Heritage Cases

The project will be conducted by Dr AM van Wyk and will be hosted by Prof. Paulette Bloomer at the Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria. Low coverage whole genome re-sequencing will be conducted through Novogene UK and consequently export permits will be required for the requested material. 1. Background: The genetic integrity of black wildebeest (Connochaetes gnou) and blue wildebeest (Connochaetes taurinus) populations in South Africa is threatened by existence of hybridization. Black wildebeest is endemic to South Africa, whereas blue wildebeest are widely distributed in southern and east Africa. Hybridization between both species was first reported in the 1960s and the hybrid offspring was determined to be fertile (Fabricius et al., 1988). Extensive translocation of both species and keeping both species on the same property has led to a potential hybrid dilemma, as natural reproductive isolation disappeared. The actual extent of hybridization is unknown; however, it was estimated that properties in South Africa contain both species (Grobler et al., 2011). In this study, I will be investigating current and historic hybridization between blue- and black wildebeest in South Africa using low coverage whole genome re-sequencing. To do this, I will collect black wildebeest samples from museums between 300 hundred and five thousand years old, before hybridization with blue wildebeest occurred, to ensure pure individuals are sampled. I will compare these ancient genomes to modern genomes of black and blue wildebeest to determine the extent of hybridization in modern populations. These ancient genomes will also be the first to be produced for black wildebeest and will allow me to investigate the population dynamics of the species before and after human populations expanded, thus contributing to our collective knowledge of how species respond to changes in human and climate pressures. 2. Aim and objectives: This study aims to investigate recent and historical hybridization in blue- and black wildebeest populations in South Africa using low coverage whole genome re-sequencing. This approach will allow me to identify ancestry informative markers across the genome, which in turn will be used for admixture mapping to determine which regions of the genome are most affected by hybridization and which genes can be found in those regions. This will ultimately assist in sound conservation and management decisions for both species. 3. Materials and Methods: Heelbo, a palaeontological site on the farm Spion Kop 932 (S28 28.039’ E27 49.058’) was identified to contain suitable material. The collection is housed by die National Museum, Bloemfontein, Free State. Teeth will predominantly be targeted, as ancient DNA is better preserved in tooth cementum (Hansen et al., 2017) and where teeth are not available dense bone will be targeted. DNA will be extracted according to an optimised protocol published by Rohland et al. 2018. All DNA extractions will take place in a dedicated ancient DNA clean lab at the University of Pretoria. Before destructive DNA extraction is performed, photographs and morphometric measurements of each sample will be taken, and casting will also be carried out if/when possible. The cementum layer of the tooth root will be targeted and in order to access this section, the tip of the tooth root will be cross sectioned with a diamond cutting disk (the crown will remain intact), followed by drilling vertically (at a low speed, to reduce friction and heat production) up into the tooth root using a hand drill with a 2 mm drill bit. The tooth powder (50 mg) will be stored in a 2 mL screw cap tube and sealed with parafilm. To obtain powder from bone, the densest section of the bone will be cleaned to remove surface contaminants followed drilling with a 2 mm drill bit. The bone powder (50 mg) will be stored in a 2 mL screw cap tube and sealed with parafilm. After DNA extraction, low coverage whole genome re-sequencing will be conducted through Novogene UK and bioinformatic and statistical analysis will be accomplished through the Centre for High Performance Computing (CHPC) of the Council for Scientific and Industrial Research (CSIR). These ancient genomes will be the first to be produced for black wildebeest and will allow me to investigate the population dynamics of the species before and after human populations expanded, thus contributing to our collective knowledge of how species respond to changes in human and climate pressures. This study will contribute to a broader project in which I am involved: “Developing genetic management guidelines for large vertebrates in southern Africa”, spearheaded by the Africa section of the International Union for the Conservation of Nature (IUCN) Species Survival Commission Conservation Genetics Specialist Group. In order to have viable populations for the future, conservation management strategies must preserve the genetic integrity, as well as conserve high levels of genetic diversity in local populations. This study, together with the genetic management guidelines developed from it, will ultimately contribute to better management practices and the conservation of the genetic integrity of both species and thus support the South African government to better conserve the biodiversity of this megadiverse country. A minimum of two high impact peer-reviewed scientific papers are intended.