A5068691883- Marine Invertebrate Physiology and Ecology
- Genomics and Phylogenetic Studies
- Marine Ecology and Invasive Species
- Genetic diversity and population structure
- Coral and Marine Ecosystems Studies
- Protist diversity and phylogeny
- HIV/AIDS Research and Interventions
- Cephalopods and Marine Biology
- HIV Research and Treatment
- HIV, Drug Use, Sexual Risk
- Evolution and Paleontology Studies
- Marine Biology and Ecology Research
- Marine Sponges and Natural Products
- Single-cell and spatial transcriptomics
- Plant and Biological Electrophysiology Studies
- Aquatic Invertebrate Ecology and Behavior
- Hippo pathway signaling and YAP/TAZ
- Gene expression and cancer classification
- Coastal wetland ecosystem dynamics
- Planarian Biology and Electrostimulation
- Chromosomal and Genetic Variations
- Marine and coastal plant biology
- bioluminescence and chemiluminescence research
- Photoreceptor and optogenetics research
- Marine Toxins and Detection Methods
Yale University
2008-2025
Robert S. Peabody Museum of Archaeology
2024
Whitney Museum of American Art
2024
Brown University
2007-2018
John Brown University
2012-2017
Oceanography Society
2017
Providence College
2015
Google (United States)
2015
Leeds Dental Hospital
2010
University of Hawaii System
2005-2008
A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity animals evolved over time. Among others, placement acoelomorph flatworms, Acoela Nemertodermatida, has fundamental implications for origin evolution various organ systems. Their position, however, been inconsistent in phylogenetic studies using one or several genes. Furthermore, among least stable taxa recent phylogenomic analyses, which simultaneously examine many genes...
The Base of the Animal Tree? identity most basal lineages animal kingdom evolutionary tree has long been contested. Ryan et al. (p. 10.1126/science.1242592 ; see Perspective by Rokas ) sequenced genome ctenophore warty comb jelly or sea walnut, Mnemiopsis leidyi , and conclude that ctenophores alone, not sponges clade consisting both cnidarians, are extant animals. results suggest a specific process likely occurred—including repeated gains loss mesoderm, expansion genes associated with cell...
Abstract Summary: Phyutility provides a set of phyloinformatics tools for summarizing and manipulating phylogenetic trees, molecular data retrieving from NCBI. Its simple command-line interface allows easy integration into scripted analyses, is able to handle large datasets with an integrated database. Availability: Phyutility, including source code, documentation, examples, executables, available at http://code.google.com/p/phyutility Contact: stephen.smith@yale.edu
Phylogenetic trees and data are often stored in incompatible inconsistent formats. The outputs of software tools that contain with analysis findings not compatible each other, making it hard to integrate the results different analyses a comparative study. treeio package is designed connect phylogenetic tree input output. It supports extracting as well commonly used analytical software. can link external phylogenies merge obtained from sources, enabling phylogeny-associated disciplines an...
In recent years, scientists have made remarkable progress reconstructing the animal phylogeny. There is broad agreement regarding many deep relationships, including monophyly of animals, Bilateria, Protostomia, Ecdysozoa, and Spiralia. This stability now allows researchers to articulate diminishing number remaining questions in terms well-defined alternative hypotheses. These include relationships at base tree, position Xenacoelomorpha, internal Recent field phylogeny has important...
Cnidaria, the sister group to Bilateria, is a highly diverse of animals in terms morphology, lifecycles, ecology, and development. How this diversity originated evolved not well understood because phylogenetic relationships among major cnidarian lineages are unclear, recent studies present contrasting hypotheses. Here, we use transcriptome data from 15 newly-sequenced species combination with 26 publicly available genomes transcriptomes assess lineages. Phylogenetic analyses using different...
Abstract Identifying our most distant animal relatives has emerged as one of the challenging problems in phylogenetics. This debate major implications for understanding origin multicellular animals and earliest events evolution, including nervous system. Some analyses identify sponges (Porifera-sister hypothesis), others comb jellies (Ctenophora-sister hypothesis). These vary many respects, making it difficult to interpret previous tests these hypotheses. To gain insight into why different...
Nearly all metazoans show signs of bilaterality, yet it is believed the bilaterians arose from radially symmetric forms hundreds millions years ago. Cnidarians (corals, sea anemones, and "jellyfish") diverged other animals before radiation Bilateria. They are diploblastic often characterized as being symmetrical around their longitudinal (oral-aboral) axis. We have studied deployment orthologs a number family members developmental regulatory genes that expressed asymmetrically during...
Gastropods are a highly diverse clade of molluscs that includes many familiar animals, such as limpets, snails, slugs and sea slugs. It is one the most abundant groups animals in only molluscan lineage has successfully colonized land. Yet relationships among within its constituent clades have remained flux for over century morphological, anatomical molecular study. Here, we re-evaluate gastropod phylogenetic by collecting new transcriptome data 40 species analysing them combination with...
In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source protein-coding gene sequences, and helped projects grow from few genes to hundreds or thousands genes. Phylogenetic studies now regularly include newly sequenced transcriptomes, as well publicly available transcriptomes genomes. Implementing such phylogenomic study, however, is computationally intensive, requires coordinated use complex software tools,...
Bivalves are an ancient and ubiquitous group of aquatic invertebrates with estimated 10 000-20 000 living species. They economically significant as a human food source, ecologically important given their biomass effects on communities. Their phylogenetic relationships have been studied for decades, unparalleled fossil record extends from the Cambrian to Recent. Nevertheless, robustly supported phylogeny deepest nodes, needed fully exploit bivalves model testing macroevolutionary theories, is...
Echinoderms (sea urchins, sea stars, brittle lilies and cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. serve as excellent model systems for developmental biology due their mechanisms, tractable laboratory use, close phylogenetic distance In addition, echinoderms very well represented fossil record, including some larval features, making valuable system studying evolutionary development. The internal relationships Echinodermata...
Significance Comparisons of genome function between species are providing important insight into the evolutionary origins diversity. Here, we show that comparative functional genomics studies can come to wrong conclusions if they do not take relationships account and instead rely on pairwise comparisons species, as is common practice. We reexamined two previously published found problems with draw both their original question. One study support for ortholog conjecture, other concluded...
Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and important constituents of global zooplankton community. They range in length from a few centimeters to tens meters. gelatinous, fragile, difficult collect, so many aspects biology these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing 32 sampled broadly across phylogeny. Sequencing depth was sufficient estimate nuclear size k-mer...
This paper examines an outbreak of five cases human monkeypox which occurred in children belonging to two families living the West Kasai region Zaire during May-July 1983. Epidemiologic investigations suggest that first case was infected from animal source, possibly a monkey, and each other four previous case. Three these presumed person-to-person transmission close household contacts. The infection either by casual contact within hospital compound, or because due use same syringe for...
Hydroidolina is a group of hydrozoans that includes Anthoathecata, Leptothecata and Siphonophorae. Previous phylogenetic analyses show strong support for monophyly, but the relationships between within its subgroups remain uncertain. In an effort to further clarify hydroidolinan relationships, we performed on 97 taxa, using DNA sequences from partial mitochondrial 16S rDNA, nearly complete nuclear 18S rDNA 28S rDNA. Our findings are consistent with previous monophyly Siphonophorae do not...