Publications by authors named "Matthew K Fujita"

36 Publications

Eye size and investment in frogs and toads correlate with adult habitat, activity pattern and breeding ecology.

Proc Biol Sci 2020 09 23;287(1935):20201393. Epub 2020 Sep 23.

Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK.

Frogs and toads (Amphibia: Anura) display diverse ecologies and behaviours, which are often correlated with visual capacity in other vertebrates. Additionally, anurans exhibit a broad range of relative eye sizes, which have not previously been linked to ecological factors in this group. We measured relative investment in eye size and corneal size for 220 species of anurans representing all 55 currently recognized families and tested whether they were correlated with six natural history traits hypothesized to be associated with the evolution of eye size. Anuran eye size was significantly correlated with habitat, with notable decreases in eye investment among fossorial, subfossorial and aquatic species. Relative eye size was also associated with mating habitat and activity pattern. Compared to other vertebrates, anurans have relatively large eyes for their body size, indicating that vision is probably of high importance. Our study reveals the role that ecology and behaviour may have played in the evolution of anuran visual systems and highlights the usefulness of museum specimens, and importance of broad taxonomic sampling, for interpreting macroecological patterns.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1098/rspb.2020.1393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7542830PMC
September 2020

Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus).

Mol Ecol 2020 08 8;29(16):2994-3009. Epub 2020 Aug 8.

Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA.

Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid-Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.15541DOI Listing
August 2020

Transcriptome sequencing reveals signatures of positive selection in the Spot-Tailed Earless Lizard.

PLoS One 2020 15;15(6):e0234504. Epub 2020 Jun 15.

Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, United States of America.

The continual loss of threatened biodiversity is occurring at an accelerated pace. High-throughput sequencing technologies are now providing opportunities to address this issue by aiding in the generation of molecular data for many understudied species of high conservation interest. Our overall goal of this study was to begin building the genomic resources to continue investigations and conservation of the Spot-Tailed Earless lizard. Here we leverage the power of high-throughput sequencing to generate the liver transcriptome for the Northern Spot-Tailed Earless Lizard (Holbrookia lacerata) and Southern Spot-Tailed Earless Lizard (Holbrookia subcaudalis), which have declined in abundance in the past decades, and their sister species, the Common Lesser Earless Lizard (Holbrookia maculata). Our efforts produced high quality and robust transcriptome assemblies validated by 1) quantifying the number of processed reads represented in the transcriptome assembly and 2) quantifying the number of highly conserved single-copy orthologs that are present in our transcript set using the BUSCO pipeline. We found 1,361 1-to-1 orthologs among the three Holbrookia species, Anolis carolinensis, and Sceloporus undulatus. We carried out dN/dS selection tests using a branch-sites model and identified a dozen genes that experienced positive selection in the Holbrookia lineage with functions in development, immunity, and metabolism. Our single-copy orthologous sequences additionally revealed significant pairwise sequence divergence (~.73%) between the Northern H. lacerata and Southern H. subcaudalis that further supports the recent elevation of the Southern Spot-Tailed Earless Lizard to full species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234504PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295237PMC
August 2020

Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads.

Mol Ecol 2020 09 10;29(18):3543-3559. Epub 2020 Jul 10.

Department of Biology, University of Texas at Arlington, Arlington, TX, USA.

Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear discordance in this complex, we used spatially explicit genetic data to test species limits and relationships, characterize demographic history, and quantify gene flow. We found extensive mitonuclear discordance among the three recognized species within this group, especially in populations within the Chortís Highlands of Honduras. Our data reveal nuclear introgression within the Chortís Highlands populations that was most probably driven by cyclical range expansions due to climatic fluctuations. Though we determined introgression occurred within the nuclear genome, our data suggest that it is not the key factor in driving mitonuclear discordance in the entire species complex. Rather, due to a lack of discernible geographic pattern between mitochondrial and nuclear DNA, as well as a relatively recent divergence time of this complex, we concluded that mitonuclear discordance has been caused by incomplete lineage sorting. Our study provides a framework to test sources of mitonuclear discordance and highlights the importance of using multiple marker types to test species boundaries in cryptic species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.15496DOI Listing
September 2020

Comparative phylogeography of West African amphibians and reptiles.

