Genomic sex identification of ancient pinnipeds using the dog genome

作者：Maiken Hemme Bro‐Jørgensen, Xénia Keighley, Hans Ahlgren, Camilla Hjorth Scharff‐Olsen, Aqqalu Rosing‐Asvid, Runé Dietz, Steven H. Ferguson, Anne Birgitte Gotfredsen, Peter Jordan, Aikaterini Glykou, Kerstin Lidén, Morten Tange Olsen · 发表于：Journal of Archaeological Science · 年份：2021 · DOI：10.1016/j.jas.2020.105321 · 被引用次数：15 · 研究领域：Wildlife Ecology and Conservation、Forensic and Genetic Research、Identification and Quantification in Food

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 (Halichoer...