campbell-Staton SC, Cheviron ZA, Rochette N, Catchen J, Losos JB, Edwards SV. Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard. Science. 2017;357 (6350) :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' 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.
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Grayson P, Sin SYW, Sackton T, Edwards SV. Comparative genomics as a foundation for evo-devo studies in birds. In: Methods in Molecular Biology: Avian and Reptilian Developmental Biology. New York: Humana Press ; 2017.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.

 

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2016
Campbell-Staton SC, Edwards SV, Losos JB. Climate-mediated adaptation after mainland colonization of an ancestrally subtropical island lizard, Anolis carolinensis. Journal of Evolutionary Biology. 2016;29 (11) :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.
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Shultz AJ, Baker AJ, Hill GE, Nolan PM, Edwards SV. SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus). Ecology and Evolution [Internet]. 2016;6 :7475–7489. Publisher's VersionAbstract
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.
Edwards SV. Inferring species trees. In: Kliman R Encyclopedia of Evolutionary Biology. Vol. 4. New York: Elsevier Inc. ; 2016. pp. 236-244.
Edwards SV, Xi Z, Janke A, Faircloth BC, McCormack JE, Glenn TC, Zhong B, Wu S, Lemmon EM, Lemmon AR. Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Molecular Phylogenetics and Evolution. 2016;94 :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 ‘‘species tree” 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’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 ‘‘first principles” 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’s claims that MSC models explain
little or none (0–15%) 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.
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Edwards SV. Phylogenomic subsampling: a brief review. Zoologica Scripta. 2016;45 (s1) :63-74. PDF
Edwards SV, Potter S, Schmitt CJ, Bragg JG, Moritz C. Reticulation, divergence, and the phylogeography–phylogenetics continuum. Proceedings of the National Academy of Sciences. 2016;113 :8025-8032.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
within loci and genomes in the form of re-
combination and across populations and species in the form of
introgression
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.
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2015
Miller HC, O'Meally D, Ezaz T, Amemiya C, Marshall-Graves JA, Edwards S. Major Histocompatibility Complex Genes Map to Two Chromosomes in an Evolutionarily Ancient Reptile, the Tuatara Sphenodon punctatus. G3-Genes, Genomes, Genetics. 2015;5 (7) :1439-1451.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.
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Liu L, Edwards SV. Comment on “Statistical binning enables an accurate coalescent-based estimation of the avian tree”. Science. 2015;350 :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—naïve, statistical, and weighted statistical—display poor performance and are statistically inconsistent in large regions of parameter space, unlike unbinned sequence data used with species tree methods.

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Liu L, Xi Z, Wu S, Davis CC, Edwards SV. Estimating phylogenetic trees from genome-scale data. Annals of the New York Academy of Sciences. 2015;1360 :36–53.Abstract

The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as “species tree” 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.

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Dierickx EG, Shultz AJ, Sato F, Hiraoka T, Edwards SV. Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation. Evolutionary Applications. 2015;8 :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.

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Edwards SV, Schultz A, Campbell-Staton S. Next-generation sequencing and the expanding domain of phylogeography. Folia Zoologica. 2015;64 :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.

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Badenhorst D, Hillier LDW, Literman R, Montiel EE, Radhakrishnan S, Shen Y, Minx P, Janes DE, Warren WC, Edwards SV, et al. Physical Mapping and Refinement of the Painted Turtle Genome ( Chrysemys picta ) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation. Genome Biology and Evolution. 2015;7 :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—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.
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Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV. Feather Development Genes and Associated Regulatory Innovation Predate the Origin of Dinosauria. Molecular Biology and Evolution [Internet]. 2015;32 (1) :23-28. Publisher's VersionAbstract
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.
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Balenger SL, Bonneaud C, Sefick SA, Edwards SV, Hill GE. Plumage color and pathogen-induced gene expression in a wild bird. Behavioral Ecology [Internet]. 2015;26 (4) :1100-1110. Publisher's Version PDF

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