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Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Der Sarkissian, Clio, Pichereau, Vianney, Dupont, Catherine, Ilsøe, Peter C., Perrigault, Mickael, Butler, Paul, Chauvaud, Laurent, Eiríksson, Jón, Scourse, James, Paillard, Christine, Orlando, Ludovic·2017·Molecular Ecology Resources
DOI 10.1111/1755-0998.12679
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Abstract

Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo‐) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro‐) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high‐throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome‐scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.

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  • New sources of archaeological material have broadened the range of ancient DNA applications, including dental calculus, wood, mollusk shells, sediments, parchments, and textiles.

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    From Ancient DNA analysis (2021) · cites this paper as [47]

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Cited by

Sorted by citations

  • Ancient DNA analysis

    Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411

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Metadata

Authors
Der Sarkissian, C., Pichereau, V., Dupont, C., Ilsøe, P. C., Perrigault, M., Butler, P., Chauvaud, L., Eiríksson, J., Scourse, J., Paillard, C., & Orlando, L.
Affiliations
  • Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Copenhagen K Denmark
  • Lemar UMR6539 CNRS/UBO/IRD/Ifremer Université de Brest, IUEM Plouzané France
  • CReAAH UMR6566 Université de Rennes 1 Rennes France
  • CGES College of Life and Environmental Sciences University of Exeter Penryn Cornwall UK
  • Institute of Earth Sciences University of Iceland Askja, Reykjavík Iceland
ORCID
Orlando, Ludovic
Venue
Molecular Ecology Resources
Publisher
Wiley
Published
2017-05-12
Volume
17
Issue
5
Pages
835-853
ISSN
  • 1755-098X
  • 1755-0998
DOI
10.1111/1755-0998.12679
Cited by
78
References
10
Language
en
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Funders
  • Centre National de la Recherche Scientifique
  • H2020 Marie Skłodowska-Curie Actions (FP7‐PEOPLE‐2013‐ITN 604802)
  • Danmarks Grundforskningsfond (DNRF94)
  • Université Européenne de Bretagne
  • Natur og Univers, Det Frie Forskningsråd (4002‐00152B)
  • Natural Environment Research Council (NE/H023356/1)

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