Genetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer)

Abstract

BackgroundAfrican wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the “genetic health” of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites.ResultsThe analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (Ar) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (Pa) of 11), low differentiation, and an absence of an inbreeding depression signal (mean FIS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (FIS = 0.062, mean Ar = 6.160, Pa = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century.ConclusionsWe showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0203-2) contains supplementary material, which is available to authorized users.

Genetic responsiveness of African buffalo to environmental stressors: A role for epigenetics in balancing autosomal and sex chromosome interactions?

“…Although the relatively high prevalence of various diseases in southern Kruger may be coincidental, we think it is important to study the potential role of male-deleterious alleles herein not only in Kruger but also in other buffalo populations from southern Africa (Mozambique, Zimbabwe, Botswana and South Africa), considering that the DE and SAE alleles observed in this study have relatively high frequencies throughout the region (SAE alleles: BM1824, CSSM19, DIK020, ILSTS026 and SPS115: Kruger = 0.568, mean other populations = 0.412, DE alleles: BM4028, ETH010, ETH225, INRA006, INRA28, TGLA227 and TGLA263: Kruger = 0.718, mean other populations = 0.634; based on raw data from 14 populations in [ 42 ]).…”

Ancient diversity and geographical sub-structuring in African buffalo Theileria parva populations revealed through metagenetic analysis of antigen-encoding loci

“…Genotyping of local populations of buffalo has revealed a high overall level of genotypic diversity and a low level of genotypic differentiation between populations at a regional level, indicating extensive historical animal movement ( Simonsen et al, 1998 , Smitz et al, 2013 , 2014). However, on a larger geographical scale, studies of 19 populations of buffalo over a large area of their southern habitat, extending from Zambia in the north to South Africa in the south, using mtDNA and microsatellite markers, identified genotypically distinct lineages, estimated to have diverged 6000–8400 years ago ( Smitz et al, 2014 ). Although not strictly related to geographical distance, the two larger lineages tended to have a north/south distribution and the authors proposed that divergence had arisen historically as a result of local geographical and/or climatic barriers.…”

Transmission of Foot-and-Mouth Disease SAT2 Viruses at the Wildlife–Livestock Interface of Two Major Transfrontier Conservation Areas in Southern Africa

“…During the 2000–2002 period, Zimbabwe went under political instability and redistribution of land, after a period in which FMDV was relatively controlled. Such situation and the establishment of private game reserves with high number of buffalos, some of them translocated from FMD-infected areas, resulted in FMD becoming endemic, affecting all neighboring countries, especially those sharing TFCAs ( Vosloo et al, 2006 ; Smitz et al, 2014 ).…”