A5062412720- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Evolution and Paleontology Studies
- Genetics, Bioinformatics, and Biomedical Research
- Prion Diseases and Protein Misfolding
- HIV Research and Treatment
- Evolution and Genetic Dynamics
- Ecology and Vegetation Dynamics Studies
- Amphibian and Reptile Biology
- Neurological diseases and metabolism
- Species Distribution and Climate Change
- Data Visualization and Analytics
- Chromosomal and Genetic Variations
- Plant Diversity and Evolution
- Herpesvirus Infections and Treatments
- Insect and Arachnid Ecology and Behavior
- Morphological variations and asymmetry
- Insect-Plant Interactions and Control
- Bioinformatics and Genomic Networks
- Alzheimer's disease research and treatments
- HIV/AIDS Research and Interventions
- Plant and animal studies
- Hemiptera Insect Studies
- Forest ecology and management
- Prenatal Screening and Diagnostics
Houston Museum of Natural Science
2015-2024
Louisiana State University
2014-2024
University of Connecticut
2014-2017
University of California, Los Angeles
1958-2017
National Museum of Natural History
2014-2017
Smithsonian Institution
2014-2017
University of Cincinnati
2012-2017
Yale University
2017
Duke University
2017
Universidad Nacional Autónoma de México
2017
Abstract Although an increasing number of phylogenetic data sets are incomplete, the effect ambiguous on accuracy is not well understood. We use 4-taxon simulations to study effects (i.e., missing characters or gaps) in maximum likelihood (ML) and Bayesian frameworks. By introducing a way that removes confounding factors, we provide first clear understanding 1 mechanism by which can mislead analyses. find both ML frameworks, among-site rate variation interact with produce misleading...
As larger, more complex data sets are being used to infer phylogenies, accuracy of these phylogenies increasingly requires models evolution that accommodate heterogeneity in the processes molecular evolution. We investigated effect improper partitioning on phylogenetic accuracy, as well type I error rate and sensitivity Bayes factors, a commonly method for choosing among different strategies Bayesian analyses. also factors test empirical need divide manner has no expected biological meaning....
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...
A surprising number of recent Bayesian phylogenetic analyses contain branch-length estimates that are several orders magnitude longer than corresponding maximum-likelihood estimates. The levels divergence implied by such branch lengths unreasonable for studies using biological data and known to be false simulated data. We conducted additional studied approximate-posterior surfaces investigate the causes underlying these large errors. manipulated starting parameter values Markov chain Monte...
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...
Ants are the world's most conspicuous and important eusocial insects their diversity, abundance, extreme behavioral specializations make them a model system for several disciplines within biological sciences. Here, we report discovery of new ant that appears to represent sister lineage all extant ants (Hymenoptera: Formicidae). The phylogenetic position this cryptic predator from soils Amazon rainforest was inferred nuclear genes, sequenced single leg. Martialis heureka (gen. et sp. nov.)...
The objective of this study is to determine whether adipose tissue functions as a reservoir for HIV-1.We examined memory CD4(+) T cells and HIV DNA in tissue-stromal vascular fraction (AT-SVF) five patients [four antiretroviral therapy (ART)-treated one untreated]. To adipocytes stimulate regulate production, primary human were cocultured with HIV-infected cells.AT-SVF studied by flow cytometry, AT-SVF (Gag Env) was nested PCR sequence analyses. T-cell activation production measured...
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...
In many animal species, the amount of care provided by parents is determined through a complex interaction offspring signals and responses to those signals. As predicted honest signaling theory, we show that in burrower bug, Sehirus cinctus , maternal provisioning responds experimental manipulations condition. Despite this environmental influence, find evidence from two cross-foster experiments variation also stems distinct genetic sources: among their ability elicit response Furthermore, as...
A large family with autosomal dominant segregation of presenile dementia, and other neurological behavioural features is described. At various times, members have carried diagnoses Alzheimer's disease, Huntington's Parkinson's myoclonic epilepsy, atypical Pick's Creutzfeldt-Jakob disease Gerstmann-Strāussler syndrome. Molecular genetic studies enabled classification this at the molecular level as one group inherited prion diseases. Here we describe phenotype (PrP 144 bp insertion).
