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

Background: African 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. Results: The 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. Conclusions: We 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.