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I determined Spearman nonparametric limited correlations ranging from ? S and KA using the R function “pcor.test,” available at yilab.gatech.edu/pcor.R, with 95% CIs obtained by bootstrapping across genes. We used the following statistics for each gene as covariates: codon use bias, measured as the proportion of optimal codons (Fop); synonymous divergence (KS), a proxy for the mutation rate of each gene; gene expression, measured using RNAseq (average log2 reads per kilobase of transcript per million mapped reads across all developmental stages of D. melanogaster); smoothed effective rates of crossing over (centimorgan per megabase) from Loess regression fits to the rates of crossing over from the D. melanogaster data of ref. 22, multiplied by one-half to correct for the absence of recombi...