Heritage Cases

TRACING HUMAN POPULATION HISTORY THROUGH ANCIENT DNA: FLORISBAD COLLECTIONS, NATIONAL MUSEUM, BLOEMFONTEIN Permit application for the sampling of human and faunal remains curated at the Florisbad Quaternary Research Station of the National Museum, Bloemfontein, and to export the resulting samples to the Jakobsson Laboratory in Uppsala (Sweden) for DNA analysis and the Beta Dating Laboratory in Oxford (United Kingdom) for carbon dating Team members Mattias Jakobsson (Swedish): Human Population Geneticist based at Uppsala University, Sweden. Group leader and PI of the Human Population Genetics group in Uppsala. Main study coordinator. Helena Malmström (Swedish): Ancient DNA genetics expert based at Uppsala University, Sweden. Head of the Ancient DNA laboratory of the Human Population Genetics group in Uppsala. Contributes expert ancient DNA knowledge and will coordinate the sampling, extraction and laboratory part of the project. Carina Schlebusch (South African working in Sweden): Human Population Geneticist based at Uppsala University, Sweden. Member of the Human Population Genetics group in Uppsala. Previously from the Soodyall lab in South Africa. Contributes expert knowledge on human population genetic structure in Africa and genetic affinities of contemporary southern African population groups. Will coordinate the analysis of the aDNA data and the comparison to contemporary human datasets. Himla Soodyall (South African): Human Population Geneticist based at the NHLS and University of the Witwatersrand, South Africa. Contributes expert knowledge on population structure and genetic affinities of contemporary southern African population groups. Marlize Lombard (South African): Stone Age Archaeologist and Director of the Micro-TrACKS research group based at the University of Johannesburg, South Africa. Contributes expert knowledge on the South African archeological record regarding Stone Age human occupation of southern Africa. South African-based project coordinator. Project proposal We propose to sample material for DNA extraction from human remains (in particular bone and teeth), curated at the Florisbad Quaternary Research Station of the National Museum, Bloemfontein. Accompanied by the curator, Dr James Brink, we inspected and photographed material between the 1st and 4th of October 2013, and found numerous specimens that could yield DNA for our envisioned project. These specimens originated from various sites spread across South Africa (see image file: Western Cape = objects 001-017; Eastern Cape = objects 018-021; Free State = objects 022-030; Northern Cape = objects 031-033; Limpopo Province = objects 034-035). Objectives of this study Our application is part of a large-scale, long-term, multi-disciplinary research project that aims to trace human population history in southern Africa through modern and ancient DNA, and to reconcile genetic data with the archaeological and palaeoanthropological records of the region. Since 2012, members of the group have already published several papers to this effect (e.g., Breton et al. 2014; Li et al. 2014; Lombard et al. 2013; Moodley et al. 2012; Schlebusch & Soodyall 2013; Schlebusch et al. 2012a, 2012b, 2013). PDFs of all these publications are available on request. Sampling the material represented in this application will have a two-pronged research purpose. First, we aim to investigate time-serial data from one locality (Matjes River), by sampling material from previously dated layers (see Sealy et al. 2006) (6 sets of human remains; image file objects 002, 003, 004, 007, 008 and 010). We will also sample and date additional material from the site (7 sets of human remains; image file objects 001, 005, 006, 009, 011, 012 and 013). This strategy will increase resolution regarding site-occupation history considerably. The time-serial data will provide an indication of how populations in this region of Western Cape changed over time, and how their DNA compares with that of current southern African populations. Based on previous criteria required by SAHRA, we will also sample 7 faunal specimens from the Matjes River collection distributed throughout the sequence (image file objects 036-042). Secondly, we aim to investigate a geographical distribution of Stone Age population groups across South Africa. By newly dating and sequencing 22 sets of human remains (image file objects 015-036) we will generate new spatiotemporal knowledge about ancient population distributions – there are no fauna associated with these remains. This research will also reveal sub-structure variation in the DNA of the ancient populations to be compared with what is known about the DNA of groups currently living in southern Africa. In addition to the above long-term research aims, the dating and DNA data generated will contribute considerably to the repository’s, and to the national database on Stone Age human remains. Minimal destructive sampling on site at the Florisbad repository Sampling will take place on site in our dedicated portable clean-room sampling tent, thus avoiding the removal of skeletal material from its original repository and curatorial authority. We will also avoid overly destructive sampling strategies, such as cutting off roots of teeth or exporting entire pieces of bone/teeth for DNA extraction. To minimize impact on the remains, we use a sampling strategy that causes little to no morphological alteration of the material. The technique comprise drilling small (~1-3mm) holes into the roots of selected teeth or bone fragments, and removing the subsequent bone/dentine powder (about 200 mg). In the first page of our image file we show Scandinavian Stone Age specimens sampled by us. It illustrates the minimal damage caused with our approach. The extracted powdered material will be completely digested during DNA extraction, so that no material will be returned to the repository. If possible, we will extract bone/teeth-material from different individuals and from different sources of each individual to increase the chance of successfully obtaining authentic ancient DNA – about 3 samples from each individual (collectively only about 200 mg). In the case of undated specimens, a small (< 2x2cm) piece of bone will be removed from the least diagnostic/obtrusive area to allow for direct dating of the specimen. The repository curator will accompany our DNA extraction team, and decisions regarding each sample will be made in close cooperation with the curator. After sampling the material at the repository, we will personally transport the samples to the ancient DNA facility at Uppsala University, Sweden. Dating samples will subsequently be couriered to the Beta Laboratory in Oxford, United Kingdom. Laboratory procedure and analysis We will use our, now well-established, protocol for extracting DNA from ancient remains (for the latest versions see, e.g., Meyer et al. 2014; Skoglund et al. 2014). We have several different approaches for DNA extraction at our disposal, which are tailored to be ideal for different DNA preservation conditions, in particular to retrieve very short fragments that are expected in old material (e.g., Dabney et al. 2013; Yang et al. 1998). We will construct DNA sequencing libraries from the DNA extracts using specific techniques, that are tailored to very challenging materials, such as the ‘blunt-end’ (Meyer and Kircher 2010) and ‘single-strand’ (Gansauge and Meyer 2013) methods. We will also apply enrichment techniques if needed, in which specific DNA sequences of interest are captured from the DNA extracts through hybridization of biotinylated oligos to streptavidine coated beads and multiplied prior to sequencing (Enk et al. 2014; Maricic et al. 2010). We, and others, have applied successfully the above methods to retrieve sequence data from Neolithic and Mesolithic humans from Scandinavia and Europe (Skoglund et al. 2012, 2014), from 300 000-year-old hominids and cave bears from Spain (Dabney et al. 2013, Meyer et al. 2014), from a 600 000-year-old horse from Canada (Orlando et al. 2013), as well as a high-coverage (30X) genome from a 30 000 to 50 000-year-old Denisovan from Siberia (Meyer et al. 2012). The DNA libraries will be sequenced at the Uppsala SNP&SEQ platform, which has worked closely together with the Jakobsson lab in order to fine-tune the sequencing of ancient DNA libraries. We will generate genomic data from the autosomes, the X-chromosome, the mitochondria and the Y-chromosome if the sample contains any ever-so-small amounts of hominid sequence data. All the labwork (DNA extraction, library construction and amplification) will be conducted at the dedicated ancient DNA facility at the Jakobsson lab at Uppsala University.