Estimation of synonymous (dS) and nonsynonymous (dN) substitutions

Our analysis of regions of conservation and variation within dsx (Fig. 3) revealed that different regions of this gene experience different evolutionary pressures. We therefore divided the gene into multiple partitions (pre-OD1, OD1, post-OD1, OD2, female-specific, and male-specific region) and estimated dN and dS separately using the AnalyzeCodonData function of HYPHY 2.3.14 (Fig. 4). We performed beta regression using betareg (v3.1-1) (38) package in R (v3.3.1) on dN using dS, gene partitions, and taxonomy as predictor variables.

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