Figure 3 : Genetic diversity and demographic model for weedy rice.

From: Genomic variation associated with local adaptation of weedy rice during de-domestication

Figure 3

(a) Boxplots of genetic diversity (π) for weedy and cultivated rice. Boxes with orange colour are japonica type (JAP), and blue for indica type (IND). Cultivated rice is labeled with ‘_C’, whereas weedy rice with ‘_W’. Genetic diversity for significant divergent windows of weedy from cultivated rice are marked in light orange or blue colour with the suffix ‘_S’. The prefixes ‘NX’, ‘LN’, ‘JS’, ‘GD’ are short for Ningxia, Liaoning, Jiangsu and Guangdong provinces, respectively. The prefixes ‘NX1’, ‘LN1’, ‘JS1’, ‘GD1’ are short for main de-domestication origin of Ningxia, Liaoning, Jiangsu and Guangdong provinces, respectively. The ‘**’ is marked if the genetic diversity of weedy rice is significantly lower than that of local cultivated rice (P<0.01 by paired t-test). (b) Demographic model for weedy rice. The model assumes that the initiate weedy rice founders split from cultivated rice (effective population size Na) and then suffered a genetic bottleneck in a Tb duration. After the bottleneck, the weedy rice founder population (effective population size Nb) recovered to the present effective population size (Nw) at time T.