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National Biodiversity Assessment 2018 Technical Report Vol National Biodiversity Assessment 2018 Technical Report Vol. 7: Genetic Diversity National Biodiversity Assessment 2018 TECHNICAL REPORT Volume 7: Genetic Diversity REPORT NUMBER: http://hdl.handle.net/20.500.12143/6376 National Biodiversity Assessment 2018 Technical Report Vol. 7: Genetic Diversity CITATION FOR THIS REPORT: Tolley, K.A., da Silva, J.M. & Jansen van Vuuren, B. 2019. South African National Biodiversity Assessment 2018 Technical Report Volume 7: Genetic Diversity. South African National Biodiversity Institute, Pretoria. http://hdl.handle.net/20.500.12143/6376 PREPARED BY: Tolley, K.A., da Silva, J.M., Jansen van Vuuren, B., Bishop, J., Dalton, D., du Plessis, M., Labuschagne, K., Kotze, A., Masehela, T., Mwale, M., Selier. J., Šmíd, J., Suleman, E., Visser, J., & von der Heyden, S. REVIEWER: Sean Hoban CONTACT PERSON: Krystal A. Tolley: [email protected] The NBA 2018 was undertaken primarily during 2015 to early 2019 and therefore the names and acronyms of government departments in existence during that period are used throughout the NBA reports. Please refer to www.gov.za to see that changes in government departments that occurred in mid-2019. 2 National Biodiversity Assessment 2018 Technical Report Vol. 7: Genetic Diversity This report forms part of a set of reports, datasets and supplementary materials that make up the South African National Biodiversity Assessment 2018. Please see the website [http://nba.sanbi.org.za/] for full accessibility to all materials. SYNTHESIS REPORT For reference in scientific publications Skowno, A.L., Poole, C.J., Raimondo, D.C., Sink, K.J., Van Deventer, H., Van Niekerk, L., Harris, L.R., Smith-Adao, L.B., Tolley, K.A., Zengeya, T.A., Foden, W.B., Midgley, G.F. & Driver, A. 2019. National Biodiversity Assessment 2018: The status of South Africa’s ecosystems and biodiversity. Synthesis Report. South African National Biodiversity Institute, an entity of the Department of Environment, Forestry and Fisheries, Pretoria. http://hdl.handle.net/20.500.12143/6362 For reference in non-scientific publications South African National Biodiversity Institute (SANBI). 2019. National Biodiversity Assessment 2018: The status of South Africa’s ecosystems and biodiversity. Synthesis Report. South African National Biodiversity Institute, an entity of the Department of Environment, Forestry and Fisheries, Pretoria. TECHNICAL REPORTS 1: Terrestrial Skowno, A.L., Raimondo, D.C., Poole, C.J., Fizzotti, B., Slingsby, J.A. (eds). 2019. South African National Biodiversity Assessment 2018 Technical Report Volume 1: Terrestrial Realm. South African National Biodiversity Institute, Pretoria. http://hdl.handle.net/20.500.12143/6370 2: Inland Aquatic (Freshwater) Van Deventer, H., Smith-Adao, L., Collins, N.B., Grenfell, M., Grundling, A., Grundling, P-L., Impson, D., Job, N., Lötter, M., Ollis, D., Petersen, C., Scherman, P., Sieben, E., Snaddon, K., Tererai, F. & Van der Colff, D. 2019. South African National Biodiversity Assessment 2018: Technical Report. Volume 2: Inland Aquatic (Freshwater) Realm. CSIR report number CSIR/NRE/ECOS/IR/2019/0004/A. South African National Biodiversity Institute, Pretoria. http://hdl.handle.net/20.500.12143/6230 3: Estuarine Van Niekerk, L., Adams, J.B., Lamberth, S.J., MacKay, F., Taljaard, S., Turpie, J.K., Weerts S. & Raimondo, D.C., 2019 (eds). South African National Biodiversity Assessment 2018: Technical Report. Volume 3: Estuarine Realm. CSIR report number CSIR/SPLA/EM/EXP/2019/0062/A. South African National Biodiversity Institute, Pretoria. Report Number: SANBI/NAT/NBA2018/2019/Vol3/A. http://hdl.handle.net/20.500.12143/6373 4: Marine Sink, K.J., Van der Bank, M.G., Majiedt, P.A., Harris, L., Atkinson, L., Kirkman, S. & Karenyi, N. (eds). 2019. South African National Biodiversity Assessment 2018 Technical Report Volume 4: Marine Realm. South African National Biodiversity Institute, Pretoria. South Africa. http://hdl.handle.net/20.500.12143/6372 5: Coast Harris, L.R., Sink, K.J., Skowno, A.L. & Van Niekerk, L. (eds). 2019. South African National Biodiversity Assessment 2018: Technical Report. Volume 5: Coast. South African National Biodiversity Institute, Pretoria. http://hdl.handle.net/20.500.12143/6374 6: Sub-Antarctic Territory Whitehead, T.O., Von der Meden, C., Skowno, A.L., Sink, K.J., Van der Merwe, S., Adams, R. & Holness, S. (eds). 