Evolution 2020 04 26;74(4):716-724. Epub 2020 Feb 26.

Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas, 76019.

Comparative phylogeographic studies often support shared divergence times for co-distributed species with similar life histories and habitat specializations. During the late Holocene, West Africa experienced aridification and the turnover of rain forest habitats into savannas. These fragmented rain forests harbor impressive numbers of endemic and threatened species. In this setting, populations of co-distributed rain forest species are expected to have diverged simultaneously, whereas divergence events for species adapted to savanna and forest-edge habitats should be absent or idiosyncratic. We conducted a Bayesian analysis of shared evolutionary events to test models of population divergence for 20 species of anurans (frogs) and squamates (lizards and snakes) that are distributed across the Dahomey Gap, a climate change-induced savanna barrier responsible for fragmenting previously contiguous rain forests of Ghana into two regions: the Togo-Volta Hills and the Southwestern Forests. A model of asynchronous diversification is supported for anurans and squamates, suggesting that drivers of diversification are not specifically related to ecological and life history associations with habitat types. Instead, the wide variability of genetic divergence histories exhibited by these species suggests that biodiversity in this region has been shaped by diversification events that extend beyond the Holocene. Comparisons of the genealogical divergence index, a measure of the genetic divergence between populations due to the combined effects of genetic isolation and gene flow, illustrate that these populations represent a broad sampling of the speciation continuum.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/evo.13941DOI Listing
April 2020

Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java.

Mol Phylogenet Evol 2018 06 27;123:101-112. Epub 2018 Feb 27.

Department of Biology, The University of Texas at Arlington, Arlington, TX 76019, USA; The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX 76010, USA.

Geological and climatological processes can drive the synchronous diversification of co-distributed species. The islands of Sumatra and Java have experienced complex geological and climatological histories, including extensive sea-level changes and the formation of valleys between northern, central, and southern components of the Barisan Mountain Range, which may have promoted diversification of their resident species. We investigate diversification on these islands using 13 species of the parachuting frog genus Rhacophorus. We use both mitochondrial and nuclear sequence data, along with genome-wide SNPs to estimate phylogenetic structure and divergence times, and to test for synchronous diversification. We find support for synchronous divergence among sister-species pairs from Sumatra and Java ∼9 Ma, as well as of populations of four co-distributed taxa on Sumatra ∼5.6 Ma. We found that sister species diverged in allopatry on Sumatra and conclude that divergence on Sumatra and Java was affected by sea-level fluctuations that promoted isolation in allopatry.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2018.02.003DOI Listing
June 2018

Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes.

Mol Ecol 2017 Oct 14;26(20):5729-5751. Epub 2017 Sep 14.

Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.

Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.14295DOI Listing
October 2017

Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection.

Mol Ecol 2017 Oct 24;26(19):5245-5263. Epub 2017 Aug 24.

Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA.

The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and then performing demographic model selection and spatially explicit analyses. We found that a majority of population divergences are best explained by allopatric models consistent with the forest refugia hypothesis and involve divergence in isolation with subsequent expansion and gene flow. These population divergences occurred simultaneously and conform to predictions based on climatically stable regions inferred through ecological niche modelling. Although forest refugia played a prominent role in the intraspecific diversification of S. gabonicus, we also find evidence for potential interactions between landscape features and historical refugia, including major rivers and elevational barriers such as the Cameroonian Volcanic Line. We outline the advantages of using genomewide variation in a model-testing framework to distinguish between alternative allopatric hypotheses, and the pitfalls of limited geographic and molecular sampling. Although phylogeographic patterns are often species-specific and related to life-history traits, additional comparative studies incorporating genomic data are necessary for separating shared historical processes from idiosyncratic responses to environmental, climatic and geological influences on diversification.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.14266DOI Listing
October 2017

Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes.

Ecol Evol 2017 06 23;7(11):3951-3966. Epub 2017 Apr 23.

Department of Biology The University of Texas at Arlington Arlington TX USA.

Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake () to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater-than-expected overlap between genes linked to lineage-specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome-scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ece3.2996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468163PMC
June 2017

Limitations of climatic data for inferring species boundaries: insights from speckled rattlesnakes.

PLoS One 2015 24;10(6):e0131435. Epub 2015 Jun 24.

Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America.

Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the "climatic niche"); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs and mitochondrial DNA), phenotypic, and climatic data for objective species delimitation in the speckled rattlesnake (Crotalus mitchellii) complex. Ordination and clustering patterns were largely congruent among intrinsic (heritable) traits (nDNA, mtDNA, phenotype), and discordance is explained by biological processes (e.g., ontogeny, hybridization). In contrast, climatic data did not produce biologically meaningful clusters that were congruent with any intrinsic dataset, but rather corresponded to regional differences in atmospheric circulation and climate, indicating an absence of inherent taxonomic signal in these data. Surrogating climate for physiological tolerances adds artificial weight to evidence of species boundaries, as these data are irrelevant for that purpose. Based on the evidence from congruent clustering of intrinsic datasets, we recommend that three subspecies of C. mitchellii be recognized as species: C. angelensis, C. mitchellii, and C. Pyrrhus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131435PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479545PMC
April 2016

Genetic divergence and diversity in the Mona and Virgin Islands Boas, Chilabothrus monensis (Epicrates monensis) (Serpentes: Boidae), West Indian snakes of special conservation concern.

Mol Phylogenet Evol 2015 Jul 30;88:144-53. Epub 2015 Mar 30.

Bureau of Fisheries and Wildlife, Department of Natural and Environmental Resources, P.O. Box 366147, San Juan, PR 00936-6147, USA; Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, P.O. Box 23341, Río Piedras, PR 00931-3341, USA. Electronic address:

Habitat fragmentation reduces the extent and connectivity of suitable habitats, and can lead to changes in population genetic structure. Limited gene flow among isolated demes can result in increased genetic divergence among populations, and decreased genetic diversity within demes. We assessed patterns of genetic variation in the Caribbean boa Chilabothrus monensis (Epicrates monensis) using two mitochondrial and seven nuclear markers, and relying on the largest number of specimens of these snakes examined to date. Two disjunct subspecies of C. monensis are recognized: the threatened C. m. monensis, endemic to Mona Island, and the rare and endangered C. m. granti, which occurs on various islands of the Puerto Rican Bank. Mitochondrial and nuclear markers revealed unambiguous genetic differences between the taxa, and coalescent species delimitation methods indicated that these snakes likely are different evolutionary lineages, which we recognize at the species level, C. monensis and C. granti. All examined loci in C. monensis (sensu stricto) are monomorphic, which may indicate a recent bottleneck event. Each population of C. granti exclusively contains private mtDNA haplotypes, but five of the seven nuclear genes assayed are monomorphic, and nucleotide diversity is low in the two remaining markers. The faster pace of evolution of mtDNA possibly reflects the present-day isolation of populations of C. granti, whereas the slower substitution rate of nuDNA may instead mirror the relatively recent episodes of connectivity among the populations facilitated by the lower sea level during the Pleistocene. The small degree of overall genetic variation in C. granti suggests that demes of this snake could be managed as a single unit, a practice that would significantly increase their effective population size.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2015.03.019DOI Listing
July 2015

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.

Gigascience 2014 12;3(1):27. Epub 2014 Dec 12.

China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100 Denmark.

Background: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri].

Results: Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology.

Conclusions: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/2047-217X-3-27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322438PMC
February 2015

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

PLoS One 2014 5;9(9):e106649. Epub 2014 Sep 5.

Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America.

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106649PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156343PMC
March 2016

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs.

Mol Ecol 2014 Jul 19;23(13):3273-91. Epub 2014 Jun 19.

Department of Biology, The University of Texas at Arlington, Arlington, TX, 76010, USA.

Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28 152 genomewide single nucleotide polymorphisms from polytypic barking frogs (Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (i) a rapid Pliocene-Pleistocene radiation that produced at least nine distinct lineages and (ii) that geographic features of the arid Central Mexican Plateau contributed to two independent northward expansions. Despite clear lineage differentiation (many private alleles and high between-lineage FST scores), D-statistic tests, which differentiate introgression from ancestral polymorphism, allowed us to identify two putative instances of reticulate gene flow. Partitioned D-statistics provided evidence that these events occurred in the same direction between clades but at different points in time. After correcting for geographic distance, we found that lineages involved in hybrid gene flow interactions had higher levels of genetic variation than independently evolving lineages. These findings suggest that the nature of hybrid compatibility can be conserved overlong periods of evolutionary time and that hybridization between diverging lineages may contribute to standing levels of genetic variation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.12814DOI Listing
July 2014

Species delimitation using genome-wide SNP data.

