HCNSO Student Theses and Dissertations

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Thesis - NSU Access Only



The burgeoning shark-fishing industry has caused severe declines in many shark populations, prompting an urgent need for conservation and management of sharks on a species-specific basis. Many fisheries are managed on the basis of species groups due to difficulty in identifying the morphologically similar requiem sharks (Carcharhinidae) and their body parts. One diagnostic trait readily discernible in landed shark carcasses is the presence or absence of an interdorsal ridge, which allows shark carcasses to be categorized as either ridgeback or non-ridgeback sharks and narrows the identification process. Further identification to species, however, remains problematic and is a major impediment to management and conservation on a species-specific basis.

To facilitate the goal of species-specific management, I have developed a rapid and cost-efficient DNA-based method for use in species identification. It employs a high-density, multiplex polymerase chain reaction (PCR) assay that combines seven species-specific primers and two universal primers to discriminate one ridgeback (Galeocerdo cuvier) and six non-ridgeback (Carcharhinus brevipinna, C. limbatus, C. acronotus, C. isodon, C. leucas, and Negaprion brevirostris) sharks common in U.S. Atlantic fisheries. The primers were designed based on species-specific nucleotide differences in the nuclear ITS2 locus. These seven primers were tested on 73 non-target species worldwide to assess their diagnostic utility on a global scale. Five of the seven primers are species-specific, with only the C. leucas and the C. limbatus primers each amplifying one other congener, C. perezi and C. tilstoni, respectively. This diagnostic assay was tested in a practical management context and successfully identified shark fins confiscated by NMFS law enforcement agents, indicating that it will be useful in management of the U.S. Atlantic shark fishery. Furthermore, the primers developed for G. cuvier, C. leucas and C. brevipinna successfully identified their respective target species from the Atlantic and Pacific Oceans, suggesting that they will also be useful for global applications such as monitoring international trade in shark products.


Accurate species delineation is essential to sound management and conservation of fishery resources. The species status of two butterfly rays, Gymnura marmorata and G. crebripunctata, occurring in the fisheries in the Gulf of California and on the Pacific Mexican coast, has long been debated. Direct sequence comparison and a phylogenetic analysis were carried out using a segment of the mitochondrial cytochrome b locus to elucidate the relationship between G. marmorata and G. crebripunctata and five other congeners. Sequence divergence between G. marmorata and G. crebripunctata was minimal compared to sequence divergence among the five other established congeners. A neighbor-joining analysis showed strong statistical (100%) support and a maximum likelihood analysis showed reasonable support (62%) for the monophyletic clade consisting. of G. marmorata and G. crebripunctata. Importantly, neither analysis supported the reciprocal monophyly of either species, as would be expected for true separate species. These data suggest that the current classification of G. marmorata and G. crebripunctata as two separate species needs to be revised to support their designation as a single species.

Genetic analysis of the cyt b locus also revealed three single-nucleotide synapomorphies that partitioned animals from the two geographic sites sampled in Mexico (Sahuimaro, Sonora and Bahia Almejas, Baja California Sur), indicating the existence of possible population genetic structure between the two sites. By analyzing cyt b sequences from seven ofthe 10 described Gymnura species, I also provide the first phylogenetic hypothesis for interspecies relationships in the genus Gymnura.

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