PCA was carried out using smartpca (45) by projecting ancient individuals onto the components inferred from modern individuals using the “lsqproject” option. Genetic affinities of ancient and modern individuals were investigated using the f-statistic framework (46). We used “outgroup f3” statistics to determine the amount of shared genetic drift between pairs of individuals and/or groups, as well as f4 statistics for allele sharing symmetry tests (tables S5 and S6). Model-based clustering implemented in ADMIXTURE was used to investigate patterns of recent admixture, in supervised mode using European (French), East Asian (Han), Oceanian (Papuan), and Australian (WCD) individuals as putative source populations.

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