(D. mel) D. melanogaster, (D. sch) D. sechellia, (D. sim) D. simulans. These three species together stand for the D. melanogaster species complex. (D. yak) D. yakuba. We calculated substitution rates between paralogs using the method described by Yang and Nielsen (2000). The standard error is shown. The detail ratio for each gene is also provided in Supplemental Tables S1–S3.