Department of Genetics

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Browsing Department of Genetics by Author "Asbury, Tamaryn Anne"

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    Marine forensics : a molecular tool for trade monitoring and compliance in southern African fisheries, with focus on commercially exploited elasmobranch species
    (Stellenbosch : Stellenbosch University, 2019-12) Asbury, Tamaryn Anne; Bester-van der Merwe, Aletta Elizabeth; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.
    ENGLISH ABSTRACT: Marine forensic science can be described as protecting fisheries resources, marine mammals and endangered species based on enforcement of the nation's laws. Species identification becomes challenging when morphological features (such as fins, scales and heads) are removed, or if confiscated samples are already in a processed state. The harvesting of elasmobranchs (sharks, rays and skates) is driven by the international shark meat and shark fin trade. In recent decades, a combination of increasing demand and economic globalisation has created a global market for elasmobranch products, especially the highly prized shark fins for Asian markets. In this study, marine forensics was assessed as a tool for complementing traditional identification methods – through the development of a mini-barcoding assay as well as investigating High Resolution Melting (HRM) analysis – for species identification, with focus on elasmobranch species occurring in the southern African region. Firstly, this involved the testing and optimisation of the standard barcoding region of the cytochrome oxidase c subunit I (COI) gene, and then using traditional barcoding primers as well as nested polymerase chain reaction (PCR) primers in a multiplex assay. Preliminary results (only a 22 % species identification success rate) indicated the limitations of using only the traditional COI primers and warranted the inclusion of alternate COI gene fragments for species identification in future related forensic cases. A mini-barcoding multiplex assay, comprising three primer sets, was optimised and applied to a wide range of forensic case studies involving confiscated shark fins, possibly for illegal trade. A significant number of CITES-listed and endangered species were identified when confiscated specimens from various regions in southern Africa were tested. Secondly, PCR amplification of a 16S ribosomal RNA (16S rRNA) gene fragment was optimised based on six southern African houndshark species and seven other commercially exploited species, including: hammerhead sharks Sphyrna lewini and Sphyrna zygaena, copper shark Carcharhinus brachyurus, dusky shark Carcharhinus obscurus, bull shark Carcharhinus leucas, blacktip shark Carcharhinus limbatus and blue shark Prionace glauca. High Resolution Melting analysis using the 16S rRNA gene region was investigated as a species identification method for these species. The HRM assay was successfully applied for the identification of seven commercially exploited shark species, including some of the top commercially important sharks and one endemic houndshark Scylliogaleus quecketti. Although further optimisation is required, this relatively fast and cost-effective approach will be a valuable tool for the initial screening of detained shipments, for possible illicit trade. Accordingly, this research presents species identification assays suitable for various shark related forensic case studies, and in future could be applied to identify most, if not all, elasmobranch species involved in trade regionally.