High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes

Abstract Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, b...

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Autores principales:	Deon de Jager, Brigitte Glanzmann, Marlo Möller, Eileen Hoal, Paul van Helden, Cindy Harper, Paulette Bloomer
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ceca7e405f3b4d349e92e10e94abacc6
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id	oai:doaj.org-article:ceca7e405f3b4d349e92e10e94abacc6
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spelling	oai:doaj.org-article:ceca7e405f3b4d349e92e10e94abacc62021-12-02T13:35:04ZHigh diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes10.1038/s41598-021-83823-82045-2322https://doaj.org/article/ceca7e405f3b4d349e92e10e94abacc62021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83823-8https://doaj.org/toc/2045-2322Abstract Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in N e between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.Deon de JagerBrigitte GlanzmannMarlo MöllerEileen HoalPaul van HeldenCindy HarperPaulette BloomerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Deon de Jager Brigitte Glanzmann Marlo Möller Eileen Hoal Paul van Helden Cindy Harper Paulette Bloomer High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes
description	Abstract Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in N e between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.
format	article
author	Deon de Jager Brigitte Glanzmann Marlo Möller Eileen Hoal Paul van Helden Cindy Harper Paulette Bloomer
author_facet	Deon de Jager Brigitte Glanzmann Marlo Möller Eileen Hoal Paul van Helden Cindy Harper Paulette Bloomer
author_sort	Deon de Jager
title	High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes
title_short	High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes
title_full	High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes
title_fullStr	High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes
title_full_unstemmed	High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes
title_sort	high diversity, inbreeding and a dynamic pleistocene demographic history revealed by african buffalo genomes
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ceca7e405f3b4d349e92e10e94abacc6
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High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes

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