PCAs were carried out based on mtDNA haplogroup frequencies. We considered 31 mtDNA haplogroups in PCA of 21 ancient populations, while in PCA with the 3 medieval populations and 53 modern-day populations, 36 mtDNA haplogroups were considered (Supplementary Tables S5 and S6). All PCAs were performed using the prcomp function for categorical PCA, implemented in R 3.1.3 (R Foundation of Statistical Computing, 2015) and plotted in a two-dimensional space, displaying the first two or the first and third principal components, respectively (Fig. 3A, Supplementary Figs S1–S3).