Fig. 2

Genetic and geographical origin of global weedy rice. a Population structure of global wild, cultivated, and weedy rice. The maximum likelihood clustering with K = 4 is presented. The cultivated rice group includes aromatic, tropical japonica, temperate japonica, indica, and aus type (ARM, TRJ, TEJ, IND, and AUS, respectively). The genetic composition of wild, TEJ, IND, and AUS are colored predominantly with dark green, orange, blue, and purple, respectively. In the weedy rice group, accessions are grouped by country to illustrate the types of weeds in each region; b The ratio of allele frequency for SNPs between targets of domestication selection vs. non-targets (estimated by Huang et al. (2012)) for temperate japonica type, indicating a similar allele frequency spectrum for japonica weedy and cultivated rice. c Effective population size (Ne) changes for the cultivated (C) and different weedy (W) rice populations of japonica type. The estimated divergence time between weedy and cultivated rice is shown with the gray-shaded bar along the x-axis and assumes one generation per year