Fig. 3: Genetic legacy of Jomon ancestry throughout Japanese populations.

Proportions of Jomon ancestry are estimated through admixture modeling under models optimal for each individual (n = 163,243). a Projection of the Jomon proportions onto the PCA plots. b Absolute values of the correlation coefficients between the Jomon proportions and PCs. The correlation coefficient is calculated using Pearson’s method. c Boxplots representing variation in the Jomon proportion across BBJ participants within each of their registered regions. d Boxplots representing variation in the Jomon proportion across the participants within each of different genetic clusters defined by PCA. In (c, d), 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, EA East Asian.