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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| Format: | Article |
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Nature Portfolio
2021-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-83823-8 |
| _version_ | 1818436097397489664 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-14T17:03:22Z |
| format | Article |
| id | doaj.art-ceca7e405f3b4d349e92e10e94abacc6 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-14T17:03:22Z |
| publishDate | 2021-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-ceca7e405f3b4d349e92e10e94abacc62022-12-21T22:53:48ZengNature PortfolioScientific 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 |
| 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 |
| title | 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_short | 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 |
| url | https://doi.org/10.1038/s41598-021-83823-8 |
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