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.

Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutierrez S, Castoe TA, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science. 2014;346 :1335-+.Abstract

To provide context for the diversification of archosaurs-the group that includes crocodilians, dinosaurs, and birds-we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346 :1320-1331.Abstract

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Dennehy JJ, Duffy S, O’Keefe KJ, Edwards SV, Turner PE. Frequent Coinfection Reduces RNA Virus Population Genetic Diversity. Journal of Heredity. 2013;104 :704-712.Abstract
The masking of deleterious mutations by complementation and the reassortment of virus segments (virus sex) are expected
to increase population genetic diversity among coinfecting viruses. Conversely, clonally reproducing or noncoinfecting virus
populations may experience clonal interference where viral clones compete with one another, preventing selective sweeps.
This dynamic reduces the efficiency of selection and increases the genetic diversity. To determine the relative influences of
these forces on population genetic diversity, we evolved 6 populations of bacteriophage φ6 under conditions promoting
or preventing coinfection. Following 300 generations, we isolated and partially sequenced 10 clones from each population.
We found greater diversity among asexual populations than sexual populations. Moreover, sexual populations did not show greater relative fitnesses than asexual populations, implying that reduced genetic variation did not result from purifying selection. However, sexual populations were less genetically robust than asexual populations and likely more prone to the deleterious epistatic effects of mutations. As such, a neutral mutation on the asexually evolved (robust) background could be profoundly deleterious on the sexually evolved (brittle) background. This could facilitate sexual populations undergoing greater purifying selection to remove deleterious mutations, but this selection is not reflected by increases in average population fitness. Our results bolster a growing literature suggesting that RNA virus segmentation is probably not a mechanism that evolved because it provides a generalized benefit of sex.
Kultz D, Clayton DF, Robinson GE, Albertson C, Carey HV, Cummings ME, Dewar K, Edwards SV, Hofmann HA, Gross LJ, et al. New Frontiers for Organismal Biology. Bioscience. 2013;63 :464-471.Abstract

Understanding how complex organisms function as integrated units that constantly interact with their environment is a long-standing challenge in biology. To address this challenge, organismal biology reveals general organizing principles of physiological systems and behavior-in particular, in complex multicellular animals. Organismal biology also focuses on the role of individual variability in the evolutionary maintenance of diversity. To broadly advance these frontiers, cross-compatibility of experimental designs, methodological approaches, and data interpretation pipelines represents a key prerequisite. It is now possible to rapidly and systematically analyze complete genomes to elucidate genetic variation associated with traits and conditions that define individuals, populations, and species. However, genetic variation alone does not explain the varied individual physiology and behavior of complex organisms. We propose that such emergent properties of complex organisms can best be explained through a renewed emphasis on the context and life-history dependence of individual phenotypes to complement genetic data.

Edwards SV. Next-generation QTL mapping: crowdsourcing SNPs, without pedigrees. Molecular Ecology. 2013;22 :3885-3887.Abstract

For many molecular ecologists, the mantra and mission
of the field of ecological genomics could be encapsulated
by the phrase ‘to find the genes that matter’ (Mitchell-
Olds 2001; Rockman 2012). This phrase of course refers to
the early hope and current increasing success in the
search for genes whose variation underlies phenotypic
variation and fitness in natural populations. In the years
since the modern incarnation of the field of ecological
genomics, many would agree that the low-hanging fruit
has, at least in principle, been plucked: we now have several
elegant examples of genes whose variation influences
key adaptive traits in natural populations, and these
examples have revealed important insights into the architecture
of adaptive variation (Hoekstra et al. 2006; Shapiro
et al. 2009; Chan et al. 2010). But how well will these
early examples, often involving single genes of large
effect on discrete or near-discrete phenotypes, represent
the dynamics of adaptive change for the totality of
phenotypes in nature? Will traits exhibiting continuous
rather than discrete variation in natural populations have
as simple a genetic basis as these early examples suggest
(Prasad et al. 2012; Rockman 2012)? Two papers in this
issue (Robinson et al. 2013; Santure et al. 2013) not only
suggest answers to these questions but also provide
useful extensions of statistical approaches for ecological
geneticists to study the genetics of continuous variation
in nature. Together these papers, by the same research
groups studying evolution in a natural population of
Great Tits (Parus major), provide a glimpse of what we
should expect as the field begins to dissect the genetic
basis of what is arguably the most common type of
variation in nature, and how genome-wide surveys of
variation can be applied to natural populations without

