TY - JOUR

T1 - Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo

AU - Quinn, Liam

AU - Garcia-Erill, Genís

AU - Santander, Cindy

AU - Brüniche-Olsen, Anna

AU - Liu, Xiaodong

AU - Sinding, Mikkel-Holger S.

AU - Heaton, Michael P.

AU - Smith, Timothy P. L.

AU - Pečnerová, Patrícia

AU - Bertola, Laura D.

AU - Hanghøj, Kristian

AU - Rasmussen, Malthe Sebro

AU - de Jager, Deon

AU - Siegismund, Hans R.

AU - Albrechtsen, Anders

AU - Heller, Rasmus

AU - Moltke, Ida

N1 - Publisher Copyright: © 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

KW - cape buffalo

KW - conservation genetics

KW - demographic history

KW - inbreeding

KW - population genetics

U2 - 10.1111/mec.16851

DO - 10.1111/mec.16851

M3 - Journal article

C2 - 36651275

AN - SCOPUS:85147454652

VL - 32

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 8

ER -