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D. Katharine Coykendall

Publications and source records attributed to D. Katharine Coykendall.

8 recordsLinked to original sources
USGS2022

The development of genetic sex identification markers and evidence of a male heterogametic sex determination system in Red Shiner

The Red Shiner Cyprinella lutrensis is of increasing management interest as an invasive species that negatively impacts many native fishes throughout North America. Trojan sex chromosome (TSC)-carrying individuals could theoretically control invasive fish populations by skewing the sex ratio to 100% male. The efficacy of TSC-based control programs requires an understanding of a population's sex determination system, yet such information is lacking for Red Shiner. We used single-digest restriction site-associated DNA sequencing to discover sex-linked single-nucleotide polymorphisms (SNPs), and we conducted a series of breeding experiments to uncover the sex determination system. All candidate sex-linked SNPs that fit our selection criteria exhibited a pattern of male heterogamety. We developed two sex-identification (sex-ID) marker assays, XY_248 and XY_170, which showed phenotype–genotype concordance scores of 77.00% and 84.35%, respectively. These sex-ID markers exhibited relatively high phenotype–genotype concordance in females (XY_248 = 96.30%; XY_170 = 98.61%), which allowed for selective breeding of phenotypically feminized genetic males. We observed a 3:1 male : female sex ratio in spawns from feminized males crossed with wild-type males, indicative of a male heterogametic sex determination system (i.e., XY male/XX female). The discovery of a male heterogametic sex determination system, in combination with our two markers, increases the likelihood of developing an effective TSC eradication strategy for invasive Red Shiner populations.

North American Journal of Aquaculture↗
USGS2017

Deepwater Program: Lophelia II, continuing ecological research on deep-sea corals and deep-reef habitats in the Gulf of Mexico

The deep sea is a rich environment composed of diverse habitat types. While deep-sea coral habitats have been discovered within each ocean basin, knowledge about the ecology of these habitats and associated inhabitants continues to grow. This report presents information and results from the Lophelia II project that examined deep-sea coral habitats in the Gulf of Mexico. The Lophelia II project focused on Lophelia pertusa habitats along the continental slope, at depths ranging from 300 to 1,000 meters. The chapters are authored by several scientists from the U.S. Geological Survey, National Oceanic and Atmospheric Administration, University of North Carolina Wilmington, and Florida State University who examined the community ecology (from microbes to fishes), deep-sea coral age, growth, and reproduction, and population connectivity of deep-sea corals and inhabitants. Data from these studies are presented in the chapters and appendixes of the report as well as in journal publications. This study was conducted by the Ecosystems Mission Area of the U.S. Geological Survey to meet information needs identified by the Bureau of Ocean Energy Management.

Gulf of Mexico↗
USGS2016

A phylogenetic perspective on diversity of Galatheoidea ( Munida, Munidopsis ) from cold-water coral and cold seep communities in the western North Atlantic Ocean

Squat lobsters (Galatheoidea and Chirostyloidea), a diverse group of decapod crustaceans, are ubiquitous members of the deep-sea fauna. Within Galatheoidea, the genera Munida and Munidopsis are the most diverse, but accurate estimates of biodiversity are difficult due to morphological complexity and cryptic diversity. Four species of Munida and nine species of Munidopsis from cold-water coral (CWC) and cold seep communities in the northwestern Atlantic Ocean (NWA) and the Gulf of Mexico (GOM) were collected over eleven years and fifteen research cruises in order to assess faunal associations and estimate squat lobster biodiversity. Identification of the majority of specimens was determined morphologically. Mitochondrial COI sequence data, obtained from material collected during these research cruises, was supplemented with published sequences of congeners from other regions. The phylogenetic analysis of Munida supports three of the four NWA and GOM species ( M. microphthalma , M. sanctipauli , and M. valida ) as closely related taxa. The fourth species, Munida iris , is basal to most other species of Munida , and is closely related to M. rutllanti, a species found in the northeastern Atlantic Ocean (NEA). The majority of the nine species of Munidopsis included in our analyses were collected from chemosynthetic cold seep sites from the GOM. While seep taxa were scattered throughout the phylogenetic tree, four of these species ( Munidopsis livida , M. similis, M. bermudezi , and M. species A ) from the NWA and the GOM were part of a large eighteen-species clade that included species collected from Pacific Ocean chemosynthetic habitats, such as hydrothermal vents and whale falls. Shinkaia crosnieri was the sister taxon to the chemosynthetic clade, and M. livida was the most basal member of this clade. Munidopsis sp. B , an undescribed species with representative individuals collected from two GOM chemosynthetic sites, exhibited the largest genetic distance from other northern Atlantic species. Generally, intraspecific diversity was lower and patterns of haplotype diversity more simple in species of Munidopsis relative to Munida . This study puts two genera of NWA and GOM squat lobsters into a population genetic and phylogenetic context with regard to biogeography and habitat to enhance understanding of the history and evolutionary trajectories of these morphologically and ecologically diverse groups.