Wu S, Song S, Liu L, Edwards SV. Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity. Proceedings of the National Academy of Sciences of the United States of America. 2013;110 :E1180. PDF
Ezaz T, Azad B, O'Meally D, Young MJ, Matsubara K, Edwards MJ, Zhang X, Holleley CE, Deakin JE, Marshall Graves JA, et al. Sequence and gene content of a large fragment of a lizard sex chromosome and evaluation of candidate sex differentiating gene R-spondin 1. Bmc Genomics. 2013;14 :899-899.Abstract

BACKGROUND: Scant genomic information from non-avian reptile sex chromosomes is available, and for only a few lizards, several snakes and one turtle species, and it represents only a small fraction of the total sex chromosome sequences in these species. RESULTS: We report a 352 kb of contiguous sequence from the sex chromosome of a squamate reptile, Pogona vitticeps, with a ZZ/ZW sex microchromosome system. This contig contains five protein coding genes (oprd1, rcc1, znf91, znf131, znf180), and major families of repetitive sequences with a high number of copies of LTR and non-LTR retrotransposons, including the CR1 and Bov-B LINEs. The two genes, oprd1 and rcc1 are part of a homologous syntenic block, which is conserved among amniotes. While oprd1 and rcc1 have no known function in sex determination or differentiation in amniotes, this homologous syntenic block in mammals and chicken also contains R-spondin 1 (rspo1), the ovarian differentiating gene in mammals. In order to explore the probability that rspo1 is sex determining in dragon lizards, genomic BAC and cDNA clones were mapped using fluorescence in situ hybridisation. Their location on an autosomal microchromosome pair, not on the ZW sex microchromosomes, eliminates rspo1 as a candidate sex determining gene in P. vitticeps. CONCLUSION: Our study has characterized the largest contiguous stretch of physically mapped sex chromosome sequence (352 kb) from a ZZ/ZW lizard species. Although this region represents only a small fraction of the sex chromosomes of P. vitticeps, it has revealed several features typically associated with sex chromosomes including the accumulation of large blocks of repetitive sequences.

Janes DE, Elsey RM, Langan EM, Valenzuela N, Edwards SV. Sex-Biased Expression of Sex-Differentiating Genes FOXL2 and FGF9 in American Alligators, Alligator mississippiensis. Sexual Development. 2013.Abstract

Across amniotes, sex-determining mechanisms exhibit great variation, yet the genes that govern sexual differentiation are largely conserved. Studies of evolution of sex-determining and sex-differentiating genes require an exhaustive characterization of functions of those genes such as FOXL2 and FGF9. FOXL2 is associated with ovarian development, and FGF9 is known to play a role in testicular organogenesis in mammals and other amniotes. As a step toward characterization of the evolutionary history of sexual development, we measured expression of FOXL2 and FGF9 across 3 developmental stages and 8 juvenile tissue types in male and female American alligators, Alligator mississippiensis. We report surprisingly high expression of FOXL2 before the stage of embryonic development when sex is determined in response to temperature, and sustained and variable expression of FGF9 in juvenile male, but not female tissue types. Novel characterization of gene expression in reptiles with temperature-dependent sex determination such as American alligators may inform the evolution of sex-determining and sex-differentiating gene networks, as they suggest alternative functions from which the genes may have been exapted. Future functional profiling of sex-differentiating genes should similarly follow other genes and other species to enable a broad comparison across sex-determining mechanisms.

