Summary: Supplementary Materials
1. Summary of surveyed loci.
2. Removing the effect of Ks using partial regression.
3. Investigating effects of possible recombination rate variation.
4. Effects of local gene density.
5. Spatial autocorrelation in the data.
6. Estimating the fraction of adaptive protein divergence.
7. Codon preference table for D. melanogaster.
Supplement 1. Summary of surveyed loci
Figure S1.1. Positions of the 137 coding regions surveyed in this study. Estimated recombination rates
based on (Charlesworth 1996) and (Andolfatto and Przeworski 2001) are plotted to the left.