2019. South African National Biodiversity Assessment 2018 Technical Report Volume 6: Sub-Antarctic Territory. South African National Biodiversity Institute, Pretoria. http://hdl.handle.net/20.500.12143/6375 7: Genetics Tolley, K.A., da Silva, J.M. & Jansen van Vuuren, B. 2019. South African National Biodiversity Assessment 2018 Technical Report Volume 7: Genetic Diversity. South African National Biodiversity Institute, Pretoria. http://hdl.handle.net/20.500.12143/6376 3 National Biodiversity Assessment 2018 Technical Report Vol. 7: Genetic Diversity ACKNOWLEDGEMENTS We would like to thank the members of the South African National Biodiversity Institute (SANBI) Molecular Laboratory who contributed ideas and feedback. Graham Alexander (University of the Witwatersrand) who provided invaluable ideas and advice regarding the phylogenetic diversity mapping, and Bianca Fizzotti and Josh Weeber (SANBI) who provided vital assistance with GIS and figures. Working space was provided by The Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg. Samples for the reptile phylogeny were generously contributed by Luke Verburgt (Enviro-Insight), John Measey (Stellenbosch University), Werner Conradie (Bayworld) and Gary Nicolau. Thanks also to Graham Alexander, Mike Bates (National Museum), Werner Conradie, Retha Hofmeyr and Bryan Maritz (University of the Western Cape) and Luke Verburgt for vetting the original geographic distribution data used in the species distribution models. A number of people contributed to the planning for this assessment, including Jaco le Roux (Stellenbosch University), Jonathan Colville (SANBI), Albert Chakona (South African Institute for Aquatic Biodiversity) and Angus McDonald (University of KwaZulu-Natal). We are grateful to Andrew Blackmore, Brent Coverdale, Craig Mulqueeny and Ian Rushworth from Ezemvelo KZN Wildlife, Johan Kruger from the Limpopo Department of Economic Development, Environment and Tourism, and Lizanne Nel South African Hunters and Game Conservation Association for contributions to section 2.3. Reviewer of the terrestrial technical report: Sean Hoban, The Morton Arboretum, Lisle, Illinois, USA 4 National Biodiversity Assessment 2018 Technical Report Vol. 7: Genetic Diversity Table of Contents Acknowledgements ......................................................................................................................................... 4 List of Tables .................................................................................................................................................... 6 List of Figures .................................................................................................................................................. 6 List of Boxes .................................................................................................................................................... 7 Glossary of terms ............................................................................................................................................ 8 Executive Summary ....................................................................................................................................... 11 1. South Africa’s Biodiversity and the National Biodiversity Assessment ......................................... 12 1.1. South Africa’s biodiversity profile ..................................................................................................... 12 1.2. The importance of biodiversity ......................................................................................................... 16 1.3. Purpose and structure of the NBA ................................................................................................... 17 1.4. Assessing genetic diversity for the National Biodiversity Assessment ............................................ 18 1.5. References....................................................................................................................................... 19 2. Risks and impacts to genetic diversity, pressure and benefits ....................................................... 20 2.1. Benefits of genetic diversity ............................................................................................................. 20 2.2. Extrinsic Benefits ............................................................................................................................. 22 2.3. Risks ................................................................................................................................................ 34 2.4. Conclusions ..................................................................................................................................... 51 2.5. References....................................................................................................................................... 51 3. Monitoring trends in genetic diversity for priority taxa in South Africa .......................................... 63 3.1. Introduction .....................................................................................................................................
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