A5007384448- Genetic diversity and population structure
- Fish Ecology and Management Studies
- Identification and Quantification in Food
- Fish Biology and Ecology Studies
- Genetic and phenotypic traits in livestock
- Genomics and Phylogenetic Studies
- Aquaculture Nutrition and Growth
- Ichthyology and Marine Biology
- Marine and fisheries research
- Aquaculture disease management and microbiota
- Marine Bivalve and Aquaculture Studies
- Genetic Mapping and Diversity in Plants and Animals
- Environmental DNA in Biodiversity Studies
- Animal Genetics and Reproduction
- Fish biology, ecology, and behavior
- Physiological and biochemical adaptations
- Aquatic Invertebrate Ecology and Behavior
- Chemical synthesis and alkaloids
- Catalysis and Hydrodesulfurization Studies
- Animal Behavior and Reproduction
- Gene expression and cancer classification
- Cephalopods and Marine Biology
- Water Quality Monitoring Technologies
- Isotope Analysis in Ecology
- Freshwater macroinvertebrate diversity and ecology
Texas A&M University – Corpus Christi
2014-2024
University of St Andrews
2018-2020
Sands
2018-2019
Horizon Discovery (United Kingdom)
2019
Washington and Lee University
2016
Harte Research Institute for Gulf of Mexico Studies
2014
Texas A&M University
2010-2012
Mitchell Institute
2012
Rensselaer Polytechnic Institute
2005
Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially non-model organisms with large effective sizes high levels of genetic polymorphism. dDocent is an analysis pipeline user-friendly, command-line interface designed process individually barcoded (with double cut sites) into...
Sequencing reduced-representation libraries of restriction site-associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming a standard methodology for molecular ecologists. Because the scale RADseq data sets, putative loci cannot be assessed individually, making process filtering noise and correctly identifying biologically meaningful signal more difficult. Artefacts introduced during library preparation and/or bioinformatic processing SNP can create...
Sex-biased dispersal is expected to homogenize nuclear genetic variation relative in material inherited through the philopatric sex. When site fidelity occurs across a heterogeneous environment, local selective regimes may alter this pattern. We assessed spatial patterns of nuclear-encoded, single nucleotide polymorphisms (SNPs) and sequences mitochondrial control region bonnethead sharks (Sphyrna tiburo), species thought exhibit female philopatry, collected from summer habitats used for...
Next-generation sequencing of reduced-representation genomic libraries provides a powerful methodology for genotyping thousands single-nucleotide polymorphisms (SNPs) among individuals nonmodel species. Utilizing genotype data in the absence reference genome, however, presents number challenges. One major challenge is trade-off between splitting alleles at single locus into separate clusters (loci), creating inflated homozygosity, and lumping multiple loci contig (locus), artefacts...
Patterns of population structure and historical genetic demography blacknose sharks in the western North Atlantic Ocean were assessed using variation nuclear-encoded microsatellites sequences mitochondrial (mt)DNA. Significant heterogeneity and/or inferred barriers to gene flow, based on mtDNA, revealed occurrence five populations localized geographic regions: southeastern U.S coast, eastern Gulf Mexico, Bay Campeche southern Mexico Bahamas. Pairwise estimates divergence between Bahamas...
Abstract Restriction site‐associated DNA (RAD) sequencing was used to characterize neutral and adaptive genetic variation among geographic samples of red drum, Sciaenops ocellatus , an estuarine‐dependent fish found in coastal waters along the southeastern coast United States (Atlantic) northern Gulf Mexico (Gulf). Analyses outlier loci revealed three genetically distinct regional clusters: one Atlantic two Gulf. Divergence indicated gradual change followed a linear pattern isolation by...
Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially organisms with large effective sizes high levels of genetic polymorphism but which genomic resources exist. dDocent is an analysis pipeline user-friendly, command-line interface designed process individually barcoded (with...
Abstract Patterns of population structure, genetic demographics, and gene flow in the small coastal shark Carcharhinus isodon (finetooth shark) sampled from two discrete nurseries along southeastern US coast (Atlantic) three northern Gulf Mexico (Gulf), were assessed using 16 nuclear-encoded microsatellites 1077 base pairs mitochondrial DNA (mtDNA) control region. Significant heterogeneity microsatellite allele distributions was detected among all localities except between Atlantic. mtDNA...
Abstract Pelagic larval duration ( PLD ) has been hypothesized to be the primary predictor of connectivity in marine fishes; however, few studies have examined effects that adult reproductive behaviour may on realized dispersal. We assessed gene flow (connectivity) by documenting variation microsatellites and mitochondrial DNA sequences two protogynous species groupers, aggregate spawning red hind, E pinephelus guttatus , single‐male, harem‐spawning coney, C ephalopholis fulva ask whether...
Genetic analysis of a female whitetip reef shark Triaenodon obesus and her stillborn pup, assumed to be parthenogenetic origin, revealed that the pup was homozygous at all 24 nuclear‐encoded microsatellites assayed, consistent with idea diploidy in had been restored via terminal fusion. Flow cytometric analysis, however, indicated genome size no more than half mother, microscopy nuclear volume c. 1·73 times larger mother pup. Together these data suggest genetically haploid, developing...
Cutting-edge DNA methylation-based epigenetic aging techniques were applied to Gulf of Mexico northern red snapper (Lutjanus campechanus; n = 10; 1–26 years old) and grouper (Epinephelus morio; 2–14 old). Bisulfite-converted restriction site-associated sequencing was used identify CpG sites (cytosines followed by guanines) that exhibit age-correlated methylation, species-specific clocks developed from hundreds in each species showed strong agreement between predicted otolith-derived age (r 2...
Abstract This article documents the addition of 473 microsatellite marker loci and 71 pairs single‐nucleotide polymorphism (SNP) sequencing primers to Molecular Ecology Resources Database. Loci were developed for following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., grandii Goidanich or gifuensis Ashmead) , Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål Sciaenops ocellatus,...
The Leon Springs pupfish (Cyprinodon bovinus) is an endangered species currently restricted to a single desert spring and separate captive habitat in southwestern North America. Following establishment of the population from wild stock 1976, has undergone natural size fluctuations, intentional culling purge genetic contamination invasive congener variegatus) augmentation/replacement fish stock. A severe decline following most recent introduction prompted us examine whether populations have...
A total of 2,206 base pairs coding sequences mitochondrial DNA from nine 10 lutjanine (Lutjanidae) species endemic to the eastern Pacific Ocean were used in a phylogenetic analysis infer relationships among lutjanines on either side Isthmus Panama. Monotypic Hoplopagrus (guentherii) appears be at all assayed date and represents first five, eastward dispersal events Indo-Pacific Americas. Diversification Americas have occurred primarily western Atlantic (Caribbean Sea) been aided by an early...
Abstract Red snapper, Lutjanus campechanus, supports one of the more important fisheries in marine waters United States. Consequently, it has been focus intensive research for than 20 years. Here, we present a genomic analysis population structure that uses landscape genetics approach to characterize patterns variation adult red snapper Gulf Mexico (GOM) alongside synoptic view decades stock-structure research. The results support Atlantic and GOM stocks indicate weak heterogeneity within...