A5059896233- Genetic diversity and population structure
- Amphibian and Reptile Biology
- Turtle Biology and Conservation
- Evolution and Paleontology Studies
- Genomics and Phylogenetic Studies
- Species Distribution and Climate Change
- Wildlife Ecology and Conservation
- Evolution and Genetic Dynamics
- Plant and animal studies
- Animal Behavior and Reproduction
- Avian ecology and behavior
- Identification and Quantification in Food
- Physiological and biochemical adaptations
- Morphological variations and asymmetry
- Fish Biology and Ecology Studies
- Ichthyology and Marine Biology
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Environmental DNA in Biodiversity Studies
- Paleontology and Evolutionary Biology
- Lepidoptera: Biology and Taxonomy
- Insect and Arachnid Ecology and Behavior
- Scarabaeidae Beetle Taxonomy and Biogeography
- Parasite Biology and Host Interactions
- Molecular Biology Techniques and Applications
- Genetics and Physical Performance
University of Hawaii System
2015-2024
University of Hawaiʻi at Mānoa
2014-2024
Natural History Museum of Los Angeles County
2020-2024
University of California, Davis
2007-2012
University of California System
2010
We describe the genome of western painted turtle, Chrysemys picta bellii, one most widespread, abundant, and well-studied turtles. place into a comparative evolutionary context, focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation determination, species' physiological capacities to withstand extreme anoxia tissue freezing.Our phylogenetic analyses confirm that turtles are sister group living archosaurs, demonstrate an extraordinarily slow rate...
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree Life, but poor resolution deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on by developing taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds conserved exons which are effective across class. After obtaining data from 220 loci 286 species (representing 94% 44% genera), estimate phylogeny extant...
Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining diversity. We investigated this hypothesis collecting a molecular dataset for 591 individual that, together, represent 80% of all turtle species, including representatives families 98% genera, used it to jointly estimate phylogeny divergence times. found the tree is relatively...
Despite considerable effort from the systematics community, delimiting species boundaries in recent radiations remains a daunting challenge. We argue that genealogical approaches, although sometimes useful, may not solve this important problem, because recently derived often have had sufficient time to achieve monophyly. Instead, we suggest population genetic approaches rely on large sets of informative markers like single nucleotide polymorphisms (SNPs) provide an alternative framework for...
As phylogenetic data sets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing directly principle provide effective syntheses of that may reveal new relationships. However, several serious difficulties exist the construction large supermatrices must be overcome before these approaches will enjoy broad utility. We present analyses examine performance sparse constructed from sequence databases for...
As the application of genomic data in phylogenetics has become routine, a number cases have arisen where alternative sets strongly support conflicting conclusions. This sensitivity to analytical decisions prevented firm resolution some most recalcitrant nodes tree life. To better understand causes and nature this sensitivity, we analyzed several phylogenomic using an measure topological (the Bayes factor) that both demonstrates averts limitations more frequently employed measures (such as...
The use of genetic data for identifying species-level lineages across the tree life has received increasing attention in field systematics over past decade. multispecies coalescent model provides a framework understanding process lineage divergence and become widely adopted delimiting species. However, because these studies lack an explicit assessment fit, many cases, accuracy inferred species boundaries are unknown. This is concerning given large amount empirical theory that highlight...
The use of large genomic data sets in phylogenetics has highlighted extensive topological variation across genes. Much this discordance is assumed to result from biological processes. However, among gene trees can also be a consequence systematic error driven by poor model fit, and the relative importance vs. methodological factors explaining tree major unresolved question. Using mitochondrial genomes control for causes variation, we estimate extent employ posterior prediction highlight role...
Recent progress in resolving the tree of life continues to expose relationships that resist resolution, which drives search for novel sources information solve these difficult phylogenetic problems. A recent example, presence and absence microRNA families, has been vigorously promoted as an ideal source data applied several perennial The utility such inference hinges critically both on developing stochastic models provide a reasonable description process give rise data, also careful...
Morphological diversification does not proceed evenly across the organism. Some body parts tend to evolve at higher rates than others, and these rate biases are often attributed sexual natural selection or genetic constraints. We hypothesized that variation in of morphological evolution among could also be related performance consequences functional systems make up body. Specifically, we tested widely held expectation for a trait is negatively correlated with strength biomechanical...
As the field of phylogeography has matured, it become clear that analyses one or a few genes may reveal more about history those than populations and species are targets study. To alleviate these concerns, discipline moved towards larger individuals genes, although little attention been paid to qualitative quantitative gains such increases in scale scope yield. Here, we increase number markers by an order magnitude over previously published work comprehensively assess phylogeographical...
Many fields of evolutionary biology now depend on stochastic mathematical models. These models are valuable for their ability to formalize predictions in the face uncertainty and provide a quantitative framework testing hypotheses. However, no model will fully capture biological complexity. Instead, these attempt important features systems using relatively simple principles. simplifications can allow us focus differences that meaningful, while ignoring those not. simplification also requires...
Hybridization between diverging lineages is associated with the generation and loss of species diversity, introgression, adaptation, changes in reproductive mode, but it unknown when why results these divergent outcomes. We estimate a comprehensive evolutionary network for largest group unisexual vertebrates use to understand outcomes hybridization. Our show that rates introgression decrease time since divergence suggest must attain threshold before hybridization transitions unisexuality....
Phylogenies often contain both well-supported and poorly supported nodes. Determining how much additional data might be required to eventually recover most or all nodes with high support is an important pragmatic goal, simulations have been used examine this question. Most based on few empirical loci, suggest that well phylogenies can determined a very modest amount of data. Here we report the results phylogenetic analysis 10 genera 25 48 species new world pond turtles (family Emydidae) one...
Abstract Accurate estimates of biodiversity are required for research in a broad array biological subdisciplines including ecology, evolution, systematics, conservation and science. The use statistical models genetic data, particularly DNA barcoding, has been suggested as an important tool remedying the large gaps our current understanding biodiversity. However, reliability obtained using these approaches depends on how well that used describe evolutionary process underlying data. In this...
A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history alleles sampled from individuals belonging to those species. This has motivated development increasingly sophisticated statistical models rooted in multispecies coalescent process. Specifically, these allow for simultaneous estimation number present a sample phylogenetic using only DNA sequence data independent loci. These methods...
The scale of data sets used to infer phylogenies has grown dramatically in the last decades, providing researchers with an enormous amount information which draw inferences about evolutionary history. However, standard approaches assessing confidence those (e.g., nonparametric bootstrap proportions [BP] and Bayesian posterior probabilities [PPs]) are still deeply influenced by statistical procedures frameworks that were developed when was much more limited. These largely quantify uncertainty...
The historical biogeography of California's taxa has been the focus extensive research effort. western pond turtle (Emys marmorata) is an example a wide-ranging taxon that spans several well-known California diversity hotspots. Using dataset comprised one mitochondrial and five nuclear loci, we elucidate major biogeographic patterns across landscape. By employing combination phylogenetic network-based approaches, recovered relatively ancient (c. 2-8 Ma) north/south split among populations E....
Tests of absolute model fit are crucial in model-based inference because poorly structured models can lead to biased parameter estimates. In Bayesian inference, posterior predictive simulations be used test fit. However, such tests have not been commonly practiced phylogenetic due a lack convenient and flexible software. Here, we describe our newly implemented using testing, based on both data- inference-based statistics, the phylogenetics software RevBayes. This new implementation makes...