Bradley Shaffer H, Minx P, Warren D, Shedlock A, Thomson R, Valenzuela N, Abramyan J, Amemiya C, Badenhorst D, Biggar K, et al. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. 2013;14 :R28.Abstract

BACKGROUND:We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing.RESULTS:Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented.CONCLUSIONS:Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

Backstroem N, Shipilina D, Blom MPK, Edwards SV. Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus). Ecology and Evolution [Internet]. 2013;3 (3) :655-666. Publisher's VersionAbstract
Characterization of the genetic basis of fitness traits in natural populations is
important for understanding how organisms adapt to the changing environ-
ment and to novel events, such as epizootics. However, candidate fitness-
influencing loci, such as regulatory regions, are usually unavailable in nonmodel
species. Here, we analyze sequence data from targeted resequencing of the cis-
regulatory regions of three candidate genes for disease resistance (CD74,
HSP90a, and LCP1) in populations of the house finch (Carpodacus mexicanus)
historically exposed (Alabama) and na
ıve (Arizona) to Mycoplasma gallisepti-
cum. Our study, the first to quantify variation in regulatory regions in wild
birds, reveals that the upstream regions of CD74 and HSP90a are GC-rich, with
the former exhibiting unusually low sequence variation for this species. We
identified two SNPs, located in a GC-rich region immediately upstream of an
inferred promoter site in the gene HSP90a, that were significantly associated
with Mycoplasma pathogen load in the two populations. The SNPs are closely
linked and situated in potential regulatory sequences: one in a binding site for
the transcription factor nuclear NFYa and the other in a dinucleotide microsat-
ellite ((GC)
). The genotype associated with pathogen load in the putative
NFYa binding site was significantly overrepresented in the Alabama birds.
However, we did not see strong effects of selection at this SNP, perhaps because
selection has acted on standing genetic variation over an extremely short time
in a highly recombining region. Our study is a useful starting point to explore
functional relationships between sequence polymorphisms, gene expression, and
phenotypic traits, such as pathogen resistance that affect fitness in the wild.
Backstroem N, Zhang Q, Edwards SV. Evidence from a House Finch (Haemorhous mexicanus) Spleen Transcriptome for Adaptive Evolution and Biased Gene Conversion in Passerine Birds. Molecular Biology and Evolution [Internet]. 2013;30 (5) :1046-1050. Publisher's VersionAbstract
Identifying genes influenced by natural selection can provid
e information about lineage-specific adaptations, and tran-
scriptomes generated by next-generation sequencing are a us
eful resource for identifying such genes. Here, we utilize a
spleen transcriptome for the house finch (
Haemorhous mexicanus
), an emerging model for sexual selection and disease
ecology, together with previously sequenced avian geno
mes (chicken, turkey, and zebra finch), to investigate
lineage-specific adaptations within birds. An analysis of 4,
398 orthologous genes revealed a significantly higher ratio
of nonsynonymous to synonymous substit
utions and significantly higher GC content in passerines than in galliforms, an
observation deviating from strictly neutral expectations b
ut consistent with an effect of biased gene conversion on the
evolutionary rate in passerines. These data also showed that ge
nes exhibiting signs of positive selection and fast evolution
in passerines have functional roles related to fat m
etabolism, neurodevelopment, and ion binding.
do Amaral FR, Albers PK, Edwards SV, Miyaki CY. Multilocus tests of Pleistocene refugia and ancient divergence in a pair of Atlantic Forest antbirds (Myrmeciza). Molecular Ecology [Internet]. 2013;22 (15) :3996-4013. Publisher's VersionAbstract
The Atlantic Forest (AF) harbours one of the most diverse vertebrate faunas of the
world, including 199 endemic species of birds. Understanding the evolutionary pro-
cesses behind such diversity has become the focus of many recent, primarily single
locus, phylogeographic studies. These studies suggest that isolation in forest refugia
may have been a major mechanism promoting diversification, although there is also
support for a role of riverine and geotectonic barriers, two sets of hypotheses that can
best be tested with multilocus data. Here we combined multilocus data (one mtDNA
marker and eight anonymous nuclear loci) from two species of parapatric antbirds,
Myrmeciza loricata
M. squamosa
, and Approximate Bayesian Computation to
