Heritage Cases

We propose to extract DNA from human remains (in particular bone and teeth) curated by the KwaZulu-Natal museum, originating from various sites in the KwaZulu-Natal Province. We have already viewed the material on a previous visit to the museum (on 16 May 2013) and found numerous specimens that could yield DNA (summarized below). To minimize impact on the remains, we will use a sampling strategy that causes minimal morphological alteration to the material. We will sand off a small portion of the surface and drill a small hole in the bones/teeth to extract small quantities of bone powder (100 mg for teeth, 200-400 mg for bone). If possible, we will extract bone/teeth-material from different individuals and different sources of each individual to increase the chance of successfully obtaining authentic ancient DNA. All, decisions regarding sampling area and quantity will be made in close cooperation with the museum curators. Sampling will take place at the museum, thus avoiding the removal of skeletal material from its original repository and curatorial authority. The samples will ultimately be destroyed during DNA extraction so that no material will be returned to the museum. Ancient DNA from humans has the potential to answer a number of important questions including, assessing genetic variation of humans in prehistoric times, assessing population affinities of past populations, their relation to current populations, and assessing the genetic impact of subsequent admixture events. We have recently developed population genetic tools that are tailor-made for analyzing ancient DNA from human remains (Malmstrom et al. 2007) that can; i) solve the issue of potential contamination from individuals handling the samples, and ii) make inferences from ancient genetic data that are incomplete by using reference samples. We will compare the genetic composition of the ancient KwaZulu-Natal individuals to genome-wide (more than 500,000 genetic markers per individual) reference data from modern populations, including worldwide collections of samples (HGDP – (Jakobsson et al. 2008), HapMap III – (Altshuler et al. 2010)), and sub-Saharan samples (Henn et al. 2011). In particular, we will be able to compare the KwaZulu-Natal ancient DNA data to one of the best current collections of genotyped southern African indigenous populations (Schlebusch et al. 2012). This collection includes eleven populations (220 individuals), of which seven are Khoe and San populations, two are Bantu-speaking populations and two are Coloured groups from different locations; and all individuals have been genotyped for 2.5 million genetic markers. These reference data from modern humans will allow us to compare the ancient DNA from southern African remains to a broad range of modern humans, including the indigenous inhabitants of southern Africa and potential sources of admixture. We propose to start our investigation by attempting to extract DNA material from eight sites (Ballito Bay A, Ballito Bay B, Ballito Bay C, Doonside, Mfongosi, Eland Cave, Newcastle and Champaigne Castle) described below. The samples were selected after an initial visit to the Museum by the team of geneticists from Uppsala University, during which material was identified that might provide the best potential DNA results. The Ballito and Doonside samples were selected because they have already been dated to ages that indicate pre-Bantu speaking and pre-colonial populations. The other samples were selected based on their geographic distribution that covers different locations in KwaZulu-Natal. We will independently date them in an effort to start generating a comparable database for dated human remains from prehistoric times in southern Africa together with their genetic data with the aim to assess genetic variation of humans in prehistoric times (pre-Bantu speaking and pre-colonial times), to assess genetic population affinities of past populations, their relation to current populations, and to assess the genetic impact of subsequent admixture events. Where possible, correlations will be made to what is known of the archaeological record. Ideally, we would like to take three samples for DNA analyses from each individual (two from teeth when possible and one from a bone), in order to be able to replicate our results. Approximately 100 mg of bone powder is needed from each tooth and between 200-400 mg of bone powder from bones is needed for one attempt to extract ancient DNA from these human remains. To visualize how the material is affected by our sampling we show pictures of bones and teeth from 5,000-10,000-year-old Scandinavian material that we have sampled previously by drilling out bone powder from the interior of the samples (Figure 1). Additionally, we show photos of the human remains from KwaZulu-Natal Museum and we have added arrows to the photos as examples of good places to sample for DNA. Since bones from Mfongosi, Eland Cave, Newcastle and Champagne Castle are not dated we furthermore want to apply for extracting additional material to be used for Radiocarbon dating. For the dating of these four sites, a single additional drilling will be considered for each specimen in collaboration with the museum curators. The dating of samples with unknown age will contribute to the completeness of the museum’s records regarding some of its human remains, without cost to the museum. Genetic scientists, Prof Jacobsson and Drs Schelebush and Malmström, will extract the samples and transport them to their specialised ancient-DNA Laboratory in Uppsala, Sweden, where the analyses will be conducted.