Population Structure of the Dusky Smoothhound Shark, Mustelus Canis, in U.S. Waters and Identification of Species in the Genus Mustelus in the Northern Gulf of Mexico

Globally, the genus Mustelus (smoothhound sharks) represents one of the most speciose groups of cartilaginous fishes. Morphological similarities and geographic overlap among species cause difficulties with species identification and taxonomy. Four morphologically conserved species (Mustelus canis canis, Mustelus sinusmexicanus, Mustelus norrisi and Mustelus higmani) are thought to occur within the northern Gulf of Mexico (Gulf). Available morphological keys are inadequate to distinguish among these species, and as such, all smoothounds in the U.S. Atlantic will be be managed as a species complex. The primary objectives of this study were to (i) develop and utilize molecular methods to distinguish among smoothhound species in the Gulf; (ii) identify morphological characters that can be used in field surveys to distinguish among the smoothhound species in the Gulf; (iii) test the null hypothesis that Mustelus canis is comprised of a single genetically panmictic stock in waters of the U.S. Atlantic (including the Gulf); (iv) assess genetic connectivity of M. canis in U.S. waters, and (v) to estimate the effective size and effective number of breeders from each locality sampled. Phylogenetic analysis of sequences of the mitochondrially-encoded NADH-2 gene resolved three reciprocally monophyletic lineages, which were identified as Mustelus canis, Mustelus norrisi, and Mustelus sinusmexicanus. Concordant with these results, comparisons of multi-locus, nuclear-encoded microsatellite genotypes also resolved three unambiguous groups. Using genetically verified voucher specimens, a field key outlining external characters was developed to aid field identification of the three species in the Gulf. Comparisons of environmental variables among specimens indicated that the three species, while co-distributed, might be partitioning the habitat based on depth and/or temperature tolerance. Comparisons of ND-2 sequences and microsatellite genotypes among M. canis from localities throughout the U.S. Atlantic (including the northern Gulf of Mexico) rejected the null hypothesis that M. canis in U.S. waters of the western Atlantic comprises one genetically panmictic stock. Low but significant genetic structure was found between M. canis in the Gulf and the Atlantic, and also within ocean basins. The results of these studies have important implications for fisheries management of smoothhound sharks in the United States

Population Structure of the Dusky Smoothhound Shark, Mustelus Canis, in U.S. Waters and Identification of Species in the Genus Mustelus in the Northern Gulf of Mexico

Globally, the genus Mustelus (smoothhound sharks) represents one of the most speciose groups of cartilaginous fishes. Morphological similarities and geographic overlap among species cause difficulties with species identification and taxonomy. Four morphologically conserved species (Mustelus canis canis, Mustelus sinusmexicanus, Mustelus norrisi and Mustelus higmani) are thought to occur within the northern Gulf of Mexico (Gulf). Available morphological keys are inadequate to distinguish among these species, and as such, all smoothounds in the U.S. Atlantic will be be managed as a species complex. The primary objectives of this study were to (i) develop and utilize molecular methods to distinguish among smoothhound species in the Gulf; (ii) identify morphological characters that can be used in field surveys to distinguish among the smoothhound species in the Gulf; (iii) test the null hypothesis that Mustelus canis is comprised of a single genetically panmictic stock in waters of the U.S. Atlantic (including the Gulf); (iv) assess genetic connectivity of M. canis in U.S. waters, and (v) to estimate the effective size and effective number of breeders from each locality sampled. Phylogenetic analysis of sequences of the mitochondrially-encoded NADH-2 gene resolved three reciprocally monophyletic lineages, which were identified as Mustelus canis, Mustelus norrisi, and Mustelus sinusmexicanus. Concordant with these results, comparisons of multi-locus, nuclear-encoded microsatellite genotypes also resolved three unambiguous groups. Using genetically verified voucher specimens, a field key outlining external characters was developed to aid field identification of the three species in the Gulf. Comparisons of environmental variables among specimens indicated that the three species, while co-distributed, might be partitioning the habitat based on depth and/or temperature tolerance. Comparisons of ND-2 sequences and microsatellite genotypes among M. canis from localities throughout the U.S. Atlantic (including the northern Gulf of Mexico) rejected the null hypothesis that M. canis in U.S. waters of the western Atlantic comprises one genetically panmictic stock. Low but significant genetic structure was found between M. canis in the Gulf and the Atlantic, and also within ocean basins. The results of these studies have important implications for fisheries management of smoothhound sharks in the United States

Africanization of a feral honey bee (Apis mellifera) population in South Texas: Does a decade make a difference?

