Population comparisons were estimated using Arlequin 3.5.146. Pairwise FST values were calculated based on 35,203 modern and 764 ancient HVS-I sequences (np 16050–16383) of 73 populations: 21 ancient and 52 modern-day populations from Eurasia. Tamura & Nei substitution model47 was assumed with a gamma value of 0.325 and 10,000 permutations were used for p-value calculation (Supplementary Tables S8 and 9). The FST values were analyzed using MDS and applied on the matrix of linearized Slatkin FST values48 (Supplementary Tables S8 and 9) and visualized in a two-dimensional space (Fig. 6) using the metaMDS function based on Euclidean distances implemented in the vegan library of R 3.1.345.