Edward J. Heist

Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea

We investigated the genetic structure of blacktip shark (Carcharhinus limbatus) continental nurseries in the northwestern Atlantic Ocean, Gulf of Mexico, and Caribbean Sea using mitochondrial DNA control region sequences and eight nuclear microsatellite loci scored in neonate and young‐of‐the‐year sharks. Significant structure was detected with both markers among nine nurseries (mitochondrial ΦST = 0.350, P < 0.001; nuclear ΦST = 0.007, P < 0.001) and sharks from the northwestern Atlantic, eastern Gulf of Mexico, western Gulf of Mexico, northern Yucatan, and Belize possessed significantly different mitochondrial DNA haplotype frequencies. Microsatellite differentiation was limited to comparisons involving northern Yucatan and Belize sharks with nuclear genetic homogeneity throughout the eastern Gulf of Mexico, western Gulf of Mexico, and northwestern Atlantic. Differences in the magnitude of maternal vs. biparental genetic differentiation support female philopatry to northwestern Atlantic, Gulf of Mexico, and Caribbean Sea natal nursery regions with higher levels of male‐mediated gene flow. Philopatry has produced multiple reproductive stocks of this commercially important shark species throughout the range of this study.

Worldwide phylogeography of the blacktip shark (Carcharhinus limbatus) inferred from mitochondrial DNA reveals isolation of western Atlantic populations coupled with recent Pacific dispersal

Although many coastal shark species have widespread distributions, the genetic relatedness of worldwide populations has been examined for few species. The blacktip shark, (Carcharhinus limbatus), inhabits tropical and subtropical coastal waters throughout the world. In this study, we examined the genetic relationships of blacktip shark populations (n = 364 sharks) throughout the majority of the species’ range using the entire mitochondrial control region (1067–1070 nucleotides). Two geographically distinct maternal lineages (western Atlantic, Gulf of Mexico, and Caribbean Sea clades, and eastern Atlantic, Indian, and Pacific Ocean clades) were identified and shallow population structure was detected throughout their geographic ranges. These findings indicate that a major population subdivision exists across the Atlantic Ocean, but not the Pacific Ocean. The historical dispersal of this widespread, coastal species may have been interrupted by the rise of the Isthmus of Panama. This scenario implies historical dispersal across the Pacific Ocean (supported by the recovery of the same common haplotype from the Philippines, Hawaii, and the Gulf of California reflecting recent/contemporary dispersal abilities) and an oceanic barrier to recent migration across the Atlantic. Genetic structure within the eastern Atlantic/Indo‐Pacific (ΦST = 0.612, P < 0.001) supports maternal philopatry throughout this area, expanding previous western Atlantic findings. Eastern Atlantic/Indo‐Pacific C. limbatus control region haplotypes were paraphyletic to Carcharhinus tilstoni haplotypes in our maximum‐parsimony analysis. The greater divergence of western Atlantic C. limbatus than C. tilstoni from eastern Atlantic/Indo‐Pacific C. limbatus reflects the taxonomic uncertainty of western Atlantic C. limbatus.

World phylogeography and male-mediated gene flow in the sandbar shark, Carcharhinus plumbeus.

The sandbar shark, Carcharhinus plumbeus, is a large, cosmopolitan, coastal species. Females are thought to show philopatry to nursery grounds while males potentially migrate long distances, creating an opportunity for male‐mediated gene flow that may lead to discordance in patterns revealed by mitochondrial DNA (mtDNA) and nuclear markers. While this dynamic has been investigated in elasmobranchs over small spatial scales, it has not been examined at a global level. We examined patterns of historical phylogeography and contemporary gene flow by genotyping 329 individuals from nine locations throughout the species’ range at eight nuclear microsatellite markers and sequencing the complete mtDNA control region. Pairwise comparisons often resulted in fixation indices and divergence estimates of greater magnitude using mtDNA sequence data than microsatellite data. In addition, multiple methods of estimation suggested fewer populations based on microsatellite loci than on mtDNA sequence data. Coalescent analyses suggest divergence and restricted migration among Hawaii, Taiwan, eastern and western Australia using mtDNA sequence data and no divergence and high migration rates, between Taiwan and both Australian sites using microsatellite data. Evidence of secondary contact was detected between several localities and appears to be discreet in time rather than continuous. Collectively, these data suggest complex spatial/temporal relationships between shark populations that may feature pulses of female dispersal and more continuous male‐mediated gene flow.

POPULATION GENETICS OF THE SANDBAR SHARK (CARCHARHINUS PLUMBEUS) IN THE GULF OF MEXICO AND MID-ATLANTIC BIGHT

Allozyme electrophoresis and restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) were performed on sandbar sharks (Carcharhinus plumbeus) from coastal waters of Virginia, including the Chesapeake Bay, and the Gulf of Mexico to test the hypothesis that individuals from the two locations comprise a single gene pool. Both techniques revealed a very low degree of genetic variability within the species (allozyme mean heterozygosity = 0.005, mean nucleotide sequence diversity = 0.036%). The small amount of genetic variation present appeared to be evenly distributed between sampling locations; and therefore, the null hypothesis of a single gene pool could not be rejected (contingency X2 = 1.344, P > 0.5, chi-square significance of mtDNA haplotype distribution = 0.81). This conclusion is consistent with the known life-history characteristics of the species, as well as the results of tagging studies.

