Publications

2008
Causey D, Edwards SV. Ecology of avian influenza virus in birds. Journal of Infectious Diseases [Internet]. 2008;197 :S29-S33. Publisher's VersionAbstract

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.

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Liu L, Pearl DK, Brumfield RT, Edwards SV. Estimating species trees using multiple-allele DNA sequence data. Evolution [Internet]. 2008;62 (8) :2080-2091. Publisher's VersionAbstract
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—yeast (
Saccharomyces
)
and birds (
Manacus
—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.
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Limaye N, Belobrajdic KA, Wandstrat AE, Bonhomme F, Edwards SV, Wakeland EK. Prevalence and evolutionary origins of autoimmune susceptibility alleles in natural mouse populations. Genes and Immunity [Internet]. 2008;9 (1) :61-68. Publisher's VersionAbstract
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.
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2007
Edwards SV, Liu L, Pearl DK. High-resolution species trees without concatenation. 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. 2007;104 :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.
Brumfield RT, Edwards SV. Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes. Evolution Int J Org Evolution. 2007;61 :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.

Organ CL, Shedlock AM, Meade A, Pagel M, Edwards SV. Origin of avian genome size and structure in non-avian dinosaurs. Nature. 2007;446 :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

Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, Liu JS, Deschavanne PJ, Edwards SV. Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proceedings of the National Academy of Sciences of the United States of America. 2007;104 :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).

Hess CM, Wang Z, Edwards SV. Evolutionary genetics of Carpodacus mexicanus, a recently colonized host of a bacterial pathogen, Mycoplasma gallisepticum. Genetica [Internet]. 2007;129 (2) :217-225. Publisher's VersionAbstract
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’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.
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2006
Fleischer RC, Kirchman JJ, Dumbacher JP, Bevier L, Dove C, Rotzel NC, Edwards SV, Lammertink M, Miglia KJ, Moore WS. Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers. Biol Lett. 2006;2 :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.

Wang Z, Miyake T, Edwards SV, Amemiya CT. Tuatara (Sphenodon) genomics: BAC library construction, sequence survey, and application to the DMRT gene family. J Hered. 2006;97 :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.

Wang ZS, Farmer K, Hill GE, Edwards SV. 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. Molecular Ecology [Internet]. 2006;15 (5) :1263-1273. Publisher's VersionAbstract
In 1994, the bacterial parasite
Mycoplasma gallisepticum
expanded its host range and
swept through populations of a novel host — 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 ‘tester’ and an infected bird as ‘driver’, 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.
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2005
Edwards SV, Birks S, Brumfield RT, Hanner R. Avian Genetic Resources Collections: Archives of Evolutionary and Environmental History. Auk [Internet]. 2005;122 :979-984. Publisher's Version PDF
Walsh HE, Edwards SV. Conservation genetics and Pacific fisheries bycatch: mitochondrial differentiation and population assignment in black-footed albatrosses ( Phoebastria nigripes ). Conservation Genetics [Internet]. 2005;6 :289-295. Publisher's Version PDF
Chapus C, Dufraigne C, Edwards S, Giron A, Fertil B, Deschavanna P. Exploration of phylogenetic data using a global sequence analysis method. BMC Evolutionary Biology [Internet]. 2005;5 :63. Publisher's VersionAbstract

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 – in particular explicit statements of homology inherent in character matrices – 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.

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Edwards SV, Jennings WB, Shedlock AM. Phylogenetics of modern birds in the era of genomics. Proceeding of the Royal Society of London series [Internet]. 2005;272 :979-992. Publisher's VersionAbstract
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 ‘community genomics’ 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—with its ability to vastly increase the number and type of molecular characters
and to provide a genomic context for these characters—will usher in a host of new perspectives and
opportunities for integrating genome evolution and avian phylogenetics.
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Edwards SV. Gene and Genome Evolution. In: Evolution. Sunderland: Sinauer Associates ; 2005.
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
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
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.
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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.

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2004
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.
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