Deep-Sea Research Part II: Topical Studies in Ocea↗
USGS2016

Deferrisoma paleochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea

A novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1 T , was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1 T grew at 30–70 °C (optimum 60 °C), 0–50 g NaCl l − 1 (optimum 15–20 g l − 1 ) and pH 5.5–8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H 2 as the energy source and CO 2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d -fructose, α- d -glucose and ( − )- d -arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini , the first species of a recently described genus in the Deltaproteobacteria . Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1 T ( = JCM 30394 T  = DSM 29363 T ).

Mediterranean Sea, Milos Island, Paleochori Bay↗
USGS2015

Nine microsatellite loci developed from the octocoral, Paragorgia arborea

Paragorgia arborea, or bubblegum coral, occurs in continental slope habitats worldwide, which are increasingly threatened by human activities such as energy development and fisheries practices. From 101 putative loci screened, nine microsatellite markers were developed from samples taken from Baltimore canyon in the western North Atlantic Ocean. The number of alleles ranged from two to thirteen per locus and each displayed equilibrium. These nuclear resources will help further research on population connectivity in threatened coral species where mitochondrial markers are known to lack fine-scale genetic diversity.

Baltimore Canyon↗
USGS2015

Population connectivity of deep-sea corals

Identifying the scale of dispersal among habitats has been a challenge in marine ecology for decades (Grantham et al., 2003; Kinlan & Gaines, 2003; Hixon, 2011). Unlike terrestrial habitats in which barriers to dispersal may be obvious (e.g. mountain ranges, rivers), few absolute barriers to dispersal are recognizable in the sea. Additionally, most marine species have complex life cycles in which juveniles are more mobile than adults. As such, the dynamics of populations may involve processes in distant habitats that are coupled by a transport mechanism. Studies of population connectivity try to quantify the transport, or dispersal of individuals, among geographically separated populations. For benthic marine species, such as corals and demersal fishes, colonization of new populations occurs primarily by dispersal of larvae (Figure 1; Shank, 2010). Successful dispersal and recruitment, followed by maturation and reproduction of these new migrants ensures individuals contribute to the gene pool (Hedgecock, 2007). Thus, successful dispersal links and cohesively maintains spatially separated sub-populations. At shorter time scales (10-100s years), connectivity regulates community structure by influencing the genetic composition, diversity and demographic stability of the population, whereas at longer time scales (1000s years), geographic distributions are affected (McClain and Hardy, 2010). Alternatively, populations may become extinct or speciation may occur if connectivity ceases (Cowen et al., 2007). Therefore, the genetic exchange of individuals between populations is fundamental to the short-term resilience and long-term maintenance of the species. However, for the vast majority of marine species, population connectivity remains poorly understood.

NOAA Technical Memorandum↗
USGS2014

Development of eighteen microsatellite loci in walleye ( Sander vitreus )

A suite of tri- and tetra-nucleotide microsatellite loci were developed for walleye ( Sander vitreus ) from 454 pyrosequencing data. Eighteen of the 50 primer sets tested amplified consistently in 35 walleye from two lakes on Isle Royale, Lake Superior: Chickenbone Lake and Whittlesey Lake. The loci displayed moderate levels of allelic diversity (average 5.5 alleles/locus) and heterozygosity (average 35.8 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring as individuals assigned back to their population of origin. Cross-species amplification within S. canadensis (sauger) was successful for 15 loci, and 11 loci were diagnostic to species. The loci characterized here will be useful for detecting fine-scale spatial structuring, resolving the taxonomic status of Sander species and sub-species, and detecting walleye/sauger hybrids.

Michigan↗