Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

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 LU orcid and Bertola, Laura D , et al. (2023) In Molecular Ecology 32(8). p.1860-1874
Abstract

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... (More)

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.

(Less)
Please use this url to cite or link to this publication:
author
; ; ; ; ; ; ; ; and , et al. (More)
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; and (Less)
publishing date
type
Contribution to journal
publication status
published
keywords
Animals, Humans, Genetics, Population, South Africa, Genetic Variation, Buffaloes/genetics, Colonialism, Rinderpest
in
Molecular Ecology
volume
32
issue
8
pages
15 pages
publisher
Wiley-Blackwell
external identifiers
  • pmid:36651275
  • scopus:85147454652
ISSN
0962-1083
DOI
10.1111/mec.16851
language
English
LU publication?
no
additional info
© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.
id
a6c116d3-705e-454c-bb3e-4c908af96330
date added to LUP
2024-10-10 15:56:47
date last changed
2025-07-05 03:37:43
@article{a6c116d3-705e-454c-bb3e-4c908af96330,
  abstract     = {{<p>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.</p>}},
  author       = {{Quinn, Liam and Garcia-Erill, Genís and Santander, Cindy and Brüniche-Olsen, Anna and Liu, Xiaodong and Sinding, Mikkel-Holger S and Heaton, Michael P and Smith, Timothy P L and Pečnerová, Patrícia and Bertola, Laura D and Hanghøj, Kristian and Rasmussen, Malthe Sebro and de Jager, Deon and Siegismund, Hans R and Albrechtsen, Anders and Heller, Rasmus and Moltke, Ida}},
  issn         = {{0962-1083}},
  keywords     = {{Animals; Humans; Genetics, Population; South Africa; Genetic Variation; Buffaloes/genetics; Colonialism; Rinderpest}},
  language     = {{eng}},
  number       = {{8}},
  pages        = {{1860--1874}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Molecular Ecology}},
  title        = {{Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo}},
  url          = {{http://dx.doi.org/10.1111/mec.16851}},
  doi          = {{10.1111/mec.16851}},
  volume       = {{32}},
  year         = {{2023}},
}