mgu FY2015 Annual Report 3.2. fig4

Figure 4. Principal components analysis and genetic distances and suggest the existence of four clusters in the sRA, located in Okinawa, the KIs, Yaeyama North, and Yaeyama South. (a) Principal components analysis (PCA) of the filtered dataset of 122 individuals and 905,561 SNPs after trimming of related samples with smartrel and outliers with smartpca. Tracy-Widom statistical significance of PC1 and PC2 was <1e⁻³⁵. Individuals from Okinawa Island, the KIs, and the YIs are shown with squares, circles, and triangles, respectively. Four subpopulations, Okinawa, Kerama, Yaeyama-North, and Yaeyama-South are circled in green, pink, blue, and purple dotted lines, respectively. (b) Heatmap showing pairwise Fst values based on Weir and Cockerham weighted estimates between sampling sites. All points were clustered by pairwise Fst values, based on the Complete Linkage Clustering method. Site combinations without boxed bold lines indicate significant differences (p-value < 0.001, ANOVA statistics across 10 eigenvectors in PCA).