Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Pere Gelabert, Susanna Sawyer, Anders Bergström, Ashot Margaryan, Thomas C. Collin, Tengiz Meshveliani, Anna Belfer-Cohen, David Lordkipanidze, Nino Jakeli, Zinovi Matskevich, Guy Bar-Oz, Daniel M. Fernandes, Olivia Cheronet, Kadir T. Özdoğan, Victoria Oberreiter, Robin N.M. Feeney, Mareike C. Stahlschmidt, Pontus Skoglund, Ron Pinhasi

Research output: Contribution to journalArticlepeer-review

Abstract

Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental “shotgun” genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.

Original languageEnglish
Pages (from-to)3564-3574.e9
JournalCurrent Biology
Volume31
Issue number16
DOIs
StatePublished - 23 Aug 2021

Bibliographical note

Funding Information:
This study makes use of data generated by the NextGen Consortium. We acknowledge Gabriel Renaud for advice on Schmutzi and on the analysis of the mitochondrial genome. We acknowledge Spencer Sawyer, Manuela Alscher, and Odin for modern DNA. We acknowledge David Reich and Iosif Lazaridis for sharing the data of the Dzudzuana2 genome and helping us with its analysis. This work has been supported by the ?Mineralogical Preservation of the Human Biome from the Depth of Time? (MINERVA) research platform, code AGB326800, from the University of Vienna. P.S. was supported by the European Research Council (852558), a Wellcome Trust Investigator award (217223/Z/19/Z), and the Vallee Foundation. P.S. and A.B. were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust. This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission T.C.C. was supported by the Medical Trainee PhD Scholarship, UCD. R.P. S.S. and P.G. conceived the study. A.B.-C. D.L. T.M. N.J. Z.M. and G.B.-O. provided samples. M.C.S. collected the samples. S.S. O.C. D.F. T.C.C. V.O. K.T.?. and R.N.M.F. performed the experimental work. P.G. S.S. A.B. A.M. and T.C.C. analyzed the data. P.G. S.S. A.B. R.P. and P.S. wrote the manuscript with inputs from all coauthors. The authors declare no competing interests.

Funding Information:
This study makes use of data generated by the NextGen Consortium. We acknowledge Gabriel Renaud for advice on Schmutzi and on the analysis of the mitochondrial genome. We acknowledge Spencer Sawyer, Manuela Alscher, and Odin for modern DNA. We acknowledge David Reich and Iosif Lazaridis for sharing the data of the Dzudzuana2 genome and helping us with its analysis. This work has been supported by the “Mineralogical Preservation of the Human Biome from the Depth of Time” (MINERVA) research platform, code AGB326800, from the University of Vienna. P.S. was supported by the European Research Council ( 852558 ), a Wellcome Trust Investigator award ( 217223/Z/19/Z ), and the Vallee Foundation . P.S. and A.B. were supported by Francis Crick Institute core funding ( FC001595 ) from Cancer Research UK , the UK Medical Research Council , and the Wellcome Trust . This research was funded in whole, or in part, by the Wellcome Trust ( FC001595 ). For the purpose of open access, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission T.C.C. was supported by the Medical Trainee PhD Scholarship, UCD .

Publisher Copyright:
© 2021 The Authors

Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.

Keywords

  • Canis
  • Caucasus
  • Upper Paleolithic
  • bison
  • enviromental DNA
  • human
  • shotgun
  • soil sequencing

ASJC Scopus subject areas

  • General Agricultural and Biological Sciences
  • General Biochemistry, Genetics and Molecular Biology
  • General Neuroscience

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