Supplementary Fig. S1: Geographic location of the five Japanese islands from which we collected samples.

Supplementary Fig. S2 : Median joining network of Y-STR haplotypes of haplogroup O-M175* highlighting samples with a microvariant of DYS627. Black nodes indicate samples
with allele 18.2 of DYS627. The link between black nodes is indicated in bold.
Supplementary Fig. S3: Median joining network of Y-STR haplotypes of haplogroup O-M122* highlighting samples with a microvariant of DYS570. Blue nodes indicate samples with
allele 18.3 of DYS570. The links between blue nodes are in bold. Red in a node indicates a sample with allele 19.3 of DYS570.
Supplementary Fig. S4: Median joining network of Y-STR haplotypes of haplogroup O-M175* highlighting samples with a microvariant of DYS385. Black in nodes indicates samples
with allele 9.2 of DYS385. The link between nodes including a sample with allele 9.2 of DYS385 is in bold.
Supplementary Fig. S5: Median joining network of Y-STR haplotypes of haplogroup O-M175* highlighting samples with a microvariant of DYS449. Black in nodes indicates samples
with allele 29.1 of DYS449. The link between nodes including a sample with allele 29.1 of DYS449 is in bold. The blue node indicates a sample with allele 29.2 of DYS449. The red
node indicates a sample with allele 30.2 of DYS449.
Supplementary Fig. S6: Multi-dimensional analysis based on pairwise RST genetic distances among the Japanese population and other Asian populations including ethnic groups in China.