Faster expression evolution of X-linked genes not directly regulated by the DCC.

<p>(A) Boxplots show the pairwise divergence in expression between 1∶1∶1 orthologs in the <i>D. melanogaster</i> (mel), <i>D. yakuba</i> (yak), and <i>D. ananassae</i> (ana) genomes measured in whole females (top) and males (bottom) on each chromosome arm. X-linked genes are divided into those that are bound and unbound by the DCC. The counts of genes on each chromosome and DCC bound and unbound genes are given along the x-axis. Boxes extend from the first to the third quartile (interquartile range; IQR), the horizontal line in the middle of the box indicates the median value, and the whiskers represent (outliers are not plotted). Error bars within each box show the location of (where is the sample size), which approximates a 95% CI of the median. The genome-wide average is represented by the horizontal gray line. X-linked genes whose median pairwise divergence is greater () or less (v) than autosomal genes are marked (there is not a significant difference in expression divergence between autosomes). Asterisks indicate significant differences in the medians between X-linked genes bound and unbound by the DCC. Mann-Whitney U tests were used to assess significant differences (one symbol = , two symbols = , three symbols = , four symbols = ). (B) Plots show the correlation between distance from the nearest HAS and the pairwise expression divergence between <i>D. melanogaster</i> (mel) and <i>D. yakuba</i> (yak) or <i>D. ananassae</i> (ana), along with the 95% CI. Expression levels were measured in females (top) and males (bottom). The dashed horizontal line shows the null expectation (). (C) Plots show the correlation between expression level in <i>D. melanogaster</i> and expression divergence between mel and yak or ana for autosomal (A) and X-linked (X, red) genes, along with the 95% CI. Expression levels were measured in females (top) and males (bottom). The solid horizontal line is the genome-wide correlation, and the dashed lines are the 95% CI of the genome-wide value. (D) Plots show the partial correlations between distance from the nearest HAS (dist), pair-wise divergence in expression between 1∶1∶1 orthologs (div), and expression level in <i>D. melanogaster</i> (level). Error bars represent the 95% CI of the partial correlations, estimated by bootstrapping. The dashed horizontal line shows the null expectation ().