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TRACING HUMAN POPULATION HISTORY THROUGH ANCIENT DNA: HAPPYLAND ARCHAEOLOGICAL SITE, HOEDSPRUIT, LIMPOPO PROVINCE

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Case Type: 

ProposalDescription: 

The sampling of human remains for ancient-DNA analysis and carbon dating. This project aims to explore the genetic affiliation of the people who inhabited the site, and will also form part of an inclusive research initiative with the objective to trace the population history of southern Africans through time and across space. The remains were archaeologically excavated from an Early Iron Age context near the town Hoedspruit in Limpopo Province.

Expanded_Motivation: 

Project proposal This being an application for both sampling and export permits, we propose to sample material for a-DNA (ancient-DNA) extraction and C14 dating from human remains (in particular bone and parts of teeth), curated at the Lydenburg Museum and retrieved from the Happyland site, interpreted as Early Iron Age (Pelser et al. 2008; van der Walt 2008). This project aims to explore the genetic affiliation of the people who inhabited the site, and will also form part of an inclusive research initiative with the objective to trace the population history of southern Africans through time and across space. In the attached project proposal, Figure 1 we show the locations of already sampled specimens, indicating the current gap in the area where the Happyland individuals were found. Team members Carina Schlebusch (population geneticist, Uppsala University and University of Johannesburg), Jean-Pierre Celliers (curator, permit applicant and archaeologist, Lydenburg Museum), Maryna Steyn (anatomist, University of the Witwatersrand) & Marlize Lombard (South African coordinator and archaeologist, University of Johannesburg).

ApplicationDate: 

Wednesday, November 8, 2017 - 11:52

CaseID: 

11893

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Heritage Reports: 

ReferenceList: 

Citation
References 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 Pelser, A. 2008. A report on archaeological Phase 2 mitigation of an early farmer site to be impacted on by development of the Zandspruit Eco Estate on the farm Happyland 241 KT Hoedspruit, Limpopo Province. South African Heritage Resources Agency: Cape Town. 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, , Edlund H, Munters AR, Vicente M, Steyn M, Soodyall H, Lombard M, Jakobsson M. (2017) Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 10.1126/science.aao6266 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 Sirak KA, Fernandes DM, Cheronet O, Novak M, Gamarra B, Balassa T, Bernert Z, Cséki A, Dani J, Gallina JZ, Kocsis-Buruzs G, Kővári I, László O, Pap I, Patay R, Petkes Z, Szenthe G, Szeniczey T, Hajdu T, Pinhasi R (2017) A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis. Biotechniques 62:283-289 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 Van der Walt, J. 2008. Ceramic analysis on material from the Happyland archaeological site, Hoedspruit, Limpopo Province. South African Heritage Resources Agency: Cape Town. 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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