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

Abstract

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.

High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes

“…D. Zimmerman 2015). AENP has the lowest genetic diversity of the three relict populations of buffalo in South Africa ( H E = 0.425 – 0.482) 16 , 17 , being lower than both KNP and HiP 16 . In contrast to KNP and HiP, the buffalo populations in AENP and MNP currently harbour no diseases of economic importance and AENP has historically also been disease-free 23 , presumably since the disease outbreaks of the 1890s and 1900s.…”

“…Population genetics studies of African buffalo, employing microsatellites and mitochondrial DNA, have found high levels of differentiation between subspecies 12 – 14 and between populations of the Cape buffalo subspecies ( S. c. caffer ) across Africa 13 , 15 – 17 . The few buffalo studies employing more modern genetics techniques have focused on disease-related variants and variant discovery, while relying on the cattle genome as reference 2 , 3 , 18 , 19 .…”

“…Comm. D. Zimmerman 2015) 17 . The breeding programme consisted of buffalo (approximately 140 cows and 10 bulls) that originated mainly from northern KNP that were contained in a fenced-off camp in KNP ( Pers.…”

“…D. Zimmerman 2015). This population has been shown to have high genetic diversity based on microsatellite data ( H E = 0.61), indicating the disease-free breeding programme likely achieved its goal of preserving the high diversity of the KNP buffalo population, although a direct comparison between MNP and KNP was not performed 17 .…”

“…Comm. D. Zimmerman 2015) 17 . There are no records of any human-mediated introduction of buffalo to AENP at any point in the history of this population ( Pers.…”