Molecular aspects of exploited sharks in South Africa: multiple paternity and identification of novel molecular markers

Sharks have existed for the past 400 million years and play an important role in the oceanic ecosystem as they occupy the upper categories of the food web. Since the 1920s they have been fished on a commercial scale as the demand for shark related products increased. This placed considerable pressure on shark populations, resulting in a global decline of many populations and an increased risk of population extinction. As the genetic diversity of a population determines it’s resilience to changing environmental factors, including such information has become paramount for short and long-term management and conservation of individual species. This study therefore aimed to add to the growing body of biological and genetic data by investigating mating strategy through assessing the presence of multiple paternity (MP) in three commercially important shark species: the common smoothhound Mustelus mustelus, dusky shark Carcharhinus obscurus and the scalloped hammerhead shark Sphyrna lewini; and by identifying potential microsatellite and single nucleotide polymorphism (SNP) markers in two of the species, M. mustelus and C. obscurus, through the use of Next-Generation Sequencing (NGS) platforms. The first aim of this study was achieved by cross-amplifying microsatellite markers developed in closely related species to the study species. A total of 22 microsatellite markers were initially tested on four litters of M. mustelus and C. obscurus in order to determine the most informative markers for parentage analysis. Reduced marker panels of five to six microsatellites were selected and parentage analysis in GERUD and COLONY revealed the presence of MP in all three species. Mustelus mustelus had the highest frequency of MP (67%), followed by S. lewini (46%) and C. obscurus (35%). The second aim of this study entailed reduced genome sequencing of one M. mustelus and one C. obscurus individual using the HiSeq Illumina and Ion Proton platforms, respectively. For M. mustelus, 51,5 million reads with an average read length of 250bp were obtained, whereas C. obscurus yielded 27,6 million reads with an average read length of 213bp. Contigs were constructed for both species in order to search for perfect repeat motifs. In total, 2 700 and 1 255 microsatellite-containing regions were identified for M. mustelus and C. obscurus respectively. In order to search for SNP-containing regions, both sample species were aligned to previously assembled scaffolds of the ghost shark Callorhinchus milii, which served as a reference genome. After quality filtering, only 767 SNP-containing regions were identified for M. mustelus, whereas the identification of potential SNPs for C. obscurus was not successful. The insights gained into the mating strategies of M. mustelus, C. obscurus and S. lewini as well as the identification of potential species-specific molecular markers add to the growing body of information and genetic resources available for exploited species. In future, this information could be used for further molecular assessment of shark populations and a more intergrated approach to conservation and management of these already vulnerable sharks.National Research Foundatio