Syst Biol 2014 Jul 12;63(4):534-42. Epub 2014 Mar 12.

Computational Evolution Group, University of Auckland, Auckland, New Zealand.

The multispecies coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden and precludes their application to genomic-scale data. Here we combine a recently introduced dynamic programming algorithm for estimating species trees that bypasses MCMC integration over gene trees with sophisticated methods for estimating marginal likelihoods, needed for Bayesian model selection, to provide a rigorous and computationally tractable technique for genome-wide species delimitation. We provide a critical yet simple correction that brings the likelihoods of different species trees, and more importantly their corresponding marginal likelihoods, to the same common denominator, which enables direct and accurate comparisons of competing species delimitation models using Bayes factors. We test this approach, which we call Bayes factor delimitation (*with genomic data; BFD*), using common species delimitation scenarios with computer simulations. Varying the numbers of loci and the number of samples suggest that the approach can distinguish the true model even with few loci and limited samples per species. Misspecification of the prior for population size θ has little impact on support for the true model. We apply the approach to West African forest geckos (Hemidactylus fasciatus complex) using genome-wide SNP data. This new Bayesian method for species delimitation builds on a growing trend for objective species delimitation methods with explicit model assumptions that are easily tested. [Bayes factor; model testing; phylogeography; RADseq; simulation; speciation.].
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/sysbio/syu018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072903PMC
July 2014

Introgression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): population genetic and phylogenetic inferences from genome-wide SNPs.

Syst Biol 2014 Mar 4;63(2):134-52. Epub 2013 Dec 4.

Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543; Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Museum of Comparative Zoology, 26 Oxford Street, Cambridge, MA 02138, USA; and Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA.

Genetic introgression is pervasive in nature and may lead to large-scale phenotypic assimilation and/or admixture of populations, but there is limited knowledge on whether large phenotypic changes are typically accompanied by high levels of introgression throughout the genome. Using bioacoustic, biometric, and spectrophotometric data from a flycatcher (Tyrannidae) system in the Neotropical genus Zimmerius, we document a mosaic pattern of phenotypic admixture in which a population of Zimmerius viridiflavus in northern Peru (henceforth "mosaic") is vocally and biometrically similar to conspecifics to the south but shares plumage characteristics with a different species (Zimmerius chrysops) to the north. To clarify the origins of the mosaic population, we used the RAD-seq approach to generate a data set of 37,361 genome-wide single nucleotide polymorphisms (SNPs). A range of population-genetic diagnostics shows that the genome of the mosaic population is largely indistinguishable from southern Z. viridiflavus and distinct from northern Z. chrysops, and the application of parsimony and species tree methods to the genome-wide SNP data set confirms the close affinity of the mosaic population with southern Z. viridiflavus. Even so, using a subset of 2710 SNPs found across all sampled lineages in configurations appropriate for a recently proposed statistical ("ABBA/BABA") test that distinguishes gene flow from incomplete lineage sorting, we detected low levels of gene flow from northern Z. chrysops into the mosaic population. Mapping the candidate loci for introgression from Z. chrysops into the mosaic population to the zebra finch genome reveals close linkage with genes significantly enriched in functions involving cell projection and plasma membranes. Introgression of key alleles may have led to phenotypic assimilation in the plumage of mosaic birds, suggesting that selection may have been a key factor facilitating introgression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/sysbio/syt070DOI Listing
March 2014

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

Proc Natl Acad Sci U S A 2013 Dec 2;110(51):20645-50. Epub 2013 Dec 2.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045.

Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1314475110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870669PMC
December 2013

Speciation on the rocks: integrated systematics of the Heteronotia spelea species complex (Gekkota; Reptilia) from Western and Central Australia.

PLoS One 2013 11;8(11):e78110. Epub 2013 Nov 11.

Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia.

