Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo

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The iconic Cape buffalo has experienced several documented population declines in recent history. These declines have been largely attributed to the late 19th century rinderpest pandemic. However, the effect of the rinderpest pandemic on their genetic diversity remains contentious, and other factors that have potentially affected this diversity include environmental changes during the Pleistocene, range expansions and recent human activity. Motivated by this, we present analyses of whole genome sequencing data from 59 individuals from across the Cape buffalo range to assess present-day levels of genome-wide genetic diversity and what factors have influenced these levels. We found that the Cape buffalo has high average heterozygosity overall (0.40%), with the two southernmost populations having significantly lower heterozygosity levels (0.33% and 0.29%) on par with that of the domesticated water buffalo (0.29%). Interestingly, we found that these lower levels are probably due to recent inbreeding (average fraction of runs of homozygosity 23.7% and 19.9%) rather than factors further back in time during the Pleistocene. Moreover, detailed investigations of recent demographic history show that events across the past three centuries were the main drivers of the exceptional loss of genetic diversity in the southernmost populations, coincident with the onset of colonialism in the southern extreme of the Cape buffalo range. Hence, our results add to the growing body of studies suggesting that multiple recent human-mediated impacts during the colonial period caused massive losses of large mammal abundance in southern Africa.

TidsskriftMolecular Ecology
Udgave nummer8
Antal sider15
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
L.Q. and I.M. were funded by the European Research Council (ERC‐2018‐STG‐804679). A.B‐O. was supported by a Carlsberg Foundation Reintegration Fellowship (grant no. CF19‐0427). M.‐H.S.S. was supported by a Carlsberg Foundation Reintegration Fellowship (grant no. CF20‐0355). U.S. Department of Agriculture, Agricultural Research Service appropriated projects 5438–32000‐034‐00D (M.P.H.) and 3040–31000‐100‐00D (T.P.L.S.). D.d.J. has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie grant agreement No. 101026951. H.R.S. was funded by Independent Research Fund Denmark (8021‐00344B).

Publisher Copyright:
© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

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