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Assessment of Genomic Diversity and Population Sub-Structuring of Kingklip (Genypterus Capensis) Off Southern Africa

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Assessment of Genomic Diversity and Population Sub-Structuring of Kingklip (Genypterus Capensis) Off Southern Africa Assessment of genomic diversity and population sub-structuring of Kingklip (Genypterus capensis) off southern Africa By Melissa Jane Schulze Thesis presented in fulfilment of the requirements of the degree of Master of Science in the Department of Botany and Zoology at Stellenbosch University Supervisor: Prof. Sophie von der Heyden Co-supervisor: Dr Romina Henriques April 2019 Stellenbosch University https://scholar.sun.ac.za DECLARATION By submitting this thesis electronically, I declare that the entirety of the work contained therein is my own, original work, that I am the sole author thereof (save to the extent explicitly otherwise stated), that reproduction and publication thereof by Stellenbosch University will not infringe any third party rights and that I have not previously in its entirety or in part submitted it for obtaining any qualifications. Date: December 2019 Copyright © 2019 Stellenbosch University All rights reserved 1 Stellenbosch University https://scholar.sun.ac.za 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. 2 Stellenbosch University https://scholar.sun.ac.za 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-nukleotied- polimorfismes - 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 SNP- databasis 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 3 Stellenbosch University https://scholar.sun.ac.za en die potensiaal vir die gebruik van die nuut ontwikkelde merkpaneel vir toekomstige Kingklip-visserybestuur. 4 Stellenbosch University https://scholar.sun.ac.za ACKNOWLEDGEMENTS I would like to thank my supervisors Prof Sophie von der Heyden and Dr Romina Henriques for allowing me this opportunity as well as for their guidance and assistance throughout my masters. I would also like to give thanks to the National Research Foundation (NRF) for their funding of this project, as well as the University and Stellenbosch and Department of Botany and Zoology for their personal sponsorship. Thank you to the Department of Agriculture Forestry and Fisheries (DAFF), CapFish and the University of Namibia for the collection of samples, without your help this project would not have been possible. Further I would like to thank the Hawaii Institute of Marine Biology for their assistance in library preparation and sequencing, as well as the Central Analytical Facility (CAF) of Stellenbosch University for their help with DNA quality and quantity control. I would also like to take this opportunity to thank my lab associates in the Evolutionary Genomics Group, especially Fawzia Gordon and Henry for their technical assistance and making sure everything runs smoothly. A special thanks to the members of the von der Heyden Lab, particularly Lisa Mertens, Nikki Phair and Erica Nielsen for their assistance with NGS, as well as Molly Czachur for the daily chats by the kettle. I would additionally like to thank my friends and “Stellenbosch family” for making the journey so enjoyable, with a special thanks to the members of 11 Piet Retief Straat for the endless stoep kuiers and support throughout the last two years. Finally, I would like to thank my mom and dad for their unwavering support and for allowing me the opportunity to continue my studies. 5 Stellenbosch University https://scholar.sun.ac.za TABLE OF CONTENTS DECLARATION…………………………………………………………………...……..1 ABSTRACT……………………………………………………………………………….2 OPSOMMING…………………………………………………………………………….3 ACKNOWLEDGEMENTS……………………………………………………………….5 TABLE OF CONTENTS………………………..……………………………...……..….6 LIST OF FIGURES…………………………………………………………………...…..9 LIST OF TABLES…….………………………………………….……………………….11 LIST OF SUPPLEMENTARY MATERIALS.……………………………...………...…13 GENERAL INTRODUCTION…………………………………………………....………14 Southern African Kingklip, Genypterus capensis…………….………………………..14 Southern African Kingklip fisheries……………………..………………….……15 Current state of knowledge and management of southern African Kingklip resources….…………………………………………………………….………….16 Fisheries Management…………………….……………………………….………….....19 Population structure and fisheries management…………….….……..19 Molecular technologies and their use in fisheries management…..….21 Aims and objectives……………………………………………………………………….24 CHAPTER 1: SNP development and identification of local adaptation in southern African Kingklip, Genypterus capensis INTRODUCTION………………….……………………………………………………….25 Restriction Site Associated Sequencing…………………….……….………….28 Single Nucleotide Polymorphisms – SNPs……………………….….…………30 Chapter aims………….………………………….…………………….………….31 METHODS…………………………...………………………………………….…………31 Sample collection……….…….………………………………………..…..……..31 DNA extraction and pooling of samples………..……………………...……….32 ezRAD Sequencing.……………………………………………………..…….....33 6 Stellenbosch University https://scholar.sun.ac.za SNP development pipeline………………………………………….………….33 Quality control……………………………...………………...………….33 Assembly and mapping of the mitochondrial DNA dataset…..…….34 Assembly and
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