The isolated uplands of the Australian arid zone are known to provide mesic refuges in an otherwise xeric landscape, and divergent lineages of largely arid zone taxa have persisted in these regions following the onset of Miocene aridification. Geckos of the genus Heteronotia are one such group, and have been the subject of many genetic studies, including H. spelea, a strongly banded form that occurs in the uplands of the Pilbara and Central Ranges regions of the Australian arid zone. Here we assess the systematics of these geckos based on detailed examination of morphological and genetic variation. The H. spelea species complex is a monophyletic lineage to the exclusion of the H. binoei and H. planiceps species complexes. Within the H. spelea complex, our previous studies based on mtDNA and nine nDNA loci found populations from the Central Ranges to be genetically divergent from Pilbara populations. Here we supplement our published molecular data with additional data gathered from central Australian samples. In the spirit of integrative species delimitation, we combine multi-locus, coalescent-based lineage delimitation with extensive morphological analyses to test species boundaries, and we describe the central populations as a new species, H. fasciolatus sp. nov. In addition, within the Pilbara there is strong genetic evidence for three lineages corresponding to northeastern (type), southern, and a large-bodied melanic population isolated in the northwest. Due to its genetic distinctiveness and extreme morphological divergence from all other Heteronotia, we describe the melanic form as a new species, H. atra sp. nov. The northeastern and southern Pilbara populations are morphologically indistinguishable with the exception of a morpho-type in the southeast that has a banding pattern resembling H. planiceps from the northern monsoonal tropics. Pending more extensive analyses, we therefore treat Pilbara H. spelea as a single species with phylogenetic structure and morphological heterogeneity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078110PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3823942PMC
July 2014

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

Genome Biol 2013 Mar 28;14(3):R28. Epub 2013 Mar 28.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2013-14-3-r28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054807PMC
March 2013

Report from the first snake genomics and integrative biology meeting.

Stand Genomic Sci 2012 Oct 24;7(1):150-2. Epub 2012 Sep 24.

Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA.

This report summarizes the proceedings of the 1st Snake Genomics and Integrative Biology Meeting held in Vail, CO USA, 5-8 October 2011. The meeting had over twenty registered participants, and was conducted as a single session of presentations. Goals of the meeting included coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4056/sigs.3106480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570801PMC
October 2012

A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia.

PLoS One 2012 7;7(11):e48990. Epub 2012 Nov 7.

Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.

In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048990PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3492174PMC
July 2013

Coalescent-based species delimitation in an integrative taxonomy.

Trends Ecol Evol 2012 Sep 25;27(9):480-8. Epub 2012 May 25.

Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.

The statistical rigor of species delimitation has increased dramatically over the past decade. Coalescent theory provides powerful models for population genetic inference, and is now increasingly important in phylogenetics and speciation research. By applying probabilistic models, coalescent-based species delimitation provides clear and objective testing of alternative hypotheses of evolutionary independence. As acquisition of multilocus data becomes increasingly automated, coalescent-based species delimitation will improve the discovery, resolution, consistency, and stability of the taxonomy of species. Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tree.2012.04.012DOI Listing
September 2012

Nonadaptive evolution of mitochondrial genome size.

Evolution 2011 Sep 10;65(9):2706-11. Epub 2011 May 10.

Department of Integrative Biology, University of California-Berkeley, 3060 Valley Life Sciences Building, Berkeley, California, 94720-3140, USA.

Genomes vary greatly in size and complexity, and identifying the evolutionary forces that have generated this variation remains a major goal in biology. A controversial proposal is that most changes in genome size are initially deleterious and therefore are linked to episodes of decrease in effective population sizes. Support for this hypothesis comes from large-scale comparative analyses, but vanishes when phylogenetic nonindependence is taken into account. Another approach to test this hypothesis involves analyzing sequence evolution among clades where duplications have recently fixed. Here we show that episodes of fixation of duplications in mitochondrial genomes of the gecko Heteronotia binoei (two independent clades) and of mantellid frogs (five distinct branches) coincide with reductions in the ability of selection to purge slightly deleterious mutations. Our results support the idea that genome complexity can arise through nonadaptive processes in tetrapods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1558-5646.2011.01322.xDOI Listing
September 2011

The genome of the green anole lizard and a comparative analysis with birds and mammals.

