Population genetics of Galeorhinus galeus, Carcharhinus brachyurus and Rhinobatos annulatus- implications for regional fisheries and elasmobranch conservation

Bitalo, Daphne Nyachaki (2016-03)

Thesis (PhDAgric)--Stellenbosch University, 2016.

Thesis

ENGLISH ABSTRACT: Elasmobranchs (sharks, skates and rays) are highly exploited world-wide and more vulnerable than most teleosts due to their life history traits (e.g. late age at maturity, low fecundity and slow growth). Most elasmobranchs are either targeted by commercial fisheries or unintentionally taken as bycatch in mixed-species fisheries. Among these, the tope shark Galeorhinus galeus, the copper shark Carcharhinus brachyurus and the southern African endemic lesser sandshark Rhinobatos annulatus, are targeted globally and locally in demersal, pelagic and recreational fisheries. Across the Southern Hemisphere, the International Union for the Conservation of Nature (IUCN) categorizes both the tope and copper sharks as “vulnerable” while the lesser sandshark as “data deficient” within its region of endemism. Information is urgently needed on their regional genetic structure and diversity to help delineate management units (MUs) for better fisheries monitoring and conserving local biodiversity. Regional and local population genetic structure of these species was assessed using previously optimised cross-species microsatellite panels and/or the mitochondrial NADH2 and NADH4 genes. Patterns of evolutionary and demographic history were inferred using coalescent and Bayesian statistical methods. For G. galeus, the data showed a lack of contemporary gene flow and deep historical divergence across the Southern Hemisphere. Two geographically distinct mitochondrial clades were recovered, one including the Atlantic and Indo-Pacific collections (ARG, SA and AUS) and one comprising the Pacific samples (NZ and CHI) as well as single divergent haplotype restricted to South Africa. Nuclear data also revealed large population subdivisions (FST = 0.050 to 0.333, P < 0.05) indicating very limited gene flow for tope sharks across ocean basins. On a local scale, F-statistics, multivariate and clustering analyses supported gene flow with substantial admixture along the South African coastline (FST = 0.016 to 0.048, P > 0.05), with some degree of genetic structure between the Atlantic and Indian Ocean samples. The east coast samples of Port Elizabeth were significantly differentiated from the rest (FST = 0.023 to 0.091, P > 0.05). For C. brachyurus, estimates of pairwise population differentiation were significant (average FST = 0.031, P = 0.000) indicating some degree of gene flow between sampling sites while the sub-structuring observed at Strandfontein indicated the existence of a possible distinct, more admixed group of individuals. Neither AMOVA (FCT = -0.011, P = 1.000) nor Bayesian clustering analyses indicated genetic discontinuity or significant population structure across the Atlantic/Indian boundary. Although the ND4 results also alluded to historical dispersal across this boundary, the population of Mossel Bay harboured four highly divergent haplotypes, indicating that this region might be a potential nursery site for C. brachyurus. The genetic diversity and genetic connectivity of R. annulatus was inferred using cross-amplified polymorphic microsatellite loci across the Agulhas bioregion that coincides with the warm temperate biogeographical province of South Africa. Significant genetic differentiation was observed over a small sampling range (FST = 0.016 to 0.094, P < 0.050) implying that the species might be highly structured throughout its entire geographical range. Overall effective population size for R. annulatus was very low (Ne = 106) and not in accordance to the abundance proposed for the species. As this is the first regional assessment for all three of these species, the findings of this study could have immediate implications for the regional management and conservation of commercial and recreational sharks.

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