Ancient DNA Analysis of Bone Samples

DNA was extracted from ∼100 mg of bone power after sodium hypochlorite treatment (SI Appendix 2). Sequencing, filtering of the data, and genotyping was carried out as previously described (ref. 3 (link) and SI Appendix 3). Present-day human DNA contamination was estimated using mitochondrial, autosomal data, and from the proportion of DNA fragment mapping on the Y chromosome (SI Appendixes 4 and 5). Demographic histories and split times were estimated using the Pairwise Sequentially Markovian Coalescent (38 (link) and SI Appendix 6) and the F(A|B) method (refs. 35 (link) and SI Appendix 7), respectively, and coestimated with momi2 (39 and SI Appendix 7). HBD tracts were computed as previously published (refs. 35 (link) and SI Appendix 8). Selection analyses were performed using the R packages GOfuncR (https://github.com/sgrote/GOfuncR), ABAEnrichment (ref. 29 (link) and SI Appendix 9), and by computing HKA and a modified PBS statistic in 25-kb windows (SI Appendix 10).