Nature 2011 Aug 31;477(7366):587-91. Epub 2011 Aug 31.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature10390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184186PMC
August 2011

The genetic legacy of aridification: climate cycling fostered lizard diversification in Australian montane refugia and left low-lying deserts genetically depauperate.

Mol Phylogenet Evol 2011 Dec 18;61(3):750-9. Epub 2011 Aug 18.

Division of Evolution, Ecology & Genetics, Research School of Biology, The Australian National University, Canberra, Australia.

It is a widely held assumption that populations historically restricted to mountain refugia tend to exhibit high levels of genetic diversity and deep coalescent histories, whereas populations distributed in surrounding low-lying regions tend to be genetically depauperate following recent expansion from refugia. These predicted genetic patterns are based largely on our understanding of glaciation history in Northern Hemisphere systems, yet remain poorly tested in analogous Southern Hemisphere arid systems because few examples in the literature allow the comparison of widespread taxa distributed across mountain and desert biomes. We demonstrate with multiple datasets from Australian geckos that topographically complex mountain regions harbor high nucleotide diversity, up to 18 times higher than that of the surrounding desert lowlands. We further demonstrate that taxa in topographically complex areas have older coalescent histories than those in the geologically younger deserts, and that both ancient and more recent aridification events have contributed to these patterns. Our results show that, despite differences in the details of climate and landscape changes that occurred in the Northern and Southern hemispheres (ice-sheets versus aridification), similar patterns emerge that illustrate the profound influence of the Pleistocene on contemporary genetic structure.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2011.08.009DOI Listing
December 2011

The Anolis lizard genome: an amniote genome without isochores.

Genome Biol Evol 2011 27;3:974-84. Epub 2011 Jul 27.

Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.

Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date. The newly sequenced genome of Anolis carolinensis provides the first opportunity to quantify isochore structure in a nonavian reptile. We find Anolis to have the most compositionally homogeneous genome of all amniotes sequenced thus far, a homogeneity exceeding that for the frog Xenopus. Based on a Bayesian algorithm, Anolis has smaller and less GC-rich isochores compared with human and chicken. Correlates generally associated with GC-rich isochores, including shorter introns and higher gene density, have all but disappeared from the Anolis genome. Using genic GC as a proxy for isochore structure so as to compare with other vertebrates, we found that GC content has substantially decreased in the lineage leading to Anolis since diverging from the common ancestor of Reptilia ∼275 Ma, perhaps reflecting weakened or reversed GC-biased gene conversion, a nonadaptive substitution process that is thought to be important in the maintenance and trajectory of isochore evolution. Our results demonstrate that GC composition in Anolis is not associated with important features of genome structure, including gene density and intron size, in contrast to patterns seen in mammal and bird genomes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gbe/evr072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184785PMC
January 2012

Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata.

Mol Phylogenet Evol 2011 Nov 1;61(2):300-7. Epub 2011 Jul 1.

Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.

As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2011.06.016DOI Listing
November 2011

Palaeoclimate change drove diversification among isolated mountain refugia in the Australian arid zone.

Mol Ecol 2011 Apr 4;20(7):1529-45. Epub 2011 Mar 4.

Division of Evolution, Ecology & Genetics, Research School of Biology, The Australian National University, Canberra, Australia.

Refugia featured prominently in shaping evolutionary trajectories during repeated cycles of glaciation in the Quaternary, particularly in the Northern Hemisphere. The Southern Hemisphere instead experienced cycles of severe aridification but little is known about the temporal presence and role of refugia for arid-adapted biota. Isolated mountain ranges located in the Australian arid zone likely provided refugia for many species following Mio/Pliocene (<15 Ma) aridification; however, the evolutionary consequences of the recent development of widespread sand deserts is largely unknown. To test alternative hypotheses of ancient vs. recent isolation, we generated a 10 gene data set to assess divergence history among saxicolous geckos in the genus Heteronotia that have distributions confined to major rocky ranges in the arid zone. Phylogenetic analyses show that each rocky range harbours a divergent lineage, and substantial intraspecific diversity is likely due to topographic complexity in these areas. Old divergences (~4 Ma) among lineages pre-date the formation of the geologically young sand deserts (<1 Ma), suggesting that Pliocene climate shifts fractured the distributions of biota long before the spread of the deserts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1365-294X.2011.05036.xDOI Listing
April 2011