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Sampling of skeletons for aDNA and C14

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Case Type: 

ProposalDescription: 

We propose to sample material for aDNA extraction (and C14 dating where relevant) from human remains (in particular bone and parts of teeth), curated at the University of Pretoria. This forms part of a larger initiative to trace the broader population history of southern Africans.

Expanded_Motivation: 

This 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, palaeoanthropological and craniometric 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; Owers et al., 2017, Schlebusch & Soodyall 2013; Schlebusch et al. 2012a, 2012b, 2013, 2016, 2017). PDFs of all these publications are available on request. Importantly, the team has proven success with extracting and reconstructing full ancient genome data from both inland and coastal regions of South Africa (Schlebusch et al. 2017). Sampling the material represented in this application will have a two-pronged research purpose. First, we aim to investigate time-serial data from southern Africa, and will increase resolution regarding site-occupation history considerably. The time-serial data will provide an indication of how populations in southern Africa changed over time, and how their DNA compares with that of current southern African populations. Samples proposed in this study would provide not only more information on the southern coastal regions, but will also include samples from less-represented areas in the northern part of the country. Secondly, we aim to investigate in particular the transition from a Stone Age hunter-gathering way of life to early farming. In previous aDNA research Iron Age remains have not received much attention. One of the questions that has been discussed is whether this transition to farming was associated with a change in the biology of people – i.e., did the Iron Age technology / farming arrive in southern Africa associated with people moving in from the north, or was it a way of life that was adopted by local inhabitants? Some of these Early Iron Age individuals (of which there are preciously few) do have morphological characteristics more commonly associated with the Khoe-San (e.g., Steyn et al. 1994). The association between culture and biology is not always clear. This research will also allow for comparison of genetic variation of the ancient populations with genetic variation in groups currently living in southern Africa, shedding light on more recent population movements. In addition to the above long-term research aims, the dating and DNA data generated will contribute considerably to the repositories, and to the national database on both Stone and Iron Age human remains. Whereas much may be known about the movements of groups or families within communities of both Khoesan and other African groups, this knowledge is seldom presented in a broader demographic context. Living and aDNA studies assist in providing scientific evidence for past admixture events and the extent to which populations across the southern African landscape interacted with each other. Such research is also able to provide relative ages for admixture and can reach into deep time for which no oral traditions are known. It therefore adds important aspects to the population histories of individuals and groups.

ApplicationDate: 

Friday, November 17, 2017 - 14:15

CaseID: 

11954

OtherReferences: 

ReferenceList: 

Citation
Breton G, Schlebusch CM, Lombard M, Sjodin P, Soodyall H, Jakobsson M (2014) Lactase Persistence alleles reveal partial East African ancestry of southern African Khoe pastoralists. Curr Biol 24:1-7 Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A, Nickel B, Valdiosera C, Garcia N, Paabo S, Arsuaga JL, Meyer M (2013) Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci U S A 110:15758-15763 Damgaard PB, Margaryan A, Schroeder H, Orlando L, Willerslev E, Allentoft ME (2015) Improving access to endogenous DNA in ancient bones and teeth. Sci Rep 5:11184 Enk JM, Devault AM, Kuch M, Murgha YE, Rouillard JM, Poinar HN (2014) Ancient whole genome enrichment using baits built from modern DNA. Mol Biol Evol 31:1292-1294 Gallego Llorente M, Jones ER, Eriksson A, Siska V, Arthur KW, et al. (2015) Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 350:820-822 Gamba C, Jones ER, Teasdale MD, McLaughlin RL, Gonzalez-Fortes G, Mattiangeli V, Domboróczki L, Kővári I, Pap I, Anders A, Whittle A, Dani J, Raczky P, Higham TF, Hofreiter M, Bradley DG, Pinhasi R (2014). Genome flux and stasis in a five millennium transect of European prehistory. Nat Commun 5:5257 Gansauge MT, Meyer M (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8:737-748 Li S, Schlebusch C, Jakobsson M (2014) Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples. Proc. R. Soc. B 281, 20141448 Lombard M, Schlebusch CM, Soodyall H (2013) Bridging disciplines to better elucidate the evolution of early Homo sapiens in southern Africa. South African Journal of Science 109:1-8 Maricic T, Whitten M, Paabo S (2010) Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One 5:e14004 Meyer M, Kircher M. 2010. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5448. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science 338:222-226 Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, Arsuaga JL, Martinez I, et al. (2014). A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505:403–406 Moodley Y, Linz B, Bond RP, Nieuwoudt M, Soodyall H, Schlebusch CM, et al. (2012) Age of the association between Helicobacter pylori and man. PLoS Pathog. 2012;8:e1002693. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, et al. (2013) Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499:74-78 Owers KA, Sjodin P, Schlebusch CM, Skoglund P, Soodyall H, et al. (2017) Adaptation to infectious disease exposure in indigenous Southern African populations. Proc Biol Sci 284 Schlebusch CM, Lombard M, Soodyall H (2013) MtDNA control region variation affirms diversity and deep sub-structure in populations from Southern Africa. BMC Evol Biol 13:56 Schlebusch CM, Skoglund P, Sjodin P, Gattepaille LM, Hernandez D, Jay F, Li S, De Jongh M, Singleton A, Blum MG, Soodyall H, Jakobsson M (2012a) Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. Science 338:374-379 Schlebusch C, Soodyall H (2013) Extensive Population Structure in San, Khoe, and Mixed Ancestry Populations from Southern Africa Revealed by 44 Short 5-SNP Haplotypes. Human Biology 84(6):article 3 Schlebusch C, Soodyall H, Jakobsson M (2012b) Genetic variation of 15 autosomal STR loci in various populations from southern Africa. Forensic Science International: Genetics 6:20-21 Schlebusch CM, Malmström H, Günther T, Sjödin P, Coutinho A, Malmström H, Günther T, Sjödin P, CoutinhoA, Edlund H, Munters AR, Steyn M, Soodyall H, Lombard M, Jakobsson M. (2017) Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago. bioRxiv Schlebusch CM, Prins F, Lombard M, Jakobsson M, Soodyall H (2016) The disappearing San of southeastern Africa and their genetic affinities. Hum Genet 135:1365-1373 Skoglund P, Malmström H, Omrak A, Raghavan M, Valdiosera C, Günther T, Hall P, Tambets K, Parik J, Sjögren K-G, Apel J, Willerslev E, Storå J, Götherström A, Jakobsson M (2014a) Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers. Science Published online 24 April 2014 [DOI:10.1126/science.1253448] Skoglund P, Malmstrom H, Raghavan M, Stora J, Hall P, Willerslev E, Gilbert MT, Gotherstrom A, Jakobsson M (2012) Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336:466-469 Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, et al. (2017) Reconstructing Prehistoric African Population Structure. Cell 171:59-71 e21 Steyn M, Loots M, Prinsloo H. (1994) An Early Iron Age human skeleton from the Soutpansberg District, South Africa. South African Journal of Science 90:552-555. Yang DY, Eng B, Waye JS, Dudar JC, Saunders SR (1998) Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am J Phys Anthropol 105:539-543
 
 

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