Genomic sex identification of ancient pinnipeds using the dog genome
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Genomic sex identification of ancient pinnipeds using the dog genome. / Bro-Jørgensen, Maiken Hemme; Keighley, Xénia; Ahlgren, Hans; Scharff-Olsen, Camilla Hjorth; Rosing-Asvid, Aqqalu; Dietz, Rune; Ferguson, Steven H.; Gotfredsen, Anne Birgitte; Jordan, Peter; Glykou, Aikaterini; Lidén, Kerstin; Olsen, Morten Tange.
In: Journal of Archaeological Science, Vol. 127, 105321, 2021.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Genomic sex identification of ancient pinnipeds using the dog genome
AU - Bro-Jørgensen, Maiken Hemme
AU - Keighley, Xénia
AU - Ahlgren, Hans
AU - Scharff-Olsen, Camilla Hjorth
AU - Rosing-Asvid, Aqqalu
AU - Dietz, Rune
AU - Ferguson, Steven H.
AU - Gotfredsen, Anne Birgitte
AU - Jordan, Peter
AU - Glykou, Aikaterini
AU - Lidén, Kerstin
AU - Olsen, Morten Tange
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
KW - Ancient DNA
KW - Shotgun sequencing
KW - X chromosome
KW - Zooarchaeology
U2 - 10.1016/j.jas.2020.105321
DO - 10.1016/j.jas.2020.105321
M3 - Journal article
AN - SCOPUS:85099434096
VL - 127
JO - Journal of Archaeological Science
JF - Journal of Archaeological Science
SN - 0305-4403
M1 - 105321
ER -
ID: 260686791