Fig. 6: Validation of the genetic legacy of Jomon ancestry and the predictive power of 132 Jomon-related variants using an independent cohort of BBJ-2nd.

a The PCA plots include all individuals from BBJ-2nd (n = 68,632), with their respective Jomon proportions overlaid. b The Jomon component prediction scores measured from all individuals within the cohort (n = 72,695) are split into the deciles. The boxplot shows the distribution of observed Jomon proportions in each decile of the predicted scores. R² indicates the squared value of the Pearson’s correlation coefficient between the prediction score and the residuals of the Jomon proportion regressed out with 10 PCs. P-value reflects a two-sided test. In (b), boxes denote the interquartile range (IQR) and the median is shown as white horizontal bars; whiskers extend to 1.5 times the IQR; outliers are shown as individual points. PC Principal component.