S and KAn excellent 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 recombination in males; GC content of short introns (<80 bp); the coding sequence (CDS) length of each gene. For further details concerning these measures, see refs. 18, 20, and 58.
For the analyses of NS sites, we applied DFE-? (24) to each of 52 (mel-yak) or 53 (mel) sets of genes binned by KA, to estimate the following parameters: ?, the shape parameter of a gamma distribution of the heterozygous fitness effects of deleterious NS mutations (the DFE); ?, the proportion of adaptive substitutions; ?Continue reading