determine whether isolation in refugia explains current patterns of genetic variation
and their status as independent evolutionary units. Patterns of population structure,
differences in intraspecific levels of divergence and coalescent estimates of historical
demography fit the predictions of a recently proposed model of refuge isolation in
which climatic stability in the northern AF sustains higher diversity and demographic
stability than in the southern AF. However, a pre-Pleistocene divergence associated
with their abutting range limits in a region of past tectonic activity also suggests a role
for rivers or geotectonic barriers. Little or no gene flow between these species suggests
the development of reproductive barriers or competitive exclusion. Our results sug-
gests that limited marker sampling in recent AF studies may compromise estimates of
divergence times and historical demography, and we discuss the effects of such sam-
pling on this and other studies.
Janes DE, Elsey RM, Langan EM, Valenzuela N, Edwards SV. Sex-Biased Expression of Sex-Differentiating Genes FOXL2 and FGF9 in American Alligators, Alligator mississippiensis. Sexual Development [Internet]. 2013;7 (5) :253-260. Publisher's Version PDF
Campbell-Staton SC, Goodman RM, Backstroem N, Edwards SV, Losos JB, Kolbe JJ. Out of Florida: mtDNA reveals patterns of migration and Pleistocene range expansion of the Green Anole lizard (Anolis carolinensis). Ecology and Evolution. 2012;2 (9) :2274-2284.Abstract
Anolis carolinensis is an emerging model species and the sole member of its genus native to the United States. Considerable morphological and physiological variation has been described in the species, and the recent sequencing of its genome makes it an attractive system for studies of genome variation. To inform future studies of molecular and phenotypic variation within A. carolinensis, a rigorous account of intraspecific population structure and relatedness is needed. Here, we present the most extensive phylogeographic study of this species to date. Phylogenetic analyses of mitochondrial DNA sequence data support the previous hypothesis of a western Cuban origin of the species. We found five well-supported, geographically distinct mitochondrial haplotype clades throughout the southeastern United States. Most Florida populations fall into one of three divergent clades, whereas the vast majority of populations outside Florida belong to a single, shallowly diverged clade. Genetic boundaries do not correspond to major rivers, but may reflect effects of Pleistocene glaciation events and the Appalachian Mountains on migration and expansion of the species. Phylogeographic signal should be examined using nuclear loci to complement these findings.
Anderson C, Liu L, Pearl D, Edwards, S. V. Tangled Trees: The challenge of inferring species trees from coalescent and non-coalescent genes. In: Anisimova M Evolutionary Genomics: Statistical and Computational Methods, volume 2. New York: Springer ; 2012. pp. 3-28.
Zhang Q, Edwards SV. The evolution of intron size in amniotes: a role for powered flight?. Genome Biology and Evolution. 2012.Abstract

Intronic DNA is a major component of eukaryotic genes and genomes and can be subject to selective constraint and have functions in gene regulation. Intron size is of particular interest given that it is thought to be the target of a variety of evolutionary forces and has been suggested to be linked ultimately to various phenotypic traits, such as powered flight. Using whole-genome analyses and comparative approaches that account for phylogenetic nonindependence, we examined interspecific variation in intron size variation in three data sets encompassing from 12 to 30 amniotes genomes and allowing for different levels of genome coverage. In addition to confirming that intron size is negatively associated with intron position and correlates with genome size, we found that on average mammals have longer introns than birds and nonavian reptiles, a trend that is correlated with the proliferation of repetitive elements in mammals. Two independent comparisons between flying and nonflying sister groups both showed a reduction of intron size in volant species, supporting an association between powered flight, or possibly the high metabolic rates associated with flight, and reduced intron/genome size. Small intron size in volant lineages is less easily explained as a neutral consequence of large effective population size. In conclusion, we found that the evolution of intron size in amniotes appears to be non-neutral, is correlated with genome size, and is likely influenced by powered flight and associated high metabolic rates.