Heritage Cases

The blue antelope (Hippotragus leucophaeus) was the first and so far only large African mammal species to become extinct during the last 350 years (Harper, 1945; Skinner & Smithers, 1990). The reasons why the blue antelope went extinct around 1800 are not sufficiently researched (Kerley et al., 2009). We will use ancient DNA sequencing of Holocene and late Pleistocene museum specimens of the extinct blue antelope in order to test the hypothesis that this species already had a non-viable population size at the end of the 18 th century, meaning hunting with firearms by European settlers was only an incidental contributor to its demise (Kerley et al., 2009). Faith & Thompson (2013) suggest that the blue antelope was a migratory species, which due to the summer/winter rainfall seasonality within the cape region migrated yearly between its calving grounds in the west, and the east. We will compare genetic variation among eastern and western South African fossil sites in order to assess whether the blue antelope was an east-west migrating species and whether climatic changes at the onset of the Holocene contributed to its eventual extinction by disrupting its migration patterns (Faith & Thompson, 2013). In addition, we will clarify its controversially discussed phylogenetic relationship. All former studies have relied on either the paleontological record, modeling or small fragments of mtDNA to make their inferences. We will apply ancient DNA sequencing techniques to blue antelope remains from museums across Europe and paleontological collections in South Africa in order to reconstruct, for the first time, the phylogeographic and population structure of this extinct species at different times in the Pleistocene and Holocene. Population genomic analyzes will test whether effective population sizes were already low thousands of years ago, and phylogeographic analysis will test whether populations of the species from eastern (e.g. Nelson Bay Cave) and western (e.g. Die Kelders Cave 1) archaeological sites were distinct or the same. Concerning the roan antelope (Hippotrgus equinus) there are two reasons why we aim to conduct ancient DNA sequencing of these specimens. First, the geographic isolation of the Western Cape population – likely isolated from the interior of South Africa by the Cape Fold Belt since the onset of the Holocene marine transgression (Compton, 2011; Faith & Behrensmeyer, 2013) – raises the possibility that it was genetically distinct from the roan antelope population found in northeast South Africa today. It follows that the Western Cape roan antelope potentially belonged to a distinct (and now extinct) sub-species or less likely to a distinct species. Because the type specimen collected by Gordon has been lost (Grubb, 1999), the fossil specimens of roan antelope provide the only means of assessing this possibility. And second, the extinction of the Cape roan antelope population has received very little attention. By assessing its demographic history through analysis of ancient DNA, we aim to provide the first detailed understanding of the prehistoric factors that contributed to its rarity in historic times. This particular project is embedded in a comprehensive project about genome analysis in connection with Pleistocene climatic cycles comprising the whole Hippotragini tribe. The project is funded by the DFG (Deutsche Forschungsgemeinschaft = German Research Foundation). Our proposed sampling techniques are based on our extensive experience with sampling and laboratory techniques, as well as published methods and protocols (e.g. Dabney et al. 2013, Gansauge & Meyer 2013, Barlow et al. 2016, Paijmans et al. 2016). Several publications in the past have shown that the best DNA preservation in ancient and historical samples can be found in dense bone. An alternative sampling place would be a section of the tooth root. The material will be processed at dedicated ancient DNA facilities in the Evolutionary Adaptive Genomics group (headed by Prof. Dr. Michael Hofreiter) at the University of Potsdam. These facilities include several isolated laboratories dedicated to the extraction and manipulation of degraded genetic material, and we hold significant expertise in processing material from a wide range of historic and archaeological samples. Our group is well-equipped to the specific challenges associated with archival specimens, and has successfully processed and analyzed samples of such nature before. Example relevant papers and reviews published by our research group that have used similar material in the palaeogenomic context include: Hofreiter (2014), Elsner et al. (2014), Shapiro & Hofreiter (2014), Campbell & Hofreiter (2015), Paijmans et al. (2016) and Wecek et al. (2016). Please see as well the uploaded detailed project description (including a detailed sample list with pictures).