A5067275965- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Protist diversity and phylogeny
- Mosquito-borne diseases and control
- Microbial Community Ecology and Physiology
- Evolution and Paleontology Studies
- Malaria Research and Control
- Genetics, Bioinformatics, and Biomedical Research
- Plant Taxonomy and Phylogenetics
- Vector-borne infectious diseases
- Parasitic Infections and Diagnostics
- RNA and protein synthesis mechanisms
- Insect symbiosis and bacterial influences
- Botany and Plant Ecology Studies
- Viral Infections and Vectors
- Bryophyte Studies and Records
- Environmental DNA in Biodiversity Studies
- Marine Ecology and Invasive Species
- Marine Biology and Ecology Research
- Amoebic Infections and Treatments
- Reproductive tract infections research
- Marine Bivalve and Aquaculture Studies
- Cephalopods and Marine Biology
- Amphibian and Reptile Biology
- Aquatic Invertebrate Ecology and Behavior
Natural History Museum
2014-2023
Queensland University of Technology
2019
University of Connecticut
2014-2017
University of California, Los Angeles
2014-2017
National Museum of Natural History
2001-2017
Smithsonian Institution
2001-2017
University of Cincinnati
2012-2017
Yale University
2017
Duke University
2017
Universidad Nacional Autónoma de México
2017
Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which a significant source morbidity mortality in developing countries. Here we present genome E. histolytica, reveals variety metabolic adaptations shared with two other amitochondrial protist pathogens: Giardia lamblia Trichomonas vaginalis. These include reduction or elimination most mitochondrial pathways use oxidative stress enzymes generally associated anaerobic prokaryotes. Phylogenomic analysis...
We describe the genome sequence of protist Trichomonas vaginalis , a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds ∼160-megabase genome, reflecting recent massive expansion genetic material. This expansion, in conjunction with shaping metabolic pathways that likely transpired through lateral gene transfer from bacteria, amplification specific families implicated pathogenesis phagocytosis host proteins may exemplify adaptations parasite...
Compositional heterogeneity among lineages can compromise phylogenetic analyses, because models in common use assume compositionally homogeneous data. Models that accommodate compositional with few extra parameters are described here, and used two examples where the true tree is known confidence. It shown using likelihood ratio tests adequate modeling of be achieved composition parameters, data may not need to modelled separate for each branch tree. Tree searching placement vectors on done a...
The origin of the eukaryotic genetic apparatus is thought to be central understanding evolution cell. Disagreement about source relevant genes has spawned competing hypotheses for origins eukaryote nuclear lineage. iconic rooted 3-domains tree life shows eukaryotes and archaebacteria as separate groups that share a common ancestor exclusion eubacteria. By contrast, eocyte hypothesis originating within sharing with particular group called Crenarchaeota or eocytes. Here, we have investigated...
Horizontal gene transfer (HGT) can radically alter the genomes of microorganisms, providing capacity to adapt new lifestyles, environments, and hosts. However, extent HGT between eukaryotes is unclear. Using whole-genome, gene-by-gene phylogenetic analysis we demonstrate an extensive pattern cross-kingdom fungi oomycetes. Comparative genomics, including de novo genome sequence Hyphochytrium catenoides , a free-living sister oomycetes, shows that these transfers largely converge within...
Significance The Archaea represent a primary domain of cellular life, play major roles in modern-day biogeochemical cycles, and are central to debates about the origin eukaryotic cells. However, understanding their origins evolutionary history is challenging because immense time spans involved. Here we apply new approach that harnesses information patterns gene family evolution find root archaeal tree resolve metabolism earliest Our robustly distinguishes between published rooting...
Plants are the primary producers of terrestrial ecosystems that dominate much natural environment. Occurring approximately 480 Ma (Sanderson 2003; Kenrick et al. 2012), evolutionary transition plants from an aquatic to a environment was accompanied by several major developmental innovations. The freshwater charophyte ancestors land have haplobiontic life cycle with single haploid multicellular stage, whereas plants, which include bryophytes (liverworts, hornworts, and mosses) tracheophytes...
Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be densely sampled. This permits better phylogenetic estimates assessment of potential biases resulting from heterogeneity in nucleotide composition rate change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies Polyphaga, altogether 97 families, including 159 newly full or partial mitogenomes. Compositional greatly affected 3rd codon...
DAVID L. SWOFFORD,1,6 PETER J. WADDELL,2 JOHN P. HUELSENBECK,3 G. FOSTER,1,7 PAUL O. LEWIS,4 AND JAMES S. ROGERS5 Laboratory of Molecular Systematics, National Museum Natural History, Smithsonian Institution Support Center, 4210 Silver Hill Road, Suitland, Maryland 20746, USA; E-mail: swofford@lms.si.edu Institute BioSciences, Massey University, Palmerston North, New Zealand; waddell@onyx.si.edu Department Biology, University Rochester, York 14627, johnh@brahms.biology.rochester.edu Ecology...
Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant enzymes have similarities to prokaryote homologues are largely active in chloroplasts, suggesting ancestry from plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived organelle, encodes with genes, including five-enzyme pentafunctional arom. These data suggests that arom either had ancient origin eukaryotes or was conveyed by...
Abstract Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries and is an important evolutionary phenomenon in ancestry many microbes. The role HGT plant history is, however, largely unexplored. Here, we compare genomes six with those 159 prokaryotic eukaryotic identify 1689 genes that show highest similarity to corresponding from fungi. We constructed a phylogeny for all identified homolog groups available rice (Oryza sativa) genome (3177...
Microsporidia are an abundant group of obligate intracellular parasites other eukaryotes, including immunocompromised humans, but the molecular basis their lifestyle and pathobiology poorly understood. New genomes from a taxonomically broad range microsporidians, complemented by published expression data, provide opportunity for comparative analyses to identify conserved lineage-specific patterns microsporidian genome evolution that have underpinned this success. In study, we infer dramatic...
Determining the relationships among major groups of cellular life is important for understanding evolution biological diversity, but difficult given enormous time spans involved. In textbook ‘three domains’ tree based on informational genes, eukaryotes and Archaea share a common ancestor to exclusion Bacteria. However, some phylogenetic analyses same data have placed within Archaea, as nearest relatives different archaeal lineages. We compared support these competing hypotheses using...
Heterogeneity among life traits in mammals has resulted considerable phylogenetic conflict, particularly concerning the position of placental root. Layered upon this are gene- and lineage-specific variation amino acid substitution rates compositional biases. Life trait variations that may impact mutational longevity, metabolic rate, body size, germ line generation time. Over past 12 years, three main conflicting hypotheses have emerged for placement These place Atlantogenata (common ancestor...
Summary Unraveling the phylogenetic relationships between four major lineages of terrestrial plants (mosses, liverworts, hornworts, and vascular plants) is essential for an understanding evolution traits specific to land plants, such as their complex life cycles, evolutionary development stomata tissue. Well supported hypotheses resulting from different data methods are often incongruent due processes nucleotide that difficult model, example substitutional saturation composition...