Sex assignment of ancient samples from shotgun sequencing data

A new article demonstrates that it's possible to assign the sex of individuals by considering the ratio of sequences aligning to chromosomes X and Y. This seems quite useful, since often ancient DNA is extracted from isolated finds  where there isn't enough of the skeleton to make a sex determination morphologically. There are additional complications mentioned in the paper (such as not all humans having a simple XX or XY pair, or contamination by males/females messing up with the ratio of ancient samples of the opposite sex).

Interestingly, many of the ancient European samples that appeared over the last couple of years turn out to be male, and so do some Neandertals; the latter might be especially important, because the available high-coverage Neandertal genome appears to be a female; while we do know about the divergence of modern human and Neandertal autosomal DNA and mtDNA, we have no clue, at the moment about the Y-chromosome MRCA of modern humans and Neandertals; it's not clear to me how good the DNA from the Neandertal males.

A version of the paper has been posted here.

Journal of Archaeological Science Available online 14 July 2013

Accurate sex identification of ancient human remains using DNA shotgun sequencing

Pontus Skoglund et al.

Accurate identification of the biological sex of ancient remains is vital for critically testing hypotheses about social structure in prehistoric societies. However, morphological methods are imprecise for juvenile individuals and fragmentary remains, and molecular methods that rely on particular sex-specific marker loci such as the amelogenin gene suffer from allelic dropout and sensitivity to modern contamination. Analyzing shotgun sequencing data from 14 present-day humans of known biological sex and 16 ancient individuals from a time span of 100 to ~70,000 years ago, we show that even relatively sparse shotgun sequencing (about 100,000 human sequences) can be used to reliably identify chromosomal sex simply by considering the ratio of sequences aligning to the X and Y chromosomes, and highlight two examples where the genetic assignments indicate morphological misassignment. Furthermore, we show that accurate sex identification of highly degraded remains can be performed in the presence of substantial amounts of present-day contamination by utilizing the signature of cytosine deamination, a characteristic feature of ancient DNA.

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