Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo
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Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo. / Quinn, Liam; Garcia-Erill, Genís; Santander, Cindy; Brüniche-Olsen, Anna; Liu, Xiaodong; Sinding, Mikkel-Holger S.; Heaton, Michael P.; Smith, Timothy P. L.; Pečnerová, Patrícia; Bertola, Laura D.; Hanghøj, Kristian; Rasmussen, Malthe Sebro; de Jager, Deon; Siegismund, Hans R.; Albrechtsen, Anders; Heller, Rasmus; Moltke, Ida.
In: Molecular Ecology, Vol. 32, No. 8, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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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 -
ID: 336528956