Fig. 2: Origin of Japanese weedy rice.

a Population structure of weedy and cultivated rice strains. Ancestry proportions for individuals with K = 5 are presented. b Demographic scenario models involving BH and SH_TEJ weedy rice and modern and landrace cultivated rice for deducing the hybridization history of SH weedy rice. Scenario 1: SH weedy rice evolved from a hybridization event between BH weedy rice and cultivated rice before the divergence of modern and landrace strains; Scenario 2: it evolved from a hybridization event between BH weedy and modern cultivated rice; and Scenario 3: it evolved from a hybridization event between BH weedy and landrace cultivated rice. Posterior Probability (95% of confidence interval) for each scenario was indicated under the title of each scenario. c Relative frequency of chloroplast genome haplotypes in weedy and cultivated rice groups. Variants of each of the chloroplast genome haplotypes are indicated in Supplementary Table 1.