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Genomic sex identification of ancient pinnipeds using the dog genome

Bro-Jørgensen, Maiken Hemme ; Keighley, Xenia ; Ahlgren, Hans ; Hjorth Scharff-Olsen, Camilla ; Rosing-Asvid, Accalu ; Dietz, Rune ; Ferguson, Steven H. ; Gotfredsen, Anne Birgitte ; Jordan, Peter LU orcid and Glykou, Aikaterini , et al. (2021) In Journal of Archaeological Science 127.
Abstract
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... (More)
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. (Less)
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publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Archaeological Science
volume
127
article number
105321
pages
7 pages
publisher
Academic Press
external identifiers
  • scopus:85099434096
ISSN
1095-9238
DOI
10.1016/j.jas.2020.105321
language
English
LU publication?
no
id
b9838d85-080a-4d9c-90f3-4d4357bbc0a9
date added to LUP
2021-08-18 15:11:46
date last changed
2023-05-18 04:05:09
@article{b9838d85-080a-4d9c-90f3-4d4357bbc0a9,
  abstract     = {{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.}},
  author       = {{Bro-Jørgensen, Maiken Hemme and Keighley, Xenia and Ahlgren, Hans and Hjorth Scharff-Olsen, Camilla and Rosing-Asvid, Accalu and Dietz, Rune and Ferguson, Steven H. and Gotfredsen, Anne Birgitte and Jordan, Peter and Glykou, Aikaterini and Lidén, Kerstin and Olsen, Morten Tange}},
  issn         = {{1095-9238}},
  language     = {{eng}},
  month        = {{03}},
  publisher    = {{Academic Press}},
  series       = {{Journal of Archaeological Science}},
  title        = {{Genomic sex identification of ancient pinnipeds using the dog genome}},
  url          = {{http://dx.doi.org/10.1016/j.jas.2020.105321}},
  doi          = {{10.1016/j.jas.2020.105321}},
  volume       = {{127}},
  year         = {{2021}},
}