Human auditory ossicles as an alternative optimal source of ancient DNA

  1. Ron Pinhasi3
  1. 1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
  2. 2Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland;
  3. 3Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria;
  4. 4CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
  5. 5Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
  6. 6The Max Planck–Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena, D-07745, Germany;
  7. 7Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA;
  8. 8Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA;
  9. 9Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary;
  10. 10Slovak National Museum–Archaeological Museum, 810 06 Bratislava 16, Slovak Republic;
  11. 11Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy;
  12. 12Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia;
  13. 13Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary;
  14. 14Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary;
  15. 15National Museum of Mongolia, Ulaanbaatar 210146, Mongolia;
  16. 16Oxford Archaeology, Oxford OX2 0ES, United Kingdom;
  17. 17Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia;
  18. 18Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Cidade Universitária 05508-090 São Paulo, Brazil;
  19. 19Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA;
  20. 20Department of Anthropology, Slovak National Museum–Natural History Museum, 810 06 Bratislava 16, Slovak Republic;
  21. 21“Fr. J. Rainer” Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania;
  22. 22Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary;
  23. 23Department of Anthropology, University of Colorado at Boulder, Boulder, Colorado 80309, USA;
  24. 24Institute of Ethnology and Anthropology, RAS, Moscow, 119991, Russia;
  25. 25Centre for Forensic Research, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada

  1. ↵26 These authors contributed equally to this work.

  • ↵Present addresses: 27Department of Anthropology, University of California, Santa Cruz, CA 95064, USA; 28Soprintendenza Archeologia, Belle Arti e Paesaggio per la Città Metropolitana di Cagliari e le Province di Oristano e Sud Sardegna, Cagliari 09124, Italy; 29Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA

  • Corresponding authors: ron.pinhasi{at}univie.ac.at, kendra_sirak{at}hms.harvard.edu, daniel.fernandes{at}univie.ac.at

    • Abstract

    DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

    Footnotes

    • Received December 10, 2019.
    • Accepted February 11, 2020.

    This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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    This Article

    1. Published in Advance February 25, 2020, doi: 10.1101/gr.260141.119 Genome Res. 30: 427-436 © 2020 Sirak et al.; Published by Cold Spring Harbor Laboratory Press

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    ORCID

    1. Profile for Sirak, K.http://orcid.org/0000-0003-2347-3479
    2. Profile for Fernandes, D.http://orcid.org/0000-0002-7434-6552

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