Figure 1.
Gene expression divergence is higher on the X chromosome in Drosophila embryos and lower in D. melanogaster strains.
The distributions of per gene expression divergence between Drosophila species separated onto each chromosome for A, embryos, and B, inbred strains of D. melanogaster. Divergence is measured per gene as the summed branch lengths for each gene tree for between-species data, and as mean log fold change for inbred strains as described in the Methods. Boxes show the upper and lower quartiles together with the median, error bars encompass data within 1.5 times the inter-quartile range, and blue circles indicate the means. Panels C and D show, for embryos and strains respectively, the distribution of 10,000 bootstrapped mean divergences for each chromosome using frequency polygons.
Figure 2.
Gene expression divergence is not higher on the X chromosome in Drosophila adults but is lower in D. melanogaster adult strains.
The distributions of per gene expression divergence between Drosophila species separated onto each chromosome for A, adult males, B, inbred adult male strains of D. melanogaster, E, adult females, and F, inbred adult female strains of D. melanogaster. Divergence is measured per gene as the summed branch lengths for each gene tree for between-species data, and as mean log fold change for inbred strains as described in the Methods. Boxes show the upper and lower quartiles together with the median, error bars encompass data within 1.5 times the inter-quartile range, and blue circles indicate the means. Panels C, D, G, and H show, for adult males, inbred adult strains, adult females, and inbred adult female strains respectively, the distribution of 10,000 bootstrapped mean divergences for each chromosome using frequency polygons.
Figure 3.
The X chromosome exhibits an excess of divergence throughout exmbryogenesis.
Bootstrapped mean X/A divergence ratios for each time point throughout embryogenesis. Genes were resampled 10,000 times on each chromosome and the X/A ratio was scored for each time point separately. Bootstrapped distributions are shown as frequency polygons. Dashed green and black lines represent adult males (AM) and adult females (AF) respectively, and the vertical dashed red line marks an X/A ratio of 1.
Figure 4.
Expression divergence is higher for the ancestral branch of the neo-X (Muller element D).
A, Per-gene, per-chromosome distributions of the length of the ancestral branch leading to the obscura sub-group (D. persimilis and D. pseudoobscura; see Figure S1) in the embryonic data divided by the sum of all branch lengths (3L is the neo-X chromosome in the obscura sub-group). B, Per-gene, per-chromosome distributions of the length of the branch leading to D. pseudoobscura in the adult data divided by the sum of all branch lengths.
Figure 5.
Gene expression mutational heritabilities are lower for the Drosophila X chromosome.
Gene expression mutational heritabilities, estimated from mutation accumulation lines of D. melanogaster [35], separated onto chromosomes. Genes with measurable mutational heritabilities are shown for the late larva (A) and the pre-pupa (B). In C and D genes are categorized as displaying zero or non-zero mutational heritabilities for late larva and pre-pupa respectively and depicted using mosaic plots where the area in the rectangles is proportional to the number in that category combination. Pearson residual shading is used to depict deviations from null expectations – blue (excess) and red (paucity) colours indicate deviations from the expectation under the null hypothesis that the two variables, mutational heritability and chromosome, are independent [85]. -values refer to the probability of independence (Chi-squared test).
Figure 6.
The faster-X effect is greatest when beneficially-interacting loci are linked on the same chromosome.
The ratio of selection gradients for X-linked models versus their equivalent autosomal cases as a function of allele frequency. Blue points represent the case where both loci are linked on the same chromosome, orange and green points represent the case where the loci are on different chromosomes, and the red points are for the one-locus scenario. Unless otherwise stated in the legend, recombination rates, , are equal to 0.5 (free recombination) and the dominance coefficient,
, is 0.01 (
is close to identical to
in the one-locus case and hence is not shown). The dashed line indicates a ratio of 1.
Figure 7.
Divergence on the X in embryos is greater using both Spearman's
and the Canberra distance. Bootstrapped distributions of A, Spearman's
(divergence is
) and B, the mean Canberra distance across chromosomes in Drosophila embryos for all pair-wise species comparisons.
Figure 8.
Divergence on the X in adults is greater using Spearman's
, but not the Canberra distance. Bootstrapped distributions of A, Spearman's
(divergence is
) and B, the mean Canberra distance across chromosomes in Drosophila males and females for a selection of pair-wise species comparisons (all pair-wise comparisons are shown in Figures S8, S9).