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.
Highlights
Sex determination of ancient zooarchaeological bones provides a valuable source of information for understanding anthropogenic im pacts on animals, notably hunting through the archaeological and cul tural aspects of prey availability, as well as hunting strategies and preferences (Weinstock, 2000, 2002; Gotfredsen and Møbjerg, 2004; Magnell, 2005)
Sex identification can contribute to essential biological insights into the ecology, behaviour, demography and life history of past animal populations including effects of human activities and environmental changes (Allentoft et al, 2010; Pecnerovaet al., 2017)
We present a comparative sexing method based on the relative read representation of chromosome X for use with shot-gun sequencing data using the annotated dog reference genome to identify the sex of a set of ancient pinnipeds consisting of walrus, grey seal and harp seal
Summary
Sex determination of ancient zooarchaeological bones provides a valuable source of information for understanding anthropogenic im pacts on animals, notably hunting through the archaeological and cul tural aspects of prey availability, as well as hunting strategies and preferences (Weinstock, 2000, 2002; Gotfredsen and Møbjerg, 2004; Magnell, 2005). Anthropogenic fragmentation prior to deposition and secondary diagenesis due to the various taphonomic processes that the skeletal remains undergo after deposition (Lyman, 1994), might alter the few morphologically sex identifiable bone parts to such a degree that sex identification is no longer reliable These limi tations make it important to seek alternative methods to investigate sex ratios of zooarchaeological material. We present a comparative sexing method based on the relative read representation of chromosome X for use with shot-gun sequencing data using the annotated dog reference genome to identify the sex of a set of ancient pinnipeds consisting of walrus, grey seal and harp seal. A data set of contemporary ringed seals with known sex was used to test the accuracy of the method
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