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).