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Results: 4

1.
Figure 1

Figure 1. Sex-biased expression in Drosophila species. From: Constraint and turnover in sex-biased gene expression in the genus Drosophila.

a–g, Sex-biased female:male expression ratio (log2) versus average expression intensity (log2) plots for each Drosophila species. Expression intensities are arbitrary, where zero represents the minimum value. Values for genes with significant (P ≤ 0.01, false-discovery-rate-corrected Mann–Whitney test) female-biased, male-biased and non-biased expression are shown. The per cent of genes with female-biased or male-biased expression is inset in each panel. D. melanogaster, D. mel; D. simulans, D. sim; D. yakuba, D. yak; D. ananassae, D. ana; D. pseudoobscura, D. pse; D. virilis, D. vir; and D. mojavensis, D. moj.

Yu Zhang, et al. Nature. ;450(7167):233-237.
2.
Figure 4

Figure 4. Relationship between sex-biased expression, gene content and sequence divergence. From: Constraint and turnover in sex-biased gene expression in the genus Drosophila.

Gene content and expression of common orthologues (a) and species-restricted (b) genes. The percentages of all genes (black) and with female (red) or male (blue) -biased expression are shown. Significant differences (P < 10−2, chi-squared test) between sex-biased classes and total genes are indicated (asterisks). See Supplementary Fig. 5 for paralogues. Average KA/KS ratios within the melanogaster subgroup for common orthologues with high or low expression-ratio s.d. (c) and for all common orthologues or species-restricted genes (d). Significant differences (P < 10−2, Mann–Whitney test) between common orthologues with constrained expression and variable expression, or between common orthologues and species-restricted genes are indicated (asterisks).

Yu Zhang, et al. Nature. ;450(7167):233-237.
3.
Figure 3

Figure 3. Expression divergence within and between species and groups. From: Constraint and turnover in sex-biased gene expression in the genus Drosophila.

a, Average female:male expression ratios for common orthologues plotted against expression divergence (expression ratio standard deviations between 7 species) for the same orthologues. b, Expression ratio standard deviations among members of the melanogaster subgroup (D. melanogaster, D. simulans and D. yakuba) plotted against standard deviations among the other four species (D. ananassae, D. pseudoobscura, D. virilis and D. mojavensis). c, K-means clustering (K=10, species-order fixed) of expression ratios where s.d.>0.5. Female-biased (red), male-biased (blue) and non-biased (black) expression is indicated. d, Examples of gene clusters that are indicated on the Eisengram (c). Species (x axis) and log2 female:male expression ratio (y axis) of common orthologues are shown.

Yu Zhang, et al. Nature. ;450(7167):233-237.
4.
Figure 2

Figure 2. Expression divergence among common orthologues. From: Constraint and turnover in sex-biased gene expression in the genus Drosophila.

Female:male expression ratios (log2) for orthologue pairs, plotted against each other: a, two different D. simulans strains; b, the melanogaster subgroup (D.melanogaster, D. simulans and D. yakuba); c, all seven Drosophila species. All the density (grey for high, black for low) scatter plots include every 1:1 pair of common orthologues for which both have an expression value. In b and c, the species A and B designation is arbitrary, but A is assigned to the species in the pair most closely related to D. melanogaster. d, Neighbour-joining trees with branch lengths inferred using sequence distance (genomic mutation distance11) and the expression distance (1–Pearson's r) for all pairs of species except the pairs between the D. ananassae outlier and other species (Supplementary Fig. 3). e, Expression distance values plotted against estimated divergence time11 for all possible species pairs and replicates within species. Quadruplicate replicates within each species were used at a time of 0 million years.

Yu Zhang, et al. Nature. ;450(7167):233-237.

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