Hierarchical clustering was performed using Ward type algorithm44 and Euclidean measurement method, where frequencies of the PCA haplogroups were used. The result was visualized as a dendrogram with the pvclust library in R.2.13.145 (Fig. 3b). Cluster significance was evaluated by 10,000 bootstrap replicates. Significance of each cluster was given as an AU (Approximately Unbiased) p-value, in percentage. Fisher tests based on absolute haplogroup frequencies used in ancient PCA (except that U1 and Y, Z remained separated) were performed using sqldf library and fisher.test function in R.3.1.3.