High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes
Date
2021
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Research (part of Springer Nature)
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 Ne 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.
Description
CITATION: De Jager, D., et al. 2021. High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes. Scientific Reports, 11:4540, doi:/10.1038/s41598-021-83823-8.
The original publication is available at https://www.nature.com
Publication of this article was funded by the Stellenbosch University Open Access Fund
The original publication is available at https://www.nature.com
Publication of this article was funded by the Stellenbosch University Open Access Fund
Keywords
African buffalo -- Ecology, Pleistocene Epoch, Paleoclimatology -- Pleistocene, Biodiversity, Inbreeding, Animal genetics, Genomics, Animal genome mapping, Demographic archaeology, Climatic change
Citation
De Jager, D., et al. 2021. High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes. Scientific Reports, 11:4540, doi:/10.1038/s41598-021-83823-8