Poster Presentation Society for Molecular Biology and Evolution Conference 2016

Retrieval of ancient mammalian mitochondrial DNA from Middle and Late Pleistocene sediment (#490)

Viviane Slon 1 , Charlotte Hopfe 1 , Marie Soressi 2 , Anatoly P. Derevianko 3 4 , Michail V. Shunkov 3 5 , Richard G. Roberts 6 , Zenobia Jacobs 6 , Bo Li 6 , Henry de Lumley 7 8 , Christian Perrenoud 7 , John R. Stewart 9 , Rebecca Miller 10 , Pavao Rudan 11 , Željko Kućan 11 , Ivan Gušić 11 , Sarah Nagel 1 , Birgit Nickel 1 , Kay Prüfer 1 , Janet Kelso 1 , Svante Pääbo 1 , Matthias Meyer 1
  1. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
  2. Faculty of Archaeology, Leiden University, Leiden, The Netherlands
  3. Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
  4. Altai State University, Barnaul , Russia
  5. Novosibirsk National Research State University, Novosibirsk, Russia
  6. Centre for Archaeological Science, School of Earth & Environmental Sciences, University of Wollongong, Wollongong, New South Wales, Australia
  7. Centre Européen de Recherches Préhistoriques de Tautavel, Tautavel, France
  8. Institut de paléontologie humaine, Paris, France
  9. School of Applied Sciences, Bournemouth University, Poole, Dorset, UK
  10. Service de Préhistoire, Université de Liège, Liège, Belgium
  11. Anthropology Center of the Croatian Academy of Sciences and Arts, Zagreb, Croatia

Sediment constitutes a ubiquitous feature of archaeological sites. Previous studies have shown that mitochondrial (mt) or chloroplast DNA can be recovered from ancient sediment by PCR [1, 2]. Here we describe the retrieval of mammalian mtDNA from sediments by hybridization capture [3].

We tested the ability of six DNA extraction methods to retrieve DNA of different sizes bound to 150 mg of clay or lime. We then extracted DNA from 83 sediment samples from six sites: Caune de l’Arago (France), Chagyrskaya Cave (Russia), Denisova Cave (Russia), Les Cottés (France), Trou Al’Wesse (Belgium) and Vindija Cave (Croatia). Aliquots of each DNA extract were converted into DNA libraries and subjected to hybridization capture using probes spanning the complete mitochondrial genomes of 242 mammals, and the isolated DNA fragments were sequenced.

We used simulated datasets composed of different proportions of mammalian and bacterial DNA sequences of different lengths, where varying levels of nucleotide substitutions typically present in ancient DNA [4] had been introduced, to test our ability to identify taxa. By comparison to a database of mammalian mtDNA sequences using BLAST [5] and assignment to taxa using MEGAN [6], taxon compositions at the family level were accurately reconstructed even in the presence of high levels of ancient DNA-like nucleotide substitutions. Biases potentially introduced by the capture procedure and the effect of sequencing depth on taxon composition were also investigated.

DNA sequences were retrieved from all archaeological sediments tested. Cytosine to thymine substitutions at terminal positions, an indication that DNA fragments are of ancient origin [4], were seen at five of the sites. A variety of taxa from twelve families were identified, including mammoths and woolly rhinoceroses. We conclude that molecular analysis of sediment by hybridization capture is a highly parallelizable and non-destructive approach to identify the past presence of animals at archaeological sites.

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