Conservation genetics of the suni antelope Nesotragus moschatus von Dueben, 1846

Abstract

The suni (Nesotragus moschatus) is a very small and secretive animal distributed in the eastern parts of Africa, from Kenya south to St. Lucia in South Africa. This antelope can also be found on small islands off the Tanzanian coast. The species is a habitat specialist associated with dense woodland, including the fragmented sand forests of southern Africa. To date six different subspecies have been described based on phenotypical features as well as distribution; since no genetic evidence was considered, there is uncertainty regarding the validity of these taxa. From phylogenetic studies performed to date, Nesotragus batesi was identified as the closest relative to the suni and they appear to be distantly related to the impala (Aepyceros melampus). A karyological study performed on captive suni individuals found cryptic variations and several cytotypes. Hybridization between the subspecies (N. m. akeleyi and N. m. zuluensis) could have contributed to the variety of chromosome numbers, as well as the decrease in fertility and increase in perinatal mortality. In addition to taxonomic uncertainties, the status and behavioural ecology from different parts of the species’ range need to be investigated. In my MSc I focussed on assessing the phylogenetic relationship between some of the suni subspecies as well as the degree of connectivity between fragmented woodland and forest patches (with emphasis on South Africa and southern Mozambique). A total of 64 samples (dung and tissue) from South Africa (Tembe Elephant Park (TEM), Ndumo Game Reserve (NDU), Phinda Private Game Reserve (PHI) and Tshanini Nature Reserve (TSH)), Mozambique and East Africa (Mnemba Island) was analysed. With the use of phylogenetic analysis of the mitochondrial cytochrome b gene and population analyses based on five microsatellite markers, I was able to identify two Evolutionarily Significant Units in southern and eastern Africa, as well as two possible Management Units in southern Africa. In addition to this, some degree of structuring was identified for the South African localities, however, finer scale resolution is needed. Within this dissertation I allocated one chapter solely for genetic non-invasive sampling, in which I have shown that DNA extraction, PCR amplification and genotyping of highly degraded dung samples are possible. To this end, I made use of 95 degraded suni dung samples to compare two extraction kits (NucleoSpin DNA Stool kit, Macherey-Nagel and QIAamp DNA mini stool kit, Qiagen), of which the NucleoSpin DNA Stool kit performed the best. With this I was able to develop guidelines for optimizing DNA extraction and PCR amplification specifically for highly degraded small dung samples. In addition, I identified and optimized 16 microsatellite markers for future use in finer ecological-scale suni research.