Genealogical and molecular studies were carried out in four families which early onset dementia is inherited as an autosomal dominant. These indicated that the derive from siblings whose parents born late 18th century South-East England. The disease was found to be closely linked a 144 bp insertion within open reading frame of prion protein (PrP) gene with maximum LOD score 11.02 at zero recombination. Within general population PrP polymorphic codon 129 (allele frequency approximately 30%...
Model checking is a critical part of Bayesian data analysis, yet it remains largely unused in systematic studies. Phylogeny estimation has recently moved into an era increasingly complex models that simultaneously account for multiple evolutionary processes, the statistical fit these to rarely been tested. Here we develop posterior predictive simulation-based model check commonly used multispecies coalescent model, implemented *BEAST, and apply 25 published sets. We show poor detectable...
Phylogenetic analysis has been widely used to test the a priori hypothesis of epidemiological clustering in suspected transmission chains HIV-1. Among studies showing strong support for relatedness between HIV samples obtained from infected individuals, evidence direction epidemiologically related pairs lacking. During HIV, genetic bottleneck occurs, resulting paraphyly source viruses with respect those recipient. This establishes transmission, which can then be inferred. Here, we present...
Topological heterogeneity among gene trees is widely observed in phylogenomic analyses and some of this variation likely caused by systematic error tree estimation. Systematic can be mitigated improving models sequence evolution to account for all evolutionary processes relevant each or identifying those genes whose best conforms existing models. However, the method such not well established. Here, we ask if filtering according their clock-likeness posterior predictive effect size (PPES, an...
Systematic phylogenetic error caused by the simplifying assumptions made in models of molecular evolution may be impossible to avoid entirely when attempting model across massive, diverse data sets. However, not all deficiencies inference result unreliable estimates. The field phylogenetics lacks a direct method identify cases where specification adversely affects inferences. Posterior predictive simulation is flexible and intuitive approach for assessing goodness-of-fit assumed priors...
In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is phylogenetic position turtles within amniotes, and 2) are relationships between three major lissamphibian (extant amphibian) groups? These have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, four branching patterns Lissamphibia. We compiled a large cDNA/EST dataset vertebrates (75 genes 129 taxa) address these outstanding questions. Gene-specific...
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...
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...
Copyedited by:TRJ MANUSCRIPT CATEGORY: Article[17:30 18/3/2014 Sysbio-syu009.tex] Page: 1 1–4Syst. Biol. 0(0):1–4, 2014© The Author(s) 2014. Published by Oxford University Press, on behalf of the Society Systematic Biologists. All rights reserved.For Permissions, please email: journals.permissions@oup.comDOI:10.1093/sysbio/syu009
1 Abstract Reconstructing the evolutionary history of different groups organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this history, providing a hypothesis events. Within Bayesian phylogenetics major step in estimating tree is choosing an appropriate model character evolution. In case most extinct species, our only source information decipher their phylogenetic relationships through morphology fossils. We...
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...
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...
Modern phylogenomic analyses often result in large collections of phylogenetic trees representing uncertainty individual gene trees, variation across genes, or both. Extracting signal from these tree sets can be challenging, as they are difficult to visualize, explore, and quantify. To overcome some challenges, we have developed TreeScaper, an application for set visualization well the identification distinct signals. GUI command-line versions TreeScaper a manual with tutorials downloaded...
Abstract Summary: The accuracy of Bayesian phylogenetic inference using molecular data depends on the use proper models sequence evolution. Although choosing best model available from a pool alternatives has become standard practice in statistical phylogenetics, assessment chosen model's adequacy is rare. Programs for have recently begun to implement evolution that account heterogeneity across sites beyond variation rates evolution, yet no program exists assess these models. PuMA implements...
Abstract Reconstructing the evolutionary history of different groups organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this history. Within Bayesian phylogenetics a major step in estimating tree is choosing an appropriate model character evolution. While most common data molecular sequence data, morphological remains vital source information. The use characters allows for incorporation fossil taxa, despite advances...