Abstract
Sex estimation of skeletons is fundamental to many archaeological studies. Currently, three approaches are available to estimate sex–osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. We present matching osteological, shotgun-genomic, and proteomic data to estimate the sex of 55 individuals, each with an independent radiocarbon date between 2,440 and 100 cal BP, from two ancestral Ohlone sites in Central California. Sex estimation was possible in 100% of this burial sample using proteomics, in 91% using genomics, and in 51% using osteology. Agreement between the methods was high, however conflicts did occur. Genomic sex estimates were 100% consistent with proteomic and osteological estimates when DNA reads were above 100,000 total sequences. However, more than half the samples had DNA read numbers below this threshold, producing high rates of conflict with osteological and proteomic data where nine out of twenty conditional DNA sex estimates conflicted with proteomics. While the DNA signal decreased by an order of magnitude in the older burial samples, there was no decrease in proteomic signal. We conclude that proteomics provides an important complement to osteological and shotgun-genomic sex estimation.
Highlights
A large-scale comparison of proteomic, genomic, and osteological methods of sex estimation provides a unique opportunity for contrasting the benefits and limits of each technique
We empirically demonstrate that the thresholds of 100,000 total and 3,000 sex chromosome reads for genomic sex estimation is impactful; all conflicts occur below this threshold and no inconsistencies occur above it
The study showed that osteological sex estimation is reliable, but has a high rate of indeterminate sex assignments when fragmentary and juvenile remains are assessed
Summary
Skoglund and c olleagues[25] developed a genomic method of sex determination that takes advantage of high-throughput shotgun-DNA sequencing. This method (RY) estimates sex using sequence reads of 30 base pairs (bp) or longer that map to human X- and Y-chromosomes. The RY method does not filter out homologous portions, but relies on a large number of total sequences to return a robust determination of sex. By artificially down-sampling sequences from these same individuals, Skoglund et al.[25] recommended that a minimum of 100,000 total chromosome reads mapped to the human reference genome (or 3,000 reads mapped to sexchromosomes) were needed for confident sex estimations
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