HCNSO Student Theses and Dissertations

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Defense Date


Document Type

Thesis - NSU Access Only

Degree Name

M.S. Marine Biology


Oceanographic Center

First Advisor

Mahmood Shivji

Second Advisor

Andrew Rogerson

Third Advisor

Richard E. Spieler


Shark populations worldwide are suspected to be in severe decline due to domestic and international markets for trade in shark products, especially dried fins in Asian markets, and as a result of bycatch mortality in multi-species fisheries. The management of sharks on a species-specific basis has become imperative for shark conservation, particularly in regions where numerous species are heavily fished, because sharks with differing life-history characteristics respond differently to exploitation. However, many commercially exploited sharks are morphologically similar and not easily identifiable to the species level. This problem is exacerbated when it comes to identifying detached fins, processed carcasses (logs), and filets or steaks at the dock or in trade.

To address these species-identification problems and make available an accurate but practical, DNA-based forensic method for use in conservation and management of sharks, I have developed a highly streamlined genetic assay based on multiplex polymerase chain reaction (PCR) and species-specific primers derived from interspecific DNA sequence differences in the nuclear ribosomal internal transcribed spacer 2 (ITS2) locus of sharks. This forensic assay allows accurate identification of body parts from ten shark species commonly exploited worldwide for their meat and/or fins. In this thesis, I report on the development and use of this assay in the form of two separate suites of species-specific PCR primers that can be used in a high-density multiplex format to achieve rapid and accurate species identification. Chapter 1 of this thesis describes a suite of species-specific primers and multiplex PCR assay that simultaneously distinguishes among seven pelagic shark species: four species of mackerel sharks: shortfin mako (Isurus oxyrinchus), longfin mako (Isurus paucus), porbeagle (Lamna nasus) and salmon (Lamna ditropis); and the three species of alopiid (thresher) sharks: common thresher (Alopias vulpinus), bigeye thresher (Alopias superciliosus) and pelagic thresher (Alopias pelagicus). The second species-specific primer suite, described in chapter 2, simultaneously identifies the three globally distributed and most commercially important species of hammerheads: the great hammerhead (Sphyrna mokarran), scalloped hammerhead (Sphyna lewini) and the smooth hammerhead (Sphyrna zygaena).

The species-specific PCR primers and forensic approach described here provide an efficient, straightforward technique that can be used in conservation and management relevant contexts where large volumes of samples need to be screened quickly. Preliminary testing of dried fins from the Hong Kong market and confiscated fins from U.S. and South African law enforcement activities suggests that this genetic technique will be useful for large-scale survey applications, such as monitoring the species composition of the fin trade as well as improving fisheries law enforcement capabilities. The efficient nature of the general forensic approach reported here may also make it useful as a model applicable to monitoring trade in other wildlife products on a global scale.


Funding provided by the Florida Sea Grant College Program with support from the NOAA Office of Sea Grant, Grant No. R/LR-B-54, the Eppley Foundation (via the Wildlife Conservation Society) and the Guy Harvey Research Institute.

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