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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Main Authors: Deon de Jager, Brigitte Glanzmann, Marlo Möller, Eileen Hoal, Paul van Helden, Cindy Harper, Paulette Bloomer
Format: Article
Language:English
Published: Nature Publishing Group 2021-02-01
Series:Scientific Reports
Online Access:https://doi.org/10.1038/s41598-021-83823-8
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spelling doaj-ceca7e405f3b4d349e92e10e94abacc62021-03-11T12:20:44ZengNature Publishing GroupScientific Reports2045-23222021-02-0111111510.1038/s41598-021-83823-8High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomesDeon de Jager0Brigitte Glanzmann1Marlo Möller2Eileen Hoal3Paul van Helden4Cindy Harper5Paulette Bloomer6Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of PretoriaDSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch UniversityDSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch UniversityDSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch UniversityDSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch UniversityVeterinary Genetics Laboratory, Faculty of Veterinary Science, University of PretoriaMolecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of PretoriaAbstract 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.https://doi.org/10.1038/s41598-021-83823-8
collection DOAJ
language English
format Article
sources DOAJ
author Deon de Jager
Brigitte Glanzmann
Marlo Möller
Eileen Hoal
Paul van Helden
Cindy Harper
Paulette Bloomer
spellingShingle 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
Scientific Reports
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 Publishing Group
series Scientific Reports
issn 2045-2322
publishDate 2021-02-01
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.
url https://doi.org/10.1038/s41598-021-83823-8
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