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Rune Dietz

Genomic sex identification of ancient pinnipeds using the dog genome

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DOI

  • Maiken Hemme Bro-Jørgensen, Stockholm University, Københavns Universitet
  • ,
  • Xénia Keighley, Københavns Universitet, University of Groningen
  • ,
  • Hans Ahlgren, Stockholm University
  • ,
  • Camilla Hjorth Scharff-Olsen, Evolutionary Genomics Section, Københavns Universitet
  • ,
  • Aqqalu Rosing-Asvid, Greenland Institute of Natural Resources
  • ,
  • Rune Dietz
  • Steven H. Ferguson, Fisheries and Oceans Canada
  • ,
  • Anne Birgitte Gotfredsen, Københavns Universitet
  • ,
  • Peter Jordan, University of Groningen
  • ,
  • Aikaterini Glykou, Stockholm University
  • ,
  • Kerstin Lidén, Stockholm University
  • ,
  • Morten Tange Olsen, Evolutionary Genomics Section, Københavns Universitet

Determining the proportion of males and females in zooarchaeological assemblages can be used to reconstruct the diversity and severity of past anthropogenic impacts on animal populations, and can also provide valuable biological insights into past animal life-histories, behaviour and demography, including the effects of environmental change. However, such inferences have often not been possible due to the fragmented nature of the zooarchaeological record and a lack of clear diagnostic skeletal markers. In this study, we test whether the dog (Canis lupus familiaris) nuclear genome is suitable for genetic sex identification in pinnipeds. We initially tested 72 contemporary ringed seal (Pusa hispida) genomes with known sex, using the proportion of X chromosome DNA reads to chromosome 1 DNA reads (i.e. chrX/chr1-ratio) to distinguish males from females. This method was found to be highly reliable, with the ratios clustering in two clearly distinguishable sex groups, allowing 69 of the 72 individuals to be correctly identified according to sex. Secondly, to determine the lower limit of DNA reads required for this method, a subset of the ringed seal genome data was randomly down-sampled. We found a lower threshold of as few as 5000 mapped DNA sequence reads required for reliable sex identification. Finally, applying this standard, sex identification was successfully carried out on a broad set of ancient pinniped samples, including walruses (Odobenus rosmarus), grey seals (Halichoerus grypus) and harp seals (Pagophilus groenlandicus). All three species showed clearly distinct male and female chrX/chr1 ratio groups, providing sex identification of 42–98% of the samples, depending on species and sample quality. The approach described in this study should aid in untangling the putative effects of human activities and environmental change on populations of pinnipeds and other animal species.

OriginalsprogEngelsk
Artikelnummer105321
TidsskriftJournal of Archaeological Science
Vol/bind127
Antal sider7
ISSN0305-4403
DOI
StatusUdgivet - mar. 2021

Bibliografisk note

Funding Information:
This project has received funding from the European Union's EU Framework Programme for Research and Innovation Horizon 2020 under Marie Curie Actions Grant Agreement No 676154 as part of “ArchSci 2020”. In addition, partial funding was obtained from the BaltHealth programme under BONUS (Art. 185), funded jointly by the EU , Innovation Fund Denmark (grants 6180-00001B and 6180-00002B ), Forschungszentrum Jülich GmbH, German Federal Ministry of Education and Research (grant number FKZ 03F0767A ), Academy of Finland (decision # 311966 ) and Swedish Foundation for Strategic Environmental Research ( MISTRA ). We would like to thank the following museums for allowing access and destructive sampling of samples: The University Museum of Bergen, The Natural History Museum of Denmark, Greenland National Museum & Archives, The National Museum of Denmark, Archäologisches Landesmuseum in der Stiftung Schleswig-Holsteinische Landesmuseen Schloss Gottorf, Ålands Landskapsregering Museibyrån, The Swedish History Museum, The National Museum of Iceland, Icelandic Institute of Natural History, Canadian Museum of History and Canadian Museum of Nature. We would further like to thank Anne Karin Hufthammer, Ulrich Schmölcke, Lembi Lõugas, Kristian Gregersen, Christian Koch Madsen, Martin Appelt, Snæbjörn Pálsson, Hilmar Malmquist, Paul Szpak and Lesley Howse for procuring samples and helping with sample authorisations. Finally, many thanks to Fátima Sánchez Barreiro and Marta Maria Ciucani for assistance with the molecular laboratory work, and to José Alfredo Samaniego for guidance in bioinformatics.

Publisher Copyright:
© 2020

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

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