Assessment of genomic diversity and population sub-structuring of kingklip (Genypterus capensis) off Southern Africa

Schulze, Melissa Jane (2019-03)

Thesis (MSc)--Stellenbosch University, 2019.

Thesis

ENGLISH ABSTRACT: Kingklip (Genypterus capensis) represents a valuable marine resource for both South Africa and Namibia. Historical exploitation levels led to substantial declines in abundance, resulting in the species being considered over-exploited in the past. Currently, there is a lack of consensus regarding kingklip stock structure, with previous studies providing evidence for both multiple and single stocks. Understanding stock structure is vital for the appropriate assessment and management of marine resources. Taking into account both the commercial importance and trans-boundary nature of this species, it is therefore evident that a consensus regarding the fine-scale genetic structure is needed in order to best inform future management decisions. Next Generation Sequencing (NGS) has revolutionised population genetics allowing for the sequencing and identification of thousands of loci at reduced costs, thereby helping to identify weak genetic differentiation and adaptive divergence even in species with high gene flow levels. By employing a pooled ezRAD sequencing technique, the first chapter of this thesis isolated and identified a novel set of genome-wide molecular markers (Single Nucleotide Polymorphisms – SNPs). Over 40 000 SNP loci were identified in chapter 1, both neutral as well as putative outlier loci, potentially under selection. The second chapter of this thesis subsequently employed the SNP database developed in chapter 1 to investigate i) the relation of previous genetic versus genomic divergence levels and patterns of sub-structuring along the South African coastline, as well as ii) genome-wide patterns of fine-scale sub-structuring along Kingklip’s southern African distribution, thereby providing novel insight into the genetic relation of Namibian and South African Kingklip. Overall, the results of chapter 2 provided evidence for a three-stock hypothesis with signficant levels of adaptive divergence identified between “Northern Benguela” (North of Lüdertiz), “Southern Benguela” (South of Lüderitz to Cape Agulhas) and “Eastern Cape (Cape Agulhas to Algoa Bay) populations. However, adaptive divergence appears to be occuring in the face of high levels of gene flow, thereby creating a dynamic system across the southern African distribution. Based on the findings of chapter 2, the third chapter addresses management recommendations and the potential for the use of the newly developed marker panel for future Kingklip fisheries management.

AFRIKAANSE OPSOMMING: Kingklip (Genypterus capensis) verteenwoordig 'n waardevolle mariene hulpbron vir beide Suid-Afrika en Namibië. Historiese uitbuitingsvlakke het gelei tot aansienlike afname, wat veroorsaak het dat die spesies in die verlede uitgenuit is. Tans is daar 'n gebrek aan konsensus oor Kingklip visbevolkings, met vorige studies wat bewyse lewer vir beide veelvuldige en enkele bevolkings. Om visbevolking struktuur te verstaan is noodsaaklik vir die toepaslike assessering en bestuur van mariene hulpbronne. Met inagneming van beide die kommersiële belang en die grensvlak van hierdie spesie, is dit dus duidelik dat 'n konsensus aangaande die fynskaalse genetiese struktuur nodig is om toekomstige bestuursbesluite die beste in te lig. Next Generation Sequencing (NGS) het populasiegenetika gerewoloseer, wat die sequencing en identifikasie van duisende loci teen verlaagde koste moontlik gemaak het, en sodoende help om swak genetiese differensiasie en adaptiewe divergensie te identifiseer selfs in spesies met hoë genevloei vlakke. Deur die gebruik van 'n saamgevoegde ezRAD-sequencingtegniek, het die eerste hoofstuk van hierdie proefskrif 'n nuwe stel genoom-wye molekulêre merkers (enkel-nukleotiedpolimorfismes - SNP's) geïsoleer en geïdentifiseer. Meer as 40 000 SNP loci is geïdentifiseer in hoofstuk 1, beide neutrale sowel as potensiële outlier loci, moontlik onder seleksie. Die tweede hoofstuk van hierdie proefskrif het daarna die SNPdatabasis wat in hoofstuk 1 ontwikkel is, aangewend om i) die verband tussen vorige genetiese versus genomiese divergensievlakke en patrone van substrukturering langs die Suid-Afrikaanse kus te ondersoek, asook ii) genoomwye patrone van fynskaalse substruktuur van Kingklip se suidelike Afrika-verspreiding, en bied dus nuwe insig in die genetiese verhouding van Namibiese en Suid-Afrikaanse Kingklip.Die algehele resultate van hoofstuk 2 het getuienis gelewer vir 'n drie-visbevolking hipotese met betekenisvolle vlakke van adaptiewe divergensie wat geïdentifiseer is tussen "Northern Benguela" (Noord van Lüdertiz), "Southern Benguela" (suid van Lüderitz tot Kaap Agulhas) en "Oos-Kaap” (Kaap Agulhas tot Algoabaai) bevolkings. Adaptiewe afwykings blyk egter voor te kom in die lig van hoë vlakke van geenvloei, en skep daardeur 'n dinamiese stelsel oor die suidelike Afrika-verspreiding. Op grond van die bevindings van hoofstuk 2 word die aanbevelings in die derde hoofstuk aangespreek en die potensiaal vir die gebruik van die nuut ontwikkelde merkpaneel vir toekomstige Kingklip-visserybestuur.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/105675
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