Publications

2003
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.

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2002
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.

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Hess CM, Edwards SV. The evolution of major histocompatibility genes in birds. Bioscience [Internet]. 2002;52 (423) :431. Publisher's VersionAbstract
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
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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 (
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.
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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.]

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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.
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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.
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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.
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2001
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.
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2000
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
Hess CM, Gasper J, Hoekstra H, Hill C, Edwards SV. MHC class II pseudogene and genomic signature of a 32-kb cosmid in the House Finch (Carpodacus mexicanus). Genome Research [Internet]. 2000;10 :13-23. Publisher's Version PDF
Edwards SV, Silva MC, Burg T, Friesen V, Warheit KI. Molecular genetic markers in the analysis of seabird bycatch populations. Seabird Bycatch: Trends, Roadblocks and Solutions [Internet]. 2000 :115-140. Publisher's Version PDF
Hoekstra HE, Edwards SV. Multiple origins of XY female mice (genus Akodon): phylogenetic and chromosomal evidence. Proceedings of the Royal Society of London Series B Biological Sciences [Internet]. 2000;267 :182-1831. Publisher's Version PDF
1999
Garrigan D, Edwards SV. Polymorphism across an exon-intron boundary in an avian Mhc class II B gene. Molecular Biology and Evolution [Internet]. 1999;16 :1599-1606. Publisher's Version PDF

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