A5046615539- Crustacean biology and ecology
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Fish biology, ecology, and behavior
- HIV Research and Treatment
- Fish Biology and Ecology Studies
- Epigenetics and DNA Methylation
- Gut microbiota and health
- Marine Biology and Ecology Research
- Chromosomal and Genetic Variations
- Cancer Genomics and Diagnostics
- Parasite Biology and Host Interactions
- Aquatic Invertebrate Ecology and Behavior
- Coral and Marine Ecosystems Studies
- Particle accelerators and beam dynamics
- HIV/AIDS drug development and treatment
- HIV/AIDS Research and Interventions
- Animal Disease Management and Epidemiology
- Species Distribution and Climate Change
- Evolution and Genetic Dynamics
- Particle Accelerators and Free-Electron Lasers
- Genetic and phenotypic traits in livestock
- Cystic Fibrosis Research Advances
- Probiotics and Fermented Foods
- Ichthyology and Marine Biology
George Washington University
2016-2025
Milken Institute
2016-2025
Smithsonian Institution
2015-2024
National Museum of Natural History
2015-2024
International Union for Conservation of Nature (Bangladesh)
2024
Brigham Young University
2006-2022
George Washington University Virginia Campus
2012-2022
National Hospital
2021
Cohort (United Kingdom)
2021
Collaborative Research Group
2021
The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits data.The package, including source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
Phylogenies are extremely useful tools, not only for establishing genealogical relationships among a group of organisms or their parts (e.g. genes), but also variety research once the phylogenies estimated. In recent review, Pagel (1999) eloquently outline number uses phylogenetic information from discovery drug resistance to reconstructing common ancestor all life. have been used predict future trends in infectious disease ( Bush et al. 1999 ) and even offered as evidence court law Vogel...
Abstract We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our was limited segments in which little recombination occurs. In such cases, cladogram can be constructed from the site sequence data represents evolutionary steps interrelate observed haplotypes. The is used define nested statistical design mutational central assumption behind this...
Recombination is a key evolutionary process that shapes the architecture of genomes and genetic structure populations. Although many statistical methods are available for detection recombination from DNA sequences, their absolute relative performance still unknown. Here we evaluated 14 different algorithms. We used coalescent with to simulate sequences levels recombination, diversity, rate variation among sites. were applied these data sets, whether they detected or not was recorded....
One of the strengths maximum likelihood method phylogenetic estimation is ease with which hypotheses can be formulated and tested. Maximum analysis DNA amino acid sequence data has been made practical recent advances in models substitution, computer programs, computational speed. Here, we describe improvements substitution. We also how ratio tests a variety biological tested using simulation to generate null distribution test statistic.
Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found major clades eukaryotic organisms. They can be easily coamplified with orthologous by using conserved universal primers; however, this is especially problematic for DNA barcoding, which attempts to characterize all living organisms a short fragment cytochrome c oxidase I (COI) gene. Here, we study effect numts on barcoding based phylogenetic and analyses numt sequences two...
Abstract Empirical data sets of intraspecific restriction site polymorphism in Drosophila have been gathered order to test hypotheses derived from coalescent theory. Three main ideas are tested: (1) haplotype frequency the sample contains information on topological position a given cladogram, (2) is related number mutational connections other haplotypes cladogram and (3) geographic location can be used infer positioning cladogram. These relationships then better estimate phylogenies two...
Despite the relevant role of models nucleotide substitution in phylogenetics, choosing among different remains a problem. Several statistical methods for selecting model that best fits data at hand have been proposed, but their absolute and relative performance has not yet characterized. In this study, we compare under various conditions hierarchical dynamic likelihood ratio tests, Akaike Bayesian information methods, best-fit substitution. We specifically examine topology used to estimate...
Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific social challenges new millennium. These require fundamental knowledge organization, evolution, functions, interactions millions planet’s organisms. Herein, we present a perspective on Earth BioGenome Project (EBP), moonshot for biology that aims to sequence, catalog, characterize genomes all eukaryotic over period 10 years. The outcomes EBP will inform broad...
We have developed a modified BOOTSCAN algorithm that may be used to screen nucleotide sequence alignments for evidence of recombination without prior identification nonrecombinant reference sequences. The is fast and includes Bonferroni corrected statistical test circumvent the multiple testing problems encountered when using method explore recombination. Using both simulated real datasets we demonstrate more powerful than other phylogenetic detection methods performs almost as well one best...
Phylogentic analysis is becoming an increasingly important tool for customized drug treatments, epidemiological studies, and evolutionary analysis. The TCS method provides dealing with genes at a population level. Existing software takes unreasonable amount of time the significant numbers Taxa. This paper presents algorithms describes initial attempts parallelization. Performance results are also presented algorithm on several data sets.
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity homologous character data across disparately related currently renders direct inference untenable. To reconstruct comprehensive life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into phylogeny. We present draft containing 2.3 million tips-the Open Tree Life. Realization this required assembly two...
The use of comparative methods to test evolutionary hypotheses has become more common at both the macro- and microevolutionary levels. application such techniques is especially troublesome interface these levels because phylogenetic relationships are often difficult estimate. a technique developed estimate intraspecific cladograms combined with traditional estimation can improve in data sets containing range diversity when lower bound approaches 0% divergence. For nucleotide sequence from...
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across globe to GISAID database up 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout entire SARS-CoV-2. Moreover,...