Figure 2.

Positive selection on genes involved in vision. (A-C) Coalescent simulations (ms) of positive selection detected by F_ST (A), Pi (B) and XP-EHH (C). (D-F) F_ST(D), Pi (E) and XP-EHH (F) values for the visual-related candidate genes compared with the values for their upstream/downstream sequences with the same length as the gene (Group A), adjacent genes (Group B) and upstream/downstream 50 kb sequences (Group C). (G) The ratio of the numbers of non-synonymous SNPs to the numbers of synonymous SNPs (pN/pS). (H) the alternative allele frequency (AAF) of the visual-related candidate genes in the village chickens and Red Junglefowl.