2.16 Gene conversion and positive selection sites of opsin genes
To investigate the mechanism of opsin gene expansion via gene conversion, with the duplication events obtained by gene synteny and gene trees, we grouped these opsin genes, and each group included at least three sequences. These groups were merged into one where distance values between groups were less than 0.4, as described (Sawyer 1989). Gene conversion per group was checked using GENECONV (Sawyer 1989). AP value <0.05 indicated statistical significance. To measure the divergence between genes with gene conversion, we obtained ꞷ values along the coding sequences of genes using a sliding window of 30 with a step size of 1 in DnaSP 6 (Rozas et al. 2017). To avoid bias toward gene clades, we calculated ꞷ values for per subfamily with more than three genes. Sequence identity of the sequence flanking the local gene was used to test if gene conversion was induced by whole-genome duplication.