Selected Sites at the Speciation and Driven by Environment
Based on the Bayesian method applied in BAYESCAN, we identified 20,796 outlier SNPs from the 151,577 filtered SNPs according to a 0.05 threshold for the q-value among the four groups. These outlier SNPs might putatively be considered to have been selected among the four groups. The outlier SNPs were located in 5954 genes, of which 677 genes were differentially expressed in different groups. Eleven genes were enriched in cytochrome P450 (ko00199, CYP450) (Figure S7), includingAqcoe2G002300 (CYP98A), Aqcoe2G223900 (CYP707A),Aqcoe4G255000 (CYP71), Aqcoe4G282900 (CYP76A),Aqcoe6G141100 (CYP707A), Aqcoe4G0100000 (CYP79D),Aqcoe5G393400 (CYP71AN), Aqcoe5G448000 (CYP90D),Aqcoe7G425500 (CYP711A), Aqcoe5G393900 (CYP71), andAqcoe4G241600 (CYP81Q).
Additionally, 1730 outlier SNPs were identified by BAYENV2 that were associated with seven environmental variables. There were 1,027 and 862 SNPs associated with Bio2 and Bio8, respectively. Considering the intersection of the SNPs identified by BAYESCAN and BAYENV2, 347 SNPs located in the intersection might be presumed to be under environmental selection and were located in 157 genes (Table S4).