Edwards SV, Kingan SB, Calkins JD, Balakrishnan CN, Jennings BW, Swanson WJ, Sorenson MD. Speciation in birds: genes, geography and sexual selection. Proc. Natl. Acad. Sci. (USA) [Internet]. 2005;102 :6550-6557. Publisher's VersionAbstract
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’s
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
mechanisms such as genetic incompatibilities, reinforcement, and
sexual selection—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—to clone speciation genes if they exist—and thereby evaluate
the relative roles of extrinsic, intrinsic, deterministic, and stochastic
causes for avian diversification.
Jennings WB, Edwards SV. Speciational history of Australian grass finches ( Poephila ) inferred from 30 gene trees. Evolution [Internet]. 2005;59 :2033-2047. Publisher's VersionAbstract

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–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.

Edwards SV, Smith M. Hitchhiking and recombination in birds: evidence from Mhc-linked and unlinked loci in red-winged blackbirds (Agelaius phoeniceus). Genetical Research. 2004;84 :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. 5–40 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’s D’ 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.
Wang Z, Hill GE, Baker AJ, Edwards SV. Reconciling actual and inferred population histories in the House FInch (Carpodacus mexicanus) by AFLP analysis. Evolution [Internet]. 2003;57 :2852-2864. Publisher's Version PDF
Edwards SV. Australo-Papuan Babblers. Encyclopedia of Birds. 2003.
Brumfield RD, Nickerson D, Beerli P, Edwards SV. The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution [Internet]. 2003;18 :249-256. Publisher's VersionAbstract

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.

Arbogast BS, Edwards SV, Wakeley J. Estimating divergence times from molecular data on population genetic and phylogenetic time scales. Annual Review of Ecology and Systematics [Internet]. 2002;33 :707-740. Publisher's VersionAbstract

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.

Hess CM, Edwards SV. The evolution of major histocompatibility genes in birds. Bioscience [Internet]. 2002;52 (423) :431. Publisher's VersionAbstract
Waltari E, Edwards SV. The evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs. American Naturalist [Internet]. 2002;106 :539-552. Publisher's VersionAbstract
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 (
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.
Edwards SV, Fertil B, Giron A, Deschavanne PJ. A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Systematic Biology [Internet]. 2002;51 :599-613. Publisher's VersionAbstract

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.]

Zelano B, Edwards SV. An Mhc component to kin recognition and mate choice in birds: predictions, progress, and prospects. American Naturalist [Internet]. 2002;106 :225-237. Publisher's VersionAbstract
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.
Edwards SV, Boles WE. Out of Gondwana: the origin of passerine birds. Trends in Ecology and Evolution [Internet]. 2002;17 :347-349. Publisher's VersionAbstract
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–Papuan Corvida and the Afro–Eurasian Passerida, as outlined in Sibley and Ahlquist’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.
Birks S, Edwards SV. A phylogeny of megapodes (Aves: Megapodidae) based on nuclear and mitochondrial DNA sequences. Molecular Phylogenetics and Evolution [Internet]. 2002;23 :408-421. Publisher's VersionAbstract
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.
Edwards SV, Silva MC, Burg T, Friesen V, Warheit KI. Molecular genetic markers in the analysis of seabird bycatch populations. (Melvin EF, Parrish JK).; 2001 pp. 115-140.
Miura G, Edwards SV. Cryptic differentiation and geographic variation in genetic diversity of Hall's Babbler (Pomatostomus halli). Journal of Avian Biology. 2001;32 :102-110.
Gasper J, Shiina T, Inoko H, Edwards SV. Songbird genomics: analysis of 45-kb upstream of a polymorphic Mhc class II gene in Red-winged Blackbird (Agelaius phoeniceus). Genomics [Internet]. 2001;75 :26-34. Publisher's VersionAbstract
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.
Edwards SV, Beerli P. Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution. 2000;54 :1839-1854.
Edwards SV, Gasper J, Garrigan D, Martindale DA, Koop BF. A 39-kb sequence around a blackbird Mhc class II B gene: ghost of selection past and songbird genome architecture. Molecular Biology and Evolution [Internet]. 2000;17 :1384-1395. Publisher's Version PDF
Edwards SV, Nusser J, Gasper J. Characterization and evolution of Mhc genes from non-model organisms, with examples from birds. In: Molecular Methods in Ecology. ; 2000. pp. 168-207. Publisher's Version
Saunders M, Edwards SV. Dynamics and phylogenetic implications of mtDNA control region in New World Jays (Aves: Corvidae). Journal of Molecular Evolution [Internet]. 2000;51 :97-109. Publisher's Version PDF