Microsatellite DNA Variation in Sandbar Sharks (Carcharhinus plumbeus) from the Gulf of Mexico and Mid-Atlantic Bight

Three polymorphic DNA microsatellite loci were developed in the sandbar shark (Carcharhinus plumbeus) and used to test the hypothesis that sharks from the midAtlantic Bight and western Gulf of Mexico comprise a single genetic stock. No significant differences in microsatellite allele frequencies were detected, a finding consistent with the null hypothesis. Polymorphic microsatellite loci appear to be scarce in sandbar sharks relative to other fish species. The three loci examined in this study had relatively low levels of heterozygosity, most likely attributable to the small number of dinucleotide repeat units per locus. T HE sandbar shark (Carcharhinus plumbeus) is

Molecular markers: progress and prospects for understanding reproductive ecology in elasmobranchs

Application of modern molecular tools is expanding the understanding of elasmobranch reproductive ecology. High-resolution molecular markers provide information at scales ranging from the identification of reproductively isolated populations in sympatry (i.e. cryptic species) to the relationships among parents, offspring and siblings. This avenue of study has not only augmented the current understanding of the reproductive biology of elasmobranchs but has also provided novel insights that could not be obtained through experimental or observational techniques. Sharing of genetic polymorphisms across ocean basins indicates that for some species there may be gene flow on global scales. The presence, however, of morphologically similar but genetically distinct entities in sympatry suggests that reproductive isolation can occur with minimal morphological differentiation. This review discusses the recent findings in elasmobranch reproductive biology like philopatry, hybridization and polyandry while highlighting important molecular and analytical techniques. Furthermore, the review examines gaps in current knowledge and discusses how new technologies may be applied to further the understanding of elasmobranch reproductive ecology.

DNA Microsatellite Loci and Genetic Structure of Red Snapper in the Gulf of Mexico

Abstract Five polymorphic microsatellite loci were developed from genomic DNA of red snapper Lutjanus campechanus and used to evaluate genetic variation among 194 red snapper sampled from three locations in the northern Gulf of Mexico and one location off the northern Yucatan Peninsula in Mexico. From 5 to 13 alleles were observed per locus, and expected heterozygosities ranged from 0.143 to 0.779. No significant departures from expectations of Hardy–Weinberg equilibrium were found at any locus either within samples or when samples were pooled across localities. Locus-by-locus tests of allele-frequency homogeneity over the four localities were nonsignificant. Weir and Cockerhams θ at each locus ranged from −0.003 to 0.012, and Statkins R ST at each locus ranged from −0.014 to 0.008. None of the estimates of θ and R ST differed significantly from zero, and magnitudes of θ and R ST did not appear to vary with geographic distance between localities. These results are consistent with the hypothesis that red...

Larval Surveys Indicate Low Levels of Endangered Pallid Sturgeon Reproduction in the Middle Mississippi River

Abstract The pallid sturgeon Scaphirhynchus albus is an endangered riverine species that is less abundant than the sympatric shovelnose sturgeon S. platorynchus with which it hybridizes. The two species are morphologically similar, and due to morphological variation within species, allometry, and the occurrence of morphological intermediates, morphological identification of specimens can be problematic. When the pallid sturgeon was listed under the U.S. Endangered Species Act in 1990, perceived threats included habitat loss due to habitat alteration (dams and channelization), hybridization, and commercial harvest. Previous studies estimated the ratio of adult pallid sturgeon to adult shovelnose sturgeon to be approximately 1:77 in the middle Mississippi River (MMR; the reach between the Missouri River confluence and the Ohio River confluence). One study using morphological identification estimated that 8–26% of Scaphirhynchus larvae collected in the MMR during May and June were pallid sturgeon. Given that...

Primordial Linkage of β2-Microglobulin to the MHC

β2-Microglobulin (β2M) is believed to have arisen in a basal jawed vertebrate (gnathostome) and is the essential L chain that associates with most MHC class I molecules. It contains a distinctive molecular structure called a constant-1 Ig superfamily domain, which is shared with other adaptive immune molecules including MHC class I and class II. Despite its structural similarity to class I and class II and its conserved function, β2M is encoded outside the MHC in all examined species from bony fish to mammals, but it is assumed to have translocated from its original location within the MHC early in gnathostome evolution. We screened a nurse shark bacterial artificial chromosome library and isolated clones containing β2M genes. A gene present in the MHC of all other vertebrates (ring3) was found in the bacterial artificial chromosome clone, and the close linkage of ring3 and β2M to MHC class I and class II genes was determined by single-strand conformational polymorphism and allele-specific PCR. This study satisfies the long-held conjecture that β2M was linked to the primordial MHC (Ur MHC); furthermore, the apparent stability of the shark genome may yield other genes predicted to have had a primordial association with the MHC specifically and with immunity in general.

Hybridization between pallid sturgeon Scaphirhynchus albus and shovelnose sturgeon Scaphirhynchus platorynchus

This study found that introgressive hybridization of the pallid sturgeon Scaphirhynchus albus with the common shovelnose sturgeon Scaphirhynchus platorynchus has probably occurred across the range of S. albus. Bayesian clustering found evidence of hybridization in all management units of S. albus. Some individuals were intermediate at both genetic and morphological characters, and some had discordant results. The results support introgressive hybridization throughout much of the range of S. albus, yet individuals consistent with being pure members of each species were detected in all management units. Simulations demonstrated that it would be very difficult to distinguish introgressed individuals from pure specimens after multiple generations of backcrossing with these microsatellite markers. Using hybrid or backcross fish as broodstock could artificially accelerate the loss of unique genetic variation in S. albus. Additional microsatellite loci or additional genetic markers, along with morphological data may be required to ensure that hybrid or backcross fish are not used. Introgressive hybridization requires at least two generations and generation lengths of S. albus are long, perhaps as long as 30 years. The proportion of individuals consistent with introgressive hybrid origins indicates that hybridization between S. albus and S. platorynchus probably has occurred for several generations and is not a recent phenomenon.