The arrival to the United States of the Africanized honey bee, a hybrid between European subspecies and the African subspecies Apis mellifera scutellata, is a remarkable model for the study of biological invasions. This immigration has created an opportunity to study the dynamics of secondary contact of honey bee subspecies from African and European lineages in a feral population in South Texas. An 11-year survey of this population (1991-2001) showed that mitochondrial haplotype frequencies changed drastically over time from a resident population of eastern and western European maternal ancestry, to a population dominated by the African haplotype. A subsequent study of the nuclear genome showed that the Africanization process included bidirectional gene flow between European and Africanized honey bees, giving rise to a new panmictic mixture of A.m.scutellata- and European-derived genes. In this study, we examined gene flow patterns in the same population 23 years after the first hybridization event occurred. We found 28 active colonies inhabiting 92 tree cavities surveyed in a 5.14 km2 area, resulting in a colony density of 5.4 colonies/km2. Of these 28 colonies, 25 were of A.m. scutellata maternal ancestry, and three were of western European maternal ancestry. No colonies of eastern European maternal ancestry were detected, although they were present in the earlier samples. Nuclear DNA revealed little change in the introgression of A.m.scutellata-derived genes into the population compared to previous surveys. Our results suggest this feral population remains an admixed swarm with continued low levels of European ancestry and a greater presence of African-derived mitochondrial genetic composition.Peer reviewedZoolog

Identification and Distribution of Morphologically Conserved Smoothhound Sharks in the Northern Gulf of Mexico

<p>Identification of sharks within the genus <i>Mustelus</i> (smoothhound sharks) is problematic because of extensive overlap in external morphology among species. Consequently, species-specific management of smoothhound shark resources is difficult when multiple species inhabit the same geographic region. The species identification and distribution of smoothhound sharks in the northern Gulf of Mexico (the Gulf) were assessed using sequences of mitochondrial DNA, nuclear-encoded microsatellites, and catch data. Phylogenetic analysis of 1,047 base pairs of mitochondrially encoded ND-2 sequences and Bayesian clustering of multilocus genotypes at 15 microsatellites revealed three genetically distinct monophyletic lineages (clades) of smoothhound sharks in the Gulf. Examination of external morphology revealed characters that distinguished each genetically distinct clade, and based on species descriptions and comparisons with the type and other specimens in established collections, the lineages were identified as Smooth Dogfish <i>Mustelus canis</i>, Florida Smoothhound <i>Mustelus norrisi</i>, and Gulf Smoothhound <i>Mustelus sinusmexicanus.</i> Two hundred and eighty-seven smoothhound sharks sampled from across the Gulf were then assigned unequivocally, based on genetic data, to one of the three species. Multifactorial analysis and homogeneity tests of species-specific means versus grand means of spatiotemporal factors (depth, longitude, and month) at capture indicated significant differences among the three species with respect to all three factors. On average, the Smooth Dogfish is found in deeper waters than the Gulf Smoothhound, whereas the Florida Smoothhound inhabits relatively shallow waters. A diagnostic key for the field identification of adult specimens of each species is provided.</p> <p>Received April 1, 2015; accepted June 30, 2015</p

Enhancer hubs and loop collisions identified from single-allele topologies

Chromatin folding contributes to the regulation of genomic processes such as gene activity. Existing conformation capture methods characterize genome topology through analysis of pairwise chromatin contacts in populations of cells but cannot discern whether individual interactions occur simultaneously or competitively. Here we present multi-contact 4C (MC-4C), which applies Nanopore sequencing to study multi-way DNA conformations of individual alleles. MC-4C distinguishes cooperative from random and competing interactions and identifies previously missed structures in subpopulations of cells. We show that individual elements of the β-globin superenhancer can aggregate into an enhancer hub that can simultaneously accommodate two genes. Neighboring chromatin domain loops can form rosette-like structures through collision of their CTCF-bound anchors, as seen most prominently in cells lacking the cohesin-unloading factor WAPL. Here, massive collision of CTCF-anchored chromatin loops is believed to reflect ‘cohesin traffic jams’. Single-allele topology studies thus help us understand the mechanisms underlying genome folding and functioning

Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer

<p>TERT-locus SNPs and leukocyte telomere measures are reportedly associated with risks of multiple cancers. Using the Illumina custom genotyping array iCOG, we analyzed similar to 480 SNPs at the TERT locus in breast (n = 103,991), ovarian (n = 39,774) and BRCA1 mutation carrier (n = 11,705) cancer cases and controls. Leukocyte telomere measurements were also available for 53,724 participants. Most associations cluster into three independent peaks. The minor allele at the peak 1 SNP rs2736108 associates with longer telomeres (P = 5.8 x 10(-7)), lower risks for estrogen receptor (ER)-negative (P = 1.0 x 10(-8)) and BRCA1 mutation carrier (P = 1.1 x 10(-5)) breast cancers and altered promoter assay signal. The minor allele at the peak 2 SNP rs7705526 associates with longer telomeres (P = 2.3 x 10(-14)), higher risk of low-malignant-potential ovarian cancer (P = 1.3 x 10(-15)) and greater promoter activity. The minor alleles at the peak 3 SNPs rs10069690 and rs2242652 increase ER-negative (P = 1.2 x 10(-12)) and BRCA1 mutation carrier (P = 1.6 x 10-14) breast and invasive ovarian (P = 1.3 x 10(-11)) cancer risks but not via altered telomere length. The cancer risk alleles of rs2242652 and rs10069690, respectively, increase silencing and generate a truncated TERT splice variant.</p>