Janes DE, Chapus C, Gondo Y, Clayton DF, Sinha S, Blatti CA, Organ CL, Fujita MK, Balakrishnan CN, Edwards SV. Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor. Genome Biology and Evolution [Internet]. 2011;3 :102-113. Publisher's VersionAbstract
Many noncoding regions of genomes appear to be essential to genome function. Conservation of large numbers of
noncoding sequences has been reported repeatedly among mammals but not thus far among birds and reptiles. By searching
genomes of chicken (
Gallus gallus
), zebra finch (
Taeniopygia guttata
), and green anole (
Anolis carolinensis
), we quantified
the conservation among birds and reptiles and across amniotes of long, conserved noncoding sequences (LCNS), which we
define as sequences
500 bp in length and exhibiting
95% similarity between species. We found 4,294 LCNS shared
between chicken and zebra finch and 574 LCNS shared by the two birds and
. The percent of genomes comprised by
LCNS in the two birds (0.0024%) is notably higher than the percent in mammals (
0.0003% to
0.001%), differences that
we show may be explained in part by differences in genome-wide substitution rates. We reconstruct a large number of LCNS
for the amniote ancestor (ca. 8,630) and hypothesize differential loss and substantial turnover of these sites in descendent
lineages. By contrast, we estimated a small role for recruitment of LCNS via acquisition of novel functions over time. Across
amniotes, LCNS are significantly enriched with transcription factor binding sites for many developmental genes, and 2.9% of
LCNS shared between the two birds show evidence of expression in brain expressed sequence tag databases. These results
show that the rate of retention of LCNS from the amniote ancestor differs between mammals and Reptilia (including birds)

and that this may reflect differing roles and constraints in gene regulation

Vo A-TE, Bank MS, Shine JP, Edwards SV. Temporal increase in organic mercury in an endangered pelagic seabird assessed by century-old museum specimens. Proceedings of the National Academy of Sciences of the United States of America [Internet]. 2011;108 (18) :7466-7471. Publisher's VersionAbstract

Methylmercury cycling in the Pacific Ocean has garnered significant attention in recent years, especially with regard to rising mercury emissions from Asia. Uncertainty exists concerning whether increases in anthropogenic emissions over time may have caused increased mercury bioaccumulation in the biota. To address this, we measured total mercury and, for a subset of samples, methylmercury (the bioaccumulated form of mercury) in museum feathers from an endangered seabird, the black-footed albatross (Phoebastria nigripes), spanning a 120-y period. We analyzed stable isotopes of nitrogen (δ15N) and carbon (δ13C) to control for temporal changes in trophic structure and diet. In post-1940 and -1990 feathers, we detected significantly higher mean methylmercury concentrations and higher proportions of samples exhibiting above deleterious threshold levels (∼40,000 ng·g−1) of methylmercury relative to prior time points, suggesting that mercury toxicity may undermine reproductive effort in the species. We also found higher levels of (presumably curator-mediated) inorganic mercury in older specimens of albatross as well as two nonpelagic species lacking historical exposure to bioavailable mercury, patterns suggesting that studies on bioaccumulation should measure methylmercury rather than total mercury when using museum collections. δ15N contributed substantially to models explaining the observed methylmercury variation. After simultaneously controlling for significant trends in δ13C over time and δ15N with methylmercury exposure, year remained a significant independent covariate with feather methylmercury levels among the albatrosses. These data show that remote seabird colonies in the Pacific basin exhibit temporal changes in methylmercury levels consistent with historical global and recent regional increases in anthropogenic emissions.

Castillo-Ramírez S, Liu L, Pearl D, Edwardsm S. V. Bayesian estimation of species trees: a practical guide to optimal sampling and analysis. In: Knowles LL, Kubatko LS Estimating Species Trees: Practical and Theoretical Aspects. New Jersey: Wiley-Blackwell ; 2010. pp. 15-33.
Balakrishnan CN, Y. LJ, Edwards SV. Phylogeography and phylogenetics in the nuclear age. In: Grant P, Grant R Searching for the Causes of Evolution: From Field Observations to Mechanisms. Princeton, NJ: Princeton University Press ; 2010. pp. 65-88.
Organ CL, Rasmussen M, Baldwin MW, Kellis M, Edwards SV. Phylogenomic approach to the evolutionary dynamics of gene duplication in birds. In: Dittmar K, Liberles D Evolution After Gene Duplication. New York: Wiley & Sons ; 2010. pp. 253-267.
Kunstner A, Wolf JBW, Backstrom N, Whitney O, Balakrishnan CN, Day L, Edwards SV, Janes DE, Schlinger BA, Wilson RK, et al. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Molecular Ecology. 2010;19 :266-276.Abstract

Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with similar to 1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.

