The greater kudu (Tragelaphus strepsiceros) is widespread throughout South Africa and occurs in higher densities in the northeastern and southern regions, with isolated populations in the Eastern Cape Province and in the Kimberley area in the Northern Cape Province. This study aimed to quantify the levels of genetic diversity and differentiation within and between individual greater kudu populations, based on neutral mitochondrial DNA regions as well as adaptive variation. A total of 116 kudu were sampled from various biomes, separated by geographic features and distance, across six South African provinces. Sampling was based on skin samples collected from taxidermists. Genetic diversity and differentiation were quanti ed using sequence data from the mitochondrial control region (mtDNA CR) and the Heat Shock Protein Subunit 5 (HSPA5) gene. A short tandem repeat (STR) sequences was identi ed at the 3'-UTR of the Bone Morphogenetic Protein 4 (BMP4) gene and used for downstream analyses. Twenty-six haplotypes were identi ed the CR dataset, three for the HSPA5 region, and 14 alleles were identi ed for the BMP4 STR. The CR phylogenetic analyses identi ed two distinct genetic clades representing an Eastern and Western group respectively. Molecular divergence dating identi ed the most recent common ancestor of the Eastern and Western South African kudu clades as older (2.237 Mya) than some well-known African antelope species. This data was further supported by the HSPA5 and BMP4 results. Environmental selective pressures, such as rainfall and ambient temperature were also identi ed as possible driving forces for evolution at the HSPA5 gene region. These results can provide support for future conservation management decisions to ensure the conservation of natural patterns of diversity in this majestic antelope species in South Africa.

The greater kudu (Tragelaphus strepsiceros) is widespread throughout South Africa and occurs in higher densities in the north-eastern and southern regions, with isolated populations in the Eastern Cape Province and in the Kimberley area in the Northern Cape Province. This study aimed to quantify the levels of genetic diversity and differentiation within and between individual greater kudu populations, based on neutral mitochondrial DNA regions as well as adaptive variation. A total of 116 kudu were sampled from various biomes, separated by geographic features and distance, across six South African provinces. Sampling was based on skin samples collected from taxidermists. Genetic diversity and differentiation were quantified using sequence data from the mitochondrial control region (mtDNA CR) and the Heat Shock Protein Subunit 5 (HSPA5) gene. A short tandem repeat (STR) sequences was identified at the 3’-UTR of the Bone Morphogenetic Protein 4 (BMP4) gene and used for downstream analyses. Twenty-six haplotypes were identified the CR dataset, three for the HSPA5 region, and 14 alleles were identified for the BMP4 STR. The CR phylogenetic analyses identified two distinct genetic clades representing an Eastern and Western group respectively. Molecular divergence dating identified the most recent common ancestor of the Eastern and Western South African kudu clades as older (2.237 Mya) than some well-known African antelope species. This data was further supported by the HSPA5 and BMP4 results. Environmental selective pressures, such as rainfall and ambient temperature were also identified as possible driving forces for evolution at the HSPA5 gene region. These results can provide support for future conservation management decisions to ensure the conservation of natural patterns of diversity in this majestic antelope species in South Africa.