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.


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
, 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.
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
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.
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.

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.

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.

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.

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.
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.
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
Zhang GJ, Li C, Li QY, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014;346 :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.

Wu SY, Zhang FC, Edwards SV, Wu WY, Ye J, Bi SD, Ni XJ, Quan C, Meng J, Organ CL. The Evolution of Bipedalism in Jerboas (Rodentia: Dipodoidea): Origin in Humid and Forested Environments. Evolution. 2014;68 :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.

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. 2014;32 :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.
Zhang Q, Hill GE, Edwards SV, Backström N. A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines. Bmc Genomics. 2014;15 :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.

Janes DE, Organ CL, Stiglec R, O'Meally D, Sarre SD, Georges A, Graves JA, Valenzuela N, Literman RA, Rutherford K, et al. Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia. Biology Letters. 2014;10.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.

Cook JA, Edwards SV, Lacey EA, Guralnick RP, Soltis PS, Soltis DE, Welch CK, Bell KC, Galbreath KE, Himes C, et al. Natural History Collections as Emerging Resources for Innovative Education. Bioscience. 2014;64 :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.

McGlothlin JW, Chuckalovcak JP, Janes DE, Edwards SV, Feldman CR, Brodie ED, Pfrender ME, Brodie ED. Parallel Evolution of Tetrodotoxin Resistance in Three Voltage-Gated Sodium Channel Genes in the Garter Snake Thamnophis sirtalis. Molecular Biology and Evolution. 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’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 (Nav1.1–1.3) showed no evidence of TTX resistance, consistent with protection from toxins by the blood–brain barrier. We also report the exon–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.

Baldwin MW, Toda Y, Nakagita T, O'Connell MJ, Klasing KC, Misaka T, Edwards SV, Liberles SD. Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor. Science (New York, N.Y.). 2014;345 :929-33.Abstract

Sensory systems define an animal'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.