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We performed demographic analysis of our ancient samples using two main approaches. PCA was conducted using smartpca When analyzing the off-target calls, individual pseudohaploid PCAs were conducted for each ancient sample separately, and then individual analyses were combined using a Procrustes transformation in R using the vegan package. Model-based clustering analysis was applied in two different ways to the 1-kb haplotypes from the 5-Mb region.
We adapted a previously described likelihood-based approach 41 for determining the most likely population of origin for a sample to our haploid SNP data, allowing ancient samples to be from any modern reference population with at least 10 individuals. To account for uncertainty, we performed 5-Mb nonoverlapping block bootstrap replicates. We visualized this uncertainty on a geographic map of Eurasia using interpolation. We calculated these sharing profiles for each ancient and modern individual independently, with the modern populations used and hence K varying across datasets, and performed jack-knifing across chromosomes to assess uncertainty.
See SI Appendixsection 16 for further details.