Data & simulation code

The Data.zip file contains all data sets (seven-generations pedigrees and microsatellite genotypes) and the annotated source codes (R scripts) for linkage map construction and smoothing, finding the optimal interference distance and for the gene-dropping simulations. The attached README provides further information on each of the files

Autocorrelation of gene expression present on the Z chromosome.

Red vertical line shows the PAR border. Blue lines represent autocorrelation values significantly different from zero. Except for the PAR region, there is no clear trend of clusters that would point at local centers of dosage compensation. Liver: upper panel. Spleen: lower panel. (TIFF)</p

Relationship between epigenetic features, gene expression and dosage balance on the Z chromosome (DB).

(A,D) Linear regression of log2(f:m) peak height to gene expression. Peak height is measured as read counts in peaks. Boxplots depicting (B,E) log2(f:m) ratios of peak height in regulatory regions of dosage balance (DB) and not DB genes. (C,F) log2(f:m) ratios of 5mC methylation in CpG islands of DB and not DB genes. Boxes in boxplots encompass interquartile ranges across genes, whiskers extend to 1.5 x the interquartile range. Wilcoxon-test statistical significance levels