Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa

S1 Appendix. Supplementary methods.

S1 Fig. Estimated effective population size (Ne) of the buffalo population from each locality. Vertical lines indicate 95% confidence intervals. Numbers inserted for GNP and GNP-MNP indicate the value of the upper bound of the 95% CI. The dashed line indicates the lower 95% CI of GNP. Values are also shown in S3 Table. PVT: Private ranches combined.

S2 Fig. Statistical support for K. The first column of graphs [L(K)] show the mean log likelihood of each value of K with its associated standard deviation, while the second column (DeltaK) shows the most likely value of K as determined by the Evanno method. Rows indicate the full data set (FDS) and the relatives removed (RR) data set. The graphs were generated using StructureHarvester and further organized in Inkscape v0.92 (https://inkscape.org/).

S3 Fig. Individual assignment plots of the STRUCTURE analyses at K = 2 and K = 3. A–full data set, B–relatives removed. The plots were generated using the online version of Clumpak and further organized in Inkscape v0.92 (https://inkscape.org/).

S4 Fig. Discriminant analysis of principal components (DAPC) of the full data set at K = 3. AENP Cluster: Addo Elephant National Park cluster, GNP-MNP Cluster: Graspan and Mokala National Park cluster, “Other” Cluster: Third, unknown origin cluster.

S1 Table. Summary statistics of microsatellite loci used in this study. Calculated in Cervus v3.0.7.

S2 Table. Mean and variance of the relatedness estimators available in COANCESTRY. TrioML (values in bold) had the lowest variance for each sampling locality and produces positive relatedness estimates between zero and one (as does DyadML).

S3 Table. Population summary statistics for each sampling locality.

S4 Table. Relatedness and individual inbreeding statistics.

S5 Table. Mean relatedness within sexes.

S6 Table. Pairwise DJOST and FST values with 95% confidence intervals.

S7 Table. Hardy-Weinberg Equilibrium (HWE) probability tests of each sampling locality, with the full data set and relatives removed. Data sets from sampling localities conformed to HWE after relatives were removed.

S8 Table. Original and Bonferroni-corrected linkage disequilibrium p-values of all pairs of loci in all sampling localities. Both the full data set (FDS) and relatives removed (RR) data set are shown.

Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist in populations with a variety of histories and management practices. We compared the genetic diversity of buffalo in national parks to private ranches and found that, except for Addo Elephant National Park, genetic diversity was high and statistically equivalent. We found that relatedness and inbreeding levels were not substantially different between ranched populations and those in national parks, indicating that breeding practices likely did not yet influence genetic diversity of buffalo on private ranches in this study. High genetic differentiation between South African protected areas highlighted their fragmented nature. Structure analysis revealed private ranches comprised three gene pools, with origins from Addo Elephant National Park, Kruger National Park and a third, unsampled gene pool. Based on these results, we recommend the Addo population be supplemented with disease-free Graspan and Mokala buffalo (of Kruger origin). We highlight the need for more research to characterize the genetic diversity and composition of ranched wildlife species, in conjunction with wildlife ranchers and conservation authorities, in order to evaluate the implications for management and conservation of these species across different systems.

DdJ hereby acknowledges the financial contribution of the National Research Foundation (https://www.nrf.ac.za/), under the grant number SFH150630122321.

http://www.plosone.org

am2021

Biochemistry

Genetics

Microbiology and Plant Pathology