Amanda M. Barker

Objective: Eastern oysters Crassostrea virginica have been harvested commercially for well over 200 years in the United States, but worldwide declines in oyster populations have led to an increased focus on conservation of oyster species in general. Among the risks to extant oyster populations, genetic containment associated with human-mediated mariculture and stock enhancement is an important consideration due to the risk posed by introducing potentially exotic or invasive genotypes to wild populations. Knowledge of wild population structure can improve strategies for ensuring genetic compatibility of cultured and wild stocks. Methods: Here, we examined genetic diversity and divergence among eastern oyster populations sampled from 386 individuals in 14 major bay systems throughout the Gulf of Mexico (Gulf), from southern Texas to southern Florida. We used a reduced representation genomic library consisting of 3,173 single nucleotide polymorphisms to make inferences about population structure and connectivity throughout the sampled range. Results: The major findings of this work were (1) deep genomic divergence among four population clusters principally centered around the western Gulf, northern Gulf, northern Florida, and southern Florida, (2) a zone of admixture between highly diverged clusters in north and south Texas, and (3) high rates of intermediate genotypes observed in oysters sampled from northern Florida compared with the northern Gulf and southern Florida. Regarding this last finding, inbreeding coefficients (FIS) in the northern Florida population were sufficiently high and heterozygosity sufficiently low that contemporary admixture seemed an unlikely explanation for the observed pattern. Conclusions: Taken as a whole, these results imply the presence of multiple discrete populations of eastern oysters in the Gulf of Mexico, and the geographic boundaries that separate them are roughly consistent with previously described studies. The presence of structured populations has implications for the selection of broodstock, and the knowledge of population boundaries will allow for more accurate assessment of risk when cultured stocks might harbor germplasm that is genomically inconsistent with wild populations in the area of culture.

Genetic polyandry was assessed in 27 litters of Blacknose Shark (Carcharhinus acronotus) from genetically distinct populations in the U.S. Atlantic (19 litters) and eastern Gulf of Mexico (eight litters) using 23 polymorphic microsatellite loci. Two methods were used to estimate genetic polyandry, and the overall observed rates were high (74% COLONY2; 81% allele counting method), with a maximum of four sires detected in a single litter. When separated by region, the rate of genetic polyandry was 63% (COLONY2) or 74% (allele counting method) in the U.S. Atlantic, and 100% (both methods) in the eastern Gulf of Mexico. Data were resampled to evaluate how the number and diversity of markers analyzed affected the estimated rate of genetic polyandry. The number of alleles per locus had a dramatic effect on the detection of polyandry, with a difference of 56% in the estimated rate of genetic polyandry (22% vs. 78%), when using only the five loci with the highest diversity (A = 21–44) versus lowest diversity (A = 3–5). The total number of markers assessed also affected the estimated rate of genetic polyandry, and the estimated rate increased by 13% when using 10 versus 20 loci (66% vs. 79%, respectively). These results suggest that unless loci are highly polymorphic, relatively large numbers of loci are required to estimate the rate of genetic polyandry accurately in elasmobranchs, particularly those with small litter sizes like the Blacknose Shark.

Hybridization between closely related species has been documented across a wide range of taxa but has not been well studied in elasmobranchs. Hammerhead sharks have drawn global conservation concern because they experience some of the highest mortality rates among sharks when interacting with fisheries. Here we report on the detection of hybrids between the globally distributed scalloped hammerhead (Sphyrna lewini) and recently described Carolina hammerhead (S. gilberti) which are only known from the western Atlantic Ocean. Using a genomics approach, 10 first-generation hybrids and 15–17 backcrosses were detected from 554 individuals. The identification of backcrosses demonstrates hybrids are viable, and all backcrosses but one involved a scalloped hammerhead. All hybrids but one possessed Carolina hammerhead mtDNA, indicating sex-biased gene flow between species. Repeated hybridization and backcrossing with scalloped hammerheads could lead to the loss of endemic Carolina hammerheads.

Two sharks, visually identified in the field as young‐of‐the‐year (YOY) scalloped hammerhead Sphyrna lewini, were identified as great hammerhead Sphyrna mokarran based on nuclear‐encoded single nucleotide polymorphisms (SNP) and sequences of mtDNA. Individuals were captured and released in Bulls Bay, SC, and Saint Joseph Bay, FL, in 2013 and 2014, respectively. These findings indicate S. mokarran may be pupping in or around these areas and highlight new regions that may be a productive focus for future research on early life history of S. mokarran.