A5063543023- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Amphibian and Reptile Biology
- Physiological and biochemical adaptations
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Mitochondrial Function and Pathology
- Animal Behavior and Reproduction
- Plant Virus Research Studies
- Insect and Pesticide Research
- Insect and Arachnid Ecology and Behavior
- Plant and animal studies
- RNA Research and Splicing
- Ion channel regulation and function
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- Congenital heart defects research
- Biochemical and Structural Characterization
- Molecular Biology Techniques and Applications
- Fish Ecology and Management Studies
- Zebrafish Biomedical Research Applications
- Ion Transport and Channel Regulation
- Wind Turbine Control Systems
- Myeloproliferative Neoplasms: Diagnosis and Treatment
Colorado State University
2014-2024
University of Colorado System
2021
University of Chicago
2010-2013
Collins College
2011
Museum of Vertebrate Zoology
2004-2008
University of California, Berkeley
1999-2008
Integra (United States)
2008
Centre for Life
2005
National Hospital for Neurology and Neurosurgery
2005
Queen Elizabeth Hospital
2005
The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits number of human viral diseases, including dengue and Chikungunya fevers. This has large genome with significant population-based size variation. complete sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes southeastern China, region within historical range origin species. comprises 1,967 Mb, largest mosquito sequenced to date, its results...
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...
The evolutionary history of the largest salamander family (Plethodontidae) is characterized by extreme morphological homoplasy. Analysis mechanisms generating such homoplasy requires an independent molecular phylogeny. To this end, we sequenced 24 complete mitochondrial genomes (22 plethodontids and two outgroup taxa), added data for three species from GenBank, performed partitioned unpartitioned Bayesian, maximum likelihood, parsimony phylogenetic analyses. We explored four dataset...
The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, it becoming increasingly possible to sequence analyze this its entirety from diverse taxa. However, sequencing entire not always desirable or feasible. Which genes should be selected best infer evolutionary history mitochondria within a group organisms, what properties gene determine performance? current study addresses these questions Bayesian framework with reference phylogeny...
Among vertebrates, most of the largest genomes are found within salamanders, a clade amphibians that includes 613 species. Salamander genome sizes range from ∼14 to ∼120 Gb. Because size is correlated with nucleus and cell sizes, as well other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, molecular mechanisms driving expansion this remain largely unknown. Here, we present first comparative analysis transposable element (TE) content...
Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial solitary life-cycle phases, some social parasite species, they especially interesting models to understand evolution, behavior, ecology. Reports many species decline point pathogen transmission, habitat loss, pesticide usage, global climate change, as interconnected causes. These threats bumblebee diversity make our reliance on handful well-studied...
Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel order, there evidence that was mediated by duplication part genome, including presence both pseudogenes and additional, presumably functional, copies duplicated genes. All rearrangement-mediating duplications include either origin light-strand replication nearby tRNA genes or regions flanking heavy-strand replication. The latter comprise nad6, trnE, cob,...
Abstract Amphibians are the most threatened group of vertebrates and in dire need conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity reproductive strategies, permeable specialized skin capable producing toxins antimicrobial compounds, multiple genetic mechanisms sex determination some lineages, ability regenerate limbs organs. Although genomic approaches would shed light on these traits aid conservation, sequencing assembly...
<b>Objective: </b> To evaluate clinical, genetic, and electrophysiologic features of patients with Andersen-Tawil syndrome (ATS) in the United Kingdom. <b>Methods: Clinical neurophysiologic evaluation was conducted 11 families suspected to have ATS. Molecular genetic analysis each proband performed by direct DNA sequencing entire coding region <i>KCNJ2</i>. Control samples were screened sequencing. The consequences several new mutations studied an oocyte expression system. <b>Results: All...
Abstract Aim The salamander Ensatina eschscholtzii Gray is a classic example of ring species, or species that has expanded around central barrier to form secondary contact characterized by species‐level divergence. In the original formulation scenario, an explicit biogeographical model was proposed account for occurrence intraspecific sympatry between two subspecies in southern California (the ‘southern closure’ model). Here we develop alternative informed geomorphological development Coast...
Evolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion deletion mutations (indels) directly impact by adding or removing sequences. Most species lose more DNA through small indels (i.e., ~1-30 bp) than they gain, which can reduction over time. Because this rate loss varies across species, indel dynamics have been suggested to contribute evolution. Species with extremely large genomes provide interesting test cases for...
Transposable elements are mobile DNA sequences that widely distributed in prokaryotic and eukaryotic genomes, where they represent a major force genome evolution. However, transposable have rarely been documented viruses, their contribution to viral evolution remains largely unexplored. Pandoraviruses recently described viruses with sizes exceed those of some prokaryotes, rivaling parasitic eukaryotes. These large genomes appear include substantial noncoding intergenic spaces, which provide...
Estimates of divergence dates between species improve our understanding processes ranging from nucleotide substitution to speciation. Such estimates are frequently based on molecular genetic differences species; therefore, they rely accurate the number such (i.e. substitutions per site, measured as branch length phylogenies). We used simulations determine effects dataset size, heterogeneity, depth, and analytical framework estimation across a range lengths. then reanalyzed an empirical for...
Mitochondria are the site for citric acid cycle and oxidative phosphorylation (OXPHOS), final steps of ATP synthesis via cellular respiration. Each mitochondrion contains its own genome; in vertebrates, this is a small, circular DNA molecule that encodes 13 subunits multiprotein OXPHOS electron transport complexes. Vertebrate lineages vary dramatically metabolic rates; thus, functional constraints on mitochondrial-encoded proteins likely differ, potentially impacting mitochondrial genome...
Salamanders have the largest nuclear genomes among tetrapods and, excepting lungfishes, vertebrates as a whole. Lynch and Conery (2003) proposed mutational-hazard hypothesis to explain variation in genome size complexity. Under this hypothesis, noncoding DNA imposes selective cost by increasing target for degenerative mutations (i.e., mutational hazard). Expansion of DNA, thus size, is driven increased levels genetic drift and/or decreased mutation rates; former determines efficiency with...
Nocturnal geckos are active at body temperatures 10-35°C below the thermal optima for maximum rate of aerobic metabolism (V.O2max) diurnal lizards. Therefore, given ancestral (diurnal) lizard physiology, nocturnality causes a substantial handicap in locomotor performance. In prior studies, we hypothesized that low minimum cost locomotion (Cmin ) was an adaptation increased endurance capacity low, nocturnal temperatures. However, Cmin is only part integrated system that, conjunction with...
Abstract Background Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different genomes. Phylogenetically diverse taxa undergo chromatin — some ciliates, nematodes, copepods, and vertebrates. In cyclopoid occurs in with massively expanded germline genomes; depending on species, genome sizes range 15 – 75 Gb, 12–74 Gb which are lost pre-somatic at soma differentiation. This more than...
Background: T‐box genes constitute a large family of transcriptional regulators involved in developmental patterning. Homozygous mutation tbx5 leads to embryonic lethal cardiac phenotypes and forelimb malformations vertebrate models. Haploinsufficiency results Holt‐Oram syndrome, human congenital disease characterized by defects. zebrafish tbx5a defects looping morphogenesis, blocks pectoral fin initiation, impairs outgrowth. Recently, second gene was described, termed tbx5b . Results: Our...
Abstract Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties genomic TE community reveal the history TE/host evolutionary dynamics and impact present-day host structure function, from to organism levels. In rare cases, community/genome size has greatly expanded in animals, associated with increased cell changes anatomy physiology. Here, we characterize landscape transcriptome an amphibian giant — caecilianIchthyophis bannanicus, which show...
Synopsis Genome size varies ∼100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation identified as a major driver of increase, but the nature constraints limiting genomes remained unclear, even traits such cell rate development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic non-metamorphic life histories, join lungfish having largest vertebrate genomes—3 40 times that...
Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), has been pushed to extreme, prompting question whether also deviates from typical conditions. To address this question, we characterize via two pathways-the piRNA pathway KRAB-ZFP transcriptional repression-in male female gonads Ranodon sibiricus, salamander ∼21 Gb...