Correlations in polymorphism data from <i>D. melanogaster</i>.

<p>(A) Levels of synonymous site diversity versus recombination rates. The effects of the rate of amino acid divergence (<i>K_a</i>) and the rate of synonymous site divergence (<i>K_s</i>) have been controlled for by partial regression, with negative values set to zero. (B) <i>K_s</i> versus recombination rates. The effect of <i>K_a</i> has been controlled for by partial regression, with negative values set to zero. (C) A summary of the allele frequency spectrum at synonymous sites versus recombination rates; more negative values of the statistic reflect a higher proportion of rare alleles. The numerator is Tajima's <i>D </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000495#pgen.1000495-Tajima1" target="_blank">[127]</a> and the denominator is the minimum value <i>D</i> (in absolute value) can take given the sample size and number of segregating sites <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000495#pgen.1000495-Schaeffer1" target="_blank">[128]</a>. (A–C) are based on the polymorphism data of Shapiro et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000495#pgen.1000495-Shapiro2" target="_blank">[34]</a>, and recombination rates estimated by Comeron et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000495#pgen.1000495-Comeron1" target="_blank">[129]</a>. For the Shapiro et al. data, 349 loci with >50 synonymous sites were used and only African individuals are included. (D) Levels of synonymous site diversity as a function of <i>K_a</i>. In red are the 137 X-linked loci surveyed by Andolfatto <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000495#pgen.1000495-Andolfatto2" target="_blank">[33]</a>. In black are autosomal loci surveyed by Shapiro et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000495#pgen.1000495-Shapiro2" target="_blank">[34]</a>. For both data sets, the effect of <i>K_s</i> has been controlled for by partial regression, with negative values set to zero. For the Shapiro et al. data, 265 loci with recombination rates >0.5 cM/Mb and >50 synonymous sites were included. The red and black dotted lines represent average levels of synonymous π in the Andolfatto and Shapiro et al. datasets, respectively. Thick red and black lines indicate Lowess fits to the data. All <i>p</i>-values are one-tailed.