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The preservation of ancient DNA in archaeological fish bone

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Author(s)

  • Giada Ferrari
  • Angélica Cuevas
  • Agata T. Gondek-Wyrozemska
  • Rachel Ballantyne
  • Oliver Kersten
  • Albína H. Pálsdóttir
  • Inge van der Jagt
  • Anne Karin Hufthammer
  • Ingrid Ystgaard
  • Stephen Wickler
  • Gerald F. Bigelow
  • Jennifer Harland
  • Rebecca Nicholson
  • David Orton
  • Benoît Clavel
  • Sanne Boessenkool
  • James H. Barrett
  • Bastiaan Star

Department/unit(s)

Publication details

JournalJournal of archaeological science
DateAccepted/In press - 21 Dec 2020
DateE-pub ahead of print (current) - 9 Jan 2021
Volume126
Early online date9/01/21
Original languageEnglish

Abstract

The field of ancient DNA is dominated by studies focusing on terrestrial vertebrates. This taxonomic bias limits our understanding of endogenous DNA preservation for species with different bone physiology, such as teleost fish. Teleost bone is typically brittle, porous, lightweight, and is characterized by a lack of bone remodeling during growth. All of these factors potentially affect DNA preservation. Using high-throughput shotgun sequencing, we here investigate the preservation of DNA in a range of different bone elements from over 200 archaeological Atlantic cod (Gadus morhua) specimens from 38 sites in northern Europe, dating up to 8000 years before present. We observe that the majority of archaeological sites (79%) yield endogenous DNA, with 40% of sites providing samples containing high levels (>20%). Library preparation success and levels of endogenous DNA depend mainly on excavation site and pre-extraction laboratory treatment. The use of pre-extraction treatments lowers the rate of libraries that can be sequenced, although — if successful — the fraction of endogenous DNA can be improved by several orders of magnitude. This trade-off between library preparation success and levels of endogenous DNA allows for alternative extraction strategies depending on the requirements of down-stream analyses and research questions. Finally, we do not find particular bone elements to yield higher levels of endogenous DNA, as is the case for denser bones in mammals. Our results highlight the potential of archaeological fish bone as a source for ancient DNA and suggest a possible role of bone remodeling in the preservation of endogenous DNA.

Bibliographical note

© 2021 The Authors. Published by Elsevier Ltd.

Funding Information:
We thank C. Amundsen for providing the Kongshavn and Skonsvika bone samples, M. Skage, S. Kollias and A. Tooming-Klunderud at the Norwegian Sequencing Centre for sequencing and processing of samples, and K. Dean for comments on the statistical analyses. This work was supported by Research Council of Norway Project “Catching the Past: Discovering the legacy of Atlantic cod exploitation using ancient DNA” (262777) and Leverhulme Trust Project “Northern Journeys: Reimagining the Medieval Revolution and its Aftermath” ( MRF-2013-065 ). Analyses were performed on the Abel Cluster at the University of Oslo and the Norwegian metacentre for High Performance Computing (NOTUR), operated by the Department for Research Computing at the University of Oslo IT-department (USIT).

Publisher Copyright:
© 2021 The Authors

Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.

    Research areas

  • Bleach, Bone element, Bone remodeling, Endogenous DNA, Petrous bone

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