Jaubert-Possamai S, Rispe C, Tanguy S, Gordon K, Walsh T, Edwards O, Tagu D. Expansion of the miRNA Pathway in the Hemipteran Insect Acyrthosiphon pisum. Molecular Biology and Evolution. 2010;27 :979-987.Abstract

The pathways that allow short noncoding RNAs such as the microRNAs (miRNAs) to mediate gene regulation and control critical cellular and developmental processes involve a limited number of key protein components. These proteins are the Dicer-like RNases, double-stranded RNA (dsRNA)-binding proteins, and the Argonaute (AGO) proteins that process stem-loop hairpin transcripts of endogenous genes to generate miRNAs or long dsRNA precursors (either exogenous or endogenous). Comparative genomics studies of metazoans have shown the pathways to be highly conserved overall; the major difference observed is that the vertebrate pathways overlap in sharing a single Dicer (DCR) and AGO proteins, whereas those of insects appear to be parallel, with distinct Dicers and AGOs required for each pathway. The genome of the pea aphid is the first available for a hemipteran insect and discloses an unexpected expansion of the miRNA pathway. It has two copies of the miRNA-specific dicr-1 and ago1 genes and four copies of pasha a cofactor of drosha involved in miRNA biosynthesis. For three of these expansions, we showed that one copy of the genes diverged rapidly and in one case (ago1b) shows signs of positive selection. These expansions occurred concomitantly within a brief evolutionary period. The pea aphid, which reproduces by viviparous parthenogenesis, is able to produce several adapted phenotypes from one single genotype. We show by reverse transcriptase-polymerase chain reaction that all the duplicated copies of the miRNA machinery genes are expressed in the different morphs. Investigating the function of these novel genes offers an exciting new challenge in aphid biology.

Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV. Genome evolution in Reptilia, the sister group of mammals. Annual Review of Genomics and Human Genetics. 2010;11 :239-64.Abstract

The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.

Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, et al. The genome of a songbird. Nature. 2010;464 :757-762.Abstract

The zebra finch is an important model organism in several fields(1,2) with unique relevance to human neuroscience(3,4). Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken(5)-the only bird with a sequenced genome until now(6). Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes(7). We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.

O'Keefe KJ, Silander OK, McCreery H, Weinreich DM, Wright KM, Chao L, Edwards SV, Remold SK, Turner PE. Geographic differences in sexual reassortment in an RNA phage. Evolution. 2010;64 :3010-3023.Abstract
The genetic structure of natural bacteriophage populations is poorly understood. Recent metagenomic studies suggest that phage biogeography is characterized by frequent migration. Using virus samples mostly isolated in Southern California, we recently showed that very little population structure exists in segmented RNA phage of the Cystoviridae family due to frequent segment reassortment (sexual genetic mixis) between unrelated virus individuals. Here we use a larger genetic dataset to examine the structure of Cystoviridae phage isolated from three geographic locations in Southern New England. We document extensive natural variation in the physical sizes of RNA genome segments for these viruses. In addition, consistent with earlier findings, our phylogenetic analyses and calculations of linkage disequilibrium (LD) show no evidence of within-segment recombination in wild populations. However, in contrast to the prior study, our analysis finds that reassortment of segments between individual phage plays a lesser role among cystoviruses sampled in New England, suggesting that the evolutionary importance of genetic mixis in Cystoviridae phage may vary according to geography. We discuss possible explanations for these conflicting results across the studies, such as differing local ecology and its impact on phage growth, and geographic differences in selection against hybrid phage genotypes.
Liu L, Yu L, Edwards S. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evolutionary Biology. 2010;10 :302.Abstract

BACKGROUND:Several phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE) of the species tree (topology, branch lengths, and population sizes) from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE) of species trees, with branch lengths of the species tree in coalescent units.RESULTS:We show that the MPE of the species tree is statistically consistent as the number M of genes goes to infinity. In addition, the probability that the MPE of the species tree matches the true species tree converges to 1 at rate O(M -1). The simulation results confirm that the maximum pseudo-likelihood approach is statistically consistent even when the species tree is in the anomaly zone. We applied our method, Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST) to a mammal dataset. The four major clades found in the MP-EST tree are consistent with those in the Bayesian concatenation tree. The bootstrap supports for the species tree estimated by the MP-EST method are more reasonable than the posterior probability supports given by the Bayesian concatenation method in reflecting the level of uncertainty in gene trees and controversies over the relationship of four major groups of placental mammals.CONCLUSIONS:MP-EST can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species.

Janes DE, Valenzuela N, Ezaz, Tariq, Amemiya, Chris, Edwards SV. Sex chromosome evolution in amniotes: applications for bacterial artificial chromosome libraries. Journal of Biomedicine and Biotechnology. 2010;2011.Abstract

Variability among sex chromosome pairs in amniotes denotes a dynamic history. Since amniotes diverged from a common
ancestor, their sex chromosome pairs and, more broadly, sex-determining mechanisms have changed reversibly and frequently.
These changes have been studied and characterized through the use of many tools and experimental approaches but perhaps
most effectively through applications for bacterial artificial chromosome (BAC) libraries. Individual BAC clones carry 100–200 kb
of sequence from one individual of a target species that can be isolated by screening, mapped onto karyotypes, and sequenced.
With these techniques, researchers have identified differences and similarities in sex chromosome content and organization across
amniotes and have addressed hypotheses regarding the frequency and direction of past changes. Here, we review studies of sex
chromosome evolution in amniotes and the ways in which the field of research has been affected by the advent of BAC libraries.

Balakrishnan CN, Edwards SV, Clayton DF. The Zebra Finch genome and avian genomics in the wild. Emu. 2010;110 :233-241.Abstract

The Zebra Finch (Taeniopygia guttata) is the first species of passerine bird with a complete genome sequence, making it an exciting time for avian evolutionary biology. Native to Australia and the Lesser Sunda Islands, this species has long played an important role in the study of ecology, behaviour and neuroscience. With the sequencing of its genome, the Zebra Finch now also represents an important model system for evolutionary and population genomics. The production of a genome sequence for the Zebra Finch will have far-reaching impacts on the study of avian biology. Here we discuss the genomic resources available for the Zebra Finch, including the genome sequence itself, and some of the ways in which they will facilitate the study of avian diversity. We also highlight recent examples from the literature that have already begun to leverage Zebra Finch genomic tools towards the study of birds in nature.

Balakrishnan CN, Ekblom R, Volker M, Westerdahl H, Godinez R, Kotkiewicz H, Burt DW, Graves T, Griffin DK, Warren WC, et al. Gene duplication and fragmentation in the zebra finch major histocompatibility complex. BMC Biology [Internet]. 2010;8 (29) :(1 April 2010)-(1 April 2010). Publisher's VersionAbstract
Due to its high polymorphism and importance for disease resistance, the major histocompatibility
complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of
particular interest because the chicken
Gallus gallus
, the avian species with the best characterized MHC, possesses a
highly streamlined
minimal essential
MHC, which is linked to resistance against specific pathogens. It remains
unclear the extent to which this organization describes the situation in other birds and whether it represents a
derived or ancestral condition. The sequencing of the zebra finch
Taeniopygia guttata
genome, in combination
with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a
highly divergent and diverse avian lineage, the passerines.
The zebra finch MHC exhibits a complex structure and history involving gene duplication and
fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be
pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the
presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome
assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to
different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content.
Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes.
The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a
complete genome sequence. The apparent lack of synteny between
and the expressed MHC Class I locus is in
fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our
analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and
translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and

organization among avian lineages

Shedlock AM, Edwards SV. Amniotes (Amniota). The timetree of life. 2009 :375-379.
Liu L, Yu L, Kubatko L, Pearl DK, Edwards SV. Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol. 2009;53 :320-8.Abstract

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.

Liu L, Yu L, Pearl DK, Edwards SV. Estimating species phylogenies using coalescence times among sequences. Systematic Biology. 2009;58 :468-477.
Liu L, Yu LL, Pearl DK, Edwards SV. Estimating species phylogenies using coalescence times among sequences. Systematic Biology. 2009;58 :468-477.Abstract

The estimation of species trees (phylogenies) is one of the most important problems in evolutionary biology, and recently, there has been greater appreciation of the need to estimate species trees directly rather than using gene trees as a surrogate. A Bayesian method constructed under the multispecies coalescent model can consistently estimate species trees but involves intensive computation, which can hinder its application to the phylogenetic analysis of large-scale genomic data. Many summary statistics-based approaches, such as shallowest coalescences (SC) and Global LAteSt Split (GLASS), have been developed to infer species phylogenies for multilocus data sets. In this paper, we propose 2 methods, species tree estimation using average ranks of coalescences (STAR) and species tree estimation using average coalescence times (STEAC), based on the summary statistics of coalescence times. It can be shown that the 2 methods are statistically consistent under the multispecies coalescent model. STAR uses the ranks of coalescences and is thus resistant to variable substitution rates along the branches in gene trees. A simulation study suggests that STAR consistently outperforms STEAC, SC, and GLASS when the substitution rates among lineages are highly variable. Two real genomic data sets were analyzed by the 2 methods and produced species trees that are consistent with previous results.

Haussler D, O'Brien SJ, Ryder OA, Barker FK, Clamp M, Crawford AJ, Hanner R, Hanotte O, Johnson WE, McGuire JA, et al. Genome 10K: A proposal to obtain whole-genome sequence for 10 000 Vertebrate Species. Journal of Heredity. 2009;100 :659-674.Abstract

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Kearns AM, Joseph L, Edwards SV, Double MC. Inferring the phylogeography and evolutionary history of the splendid fairy‐wren Malurus splendens from mitochondrial DNA and spectrophotometry. Journal of Avian Biology. 2009;40 :7-17.