Summary of population genetics analyses.

<p>In each figure, red is used for <i>O. rufipogon</i>, blue for <i>indica</i>, and green for <i>japonica.</i> (A) Distribution of π of protein coding genes. The first 1000 synonymous sites from the translation start site were used for each gene to correct for the difference in length in each gene. 13,471 genes with 1,000 sites with reliable SNP data are used. (B) Neighbor-joining tree of all sequenced strains. (C) Population structure estimated by PCA. (D) Population structure estimated by the bayesian clustering program STRUCTURE (<i>K</i> = 3). The results of <i>K</i> = 2∼6 are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083720#pone.0083720.s001" target="_blank">Figure S1</a>. (E) Decay of LD against distance. The bin size is 2000 bp (measured until 1000 kb).