PMC

Gene expression measurements from head using microarrays were used to calculate the correlation of expression levels between D. melanogaster (mel), D. pseudoobscura (pse), and D. mojavensis (moj). Expression was measured in females (top) and males (bottom). Graphs are the same as in .

Expression level of a gene (dashed blue line) and relative fitness (solid green curve) are plotted for genotypes at a locus with two alleles ( and ). The alleles have additive phenotypic effects, with each copy of increasing expression level. (A) The locus is autosomal with phenotypic and fitness measurements collected in females or males, or it is X-linked with measurements collected in females. (B) The locus is X-linked and not dosage compensated with measurements collected in males.

Correlations of expression between D. melanogaster (mel) and either D. yakuba (yak) or D. ananassae (ana) are plotted for each chromosome arm using expression measurements from whole females (top) or males (bottom). Genes were included if they are narrowly expressed in non-reproductive tissues (black), female reproductive tissues (purple, top), or male reproductive tissues (purple, bottom). Graphs are the same as in .

Pairwise correlations of gene expression are shown for genes on each chromosome arm, using expression measurements from (A) females or (B) males. In each graph, the solid horizontal line is the genome-wide correlation, and the dashed lines are the 95% confidence interval (CI). Each point represents the correlation for a chromosome arm, and the error bars are the 95% CI. Chromosome arms are represented with their Muller element nomenclature. Muller element A is is the X chromosome (red), and Muller element D is the D. pseudoobscura neo-X chromosome. Species names were abbreviated as follows: mel =  D. melanogaster, yak =  D. yakuba, ana = D. ananassae, pse = D. pseudoobscura, moj = D. mojavensis, vir = D. virilis.

Genes were classified based on their expression breadth, whether they are bound by the DCC, and whether they are in transcriptionally active or repressive (repr) chromatin (based on data from S2 cells). (A) Boxplots show the pairwise divergence in expression between 1∶1∶1 orthologs in the D. melanogaster (mel) and D. yakuba (yak) or D. ananassae (ana) genomes for broadly and narrowly expressed genes (see ). Mann-Whitney U tests were used to assess significant differences in expression divergence between broadly and narrowly expressed genes (***** ). (B) X-linked broadly expressed (gray) and narrowly expressed (white) genes were divided into those that are bound and unbound by the DCC. (C) Broadly expressed (gray) and narrowly expressed (white) genes were divided into those that are in transcriptionally active and repressive chromatin. (B–C) Fisher's exact test was used to determine if there is a non-random distribution of genes in the four classes.

(A) Pairwise correlations of gene expression between the sexes are shown for genes on each chromosome arm, using expression measurements from six species. Correlations are represented as in . (B–E) Boxplots show the distribution of of expression level in D. melanogaster females or males for genes with significant heritability. Horizontal dashed lines show the genome-wide average . Asterisks indicate significant differences between subsets of genes. Groups of genes whose is greater or less (v) than the rest of the genome are marked. Mann-Whitney U tests were used to assess significant differences (one symbol = , two symbols = , three symbols = , four symbols = , five symbols = ). (B) Genes were divided into those that are X-linked (X, red) and those that are autosomal (A). (C) X-linked genes were divided into those that are bound by the DCC and those that are not. (D–E) Genes were further divided into (D) those that are broadly or narrowly expressed and (E) those that are in transcriptionally active or repressive (repr) chromatin measured in either BG3 or S2 cells.

Boxplots show the pairwise divergence in expression between 1∶1∶1 orthologs in the D. melanogaster and D. yakuba or D. ananassae genomes measured in whole females and males (see ). X-linked (X, red) and autosomal (A) genes were assigned to transcriptionally active and repressive chromatin based on the results of ChIP-chip experiments in one of two cell lines (BG3 and S2) . Counts of genes in each chromatin state are given for data collected from each of the cell lines in the top left quadrants. Groups of genes whose pairwise divergence is greater () or less (v) than the rest of the genome are marked. Comparisons were also made between genes in active and repressive chromatin on the X chromosome or autosomes, and comparisons were made between autosomal and X-linked genes in active or repressive chromatin. Mann-Whitney U tests were used to assess significant differences (one symbol = , two symbols = , three symbols = , four symbols = ).

Boxplots show the pairwise divergence in expression between 1∶1∶1 orthologs in the D. melanogaster (mel) and D. yakuba (yak) or D. ananassae (ana) genomes measured in whole females and males (see , ). X-linked (X, red) and Autosomal (A) genes were assigned to transcriptionally active and repressive chromatin based on the results of experiments in S2 cells (for the results from BG3 cells see ). Groups of genes whose pairwise divergence is greater or less (v) than the rest of the genome are marked. Subsets of narrowly expressed genes whose pairwise divergence is significantly different than all other narrowly expressed genes are marked (N). The same was done for subsets of genes in repressive chromatin (R). Significant differences between X-linked and autosomal genes in the same chromatin state and with the same expression breadth are marked with asterisks. Mann-Whitney U tests were used to assess significant differences (one symbol = , two symbols = , three symbols = , four symbols = , five symbols = ).

Overlaid on each branch of the phylogeny are the branch lengths estimated from the pairwise correlations in expression (measured in whole flies with microarrays) using the Fitch and Margoliash method. In each graph, the solid horizontal line is the genome-wide branch length, and the dashed lines are the 95% CI. Each point represents the branch length estimate for a chromosome arm (X is in red), and the error bars are the 95% CI. Bootstrap supports for the nodes are listed in the boxes adjacent to the nodes. The first number, in bold, is the bootstrap support using all orthologs, and the subsequent five values are for genes on each chromosome arm (X is in red). The last value, in italics, is the bootstrap support using genes on the four autosomes (Muller elements B–E). Chromosome arms are represented with their Muller element nomenclature, as described in . The Fitch and Margoliash algorithm treats the phylogeny as unrooted, so there is a single branch length and bootstrap value for the lineage connecting the Sophophora (D. melanogaster, D. yakuba, D. ananassae, and D. pseudoobscura) and Drosophila (D. mojavensis and D. virilis) subgenera. Branch lengths and bootstrap support were estimated using expression measurements from (panel A) females and (panel B) males.

(A) Boxplots show the pairwise divergence in expression between 1∶1∶1 orthologs in the D. melanogaster (mel), D. yakuba (yak), and D. ananassae (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 D. melanogaster (mel) and D. yakuba (yak) or D. ananassae (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 D. melanogaster 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 D. melanogaster (level). Error bars represent the 95% CI of the partial correlations, estimated by bootstrapping. The dashed horizontal line shows the null expectation ().