Fig 1.
Geographic distribution of the Japanese genetic clusters.
Each population is mapped to its geographic location. The individuals in a population are represented by circles colored according to their assigned genetic clusters. The figure map was generated using the packages maps v3.1.0 and mapdata v2.2–6 in the R software.
Fig 2.
Genetic clustering of an extended set of individuals from the Shimane prefecture.
a) For each municipality, the individuals therein are represented by diamonds colored according to their assigned genetic clusters. b) Re-classification of the individuals in the Shimane 1, 2 clusters of Fig 1 into the finer clusters Shimane A–E. The map of Shimane prefecture (https://commons.wikimedia.org/wiki/File%3AMap_of_Shimane_Prefecture_Ja.svg) is licensed under the Attribution-ShareAlike 3.0 Unported license. The license terms can be found on the following link: https://creativecommons.org/licenses/by-sa/3.0/.
Fig 3.
Ancestry profile of the Japanese genetic clusters.
For each Japanese cluster, the non-Japanese genetic components are represented as a mixture of continental Asian clusters. The bar graph indicates the proportion of continental Asian clusters contributing to a given Japanese cluster. Continental Asian clusters with ≥1% contribution to at least one Japanese cluster are shown. The map indicates geographic locations of the populations included in continental Asian clusters. See S4 Table for details. The figure map was generated using the packages maps v2.3–9 and mapdata v2.2–3 in the R software.
Table 1.
Admixture events detected in the Japanese clusters.
Fig 4.
Ancestry populations for the Japanese and continental Asians modeled using the ADMIXTURE program.
Eight ancestry populations are inferred. In this bar plot, each individual is represented by a vertical bar, which is colored by eight segments that indicate the proportion contributed by the corresponding ancestry populations. The individuals are sorted by 23 continental Asian clusters (see S4 Table for details) and nine Japanese clusters. The bar widths are halved for Japanese individuals, to fit the plot in space. The inset shows color-codes for eight ancestry populations and geographic areas of clusters, to which the individual population mainly contributes.
Fig 5.
Relation between locus-specific genetic differentiation and positive selection in East Asia.
a) Genetic differentiation is analyzed in four areas, consisting of different sets of populations. b) Neighbor-joining phylogenetic tree of the genetic clusters. c) Genetic similarity among the individuals is plotted by the first two principal components of EIGENSOFT PCA. d) For each area, 4-SNP windows of the genome are sorted into 20 equal-sized bins arranged according to locus-specific HFST in the corresponding populations. The proportion of positively selected windows (in vertical axis) is plotted across 20 HFST bins (in horizontal axis); the average proportion (1.3%) is indicated by a gray line. Asterisk (*) indicates significant enrichment of positively selected windows in a specific bin, compared to the whole-genome average (Fisher’s exact test P < 0.01/20). The highest (or rightmost) HFST bin in A1 and second to lowest (leftmost) HFST bins in A2 and A3 are significantly enriched. Triangles above the plot indicate the HFST bins, to which genes known to be under selection belong [29–41]. The figure map was generated using the packages maps v3.1.0 and mapdata v2.2–6 in the R software.
Fig 6.
Relation between locus-specific genetic differentiation and positive selection in Southeast Asia and South Asia.
a and c) Neighbor-joining phylogenetic tree of the genetic clusters. b and d) The proportion of positively selected windows (in vertical axis) is plotted across 20 HFST bins of 4-SNP windows (in horizontal axis); the average proportion is indicated by a gray line. Asterisk (*) indicates significant enrichment of positively selected windows in a specific bin, compared to the whole-genome average (Fisher’s exact test P < 0.01/20). Triangles above the plot indicate the HFST bins, to which genes known to be under selection belong [29,34–36,39].