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.

DRYAD-SYNCERUSThe African buffalo microsatellite database is presented as an excel file with two sheets. The first sheet displays the allelic composition of the 14 autosomal microsatellites used within the present study, which is concentrated on southern African sampling localities. The first four lines of this first sheet refer to the title attributed to the present database sheet, the number of clusters identified with the STRUCTURE software, the number of loci studied, as well as the total number of individuals studied, respectively. The table below covers the following information for each specimen involved in the present study: species name, country of origin, sampling locality (protected area), gender, sample ID, cluster affiliation (result from the STRUCTURE analysis), followed by the allele composition for each 14 loci (diploid species). The second sheet displays the allelic composition of the 3 Y-chromosomal microsatellites used within the present study. The first three lines refer to the title attributed to the present database sheet, the number of loci studied, as well as the number of male individuals studied within the present study, respectively. The table below cover the following information for each male specimen genotyped in the present study: sample ID, alleles composition for each three Y-chromosomal microsatellites, haplotype designation for each three Y-chromosomal microsatellites, and final haplogroup determination. The haplotype designation is a number attributed to designate the combination of alleles for each of the three loci because they can appear as multicopies on the Y-chromosome. The haplogroup is thus defined as the combination of the haplotypes, written as {n UMN1113 haplotype, n UMN0304 haplotype, n INRA189 haplotype}, where n UMN1113 haplotype = 1,...,15, n UMN0304 haplotype = 1,...,9, and n INRA189 haplotype = 1,...,12. For further information, please see the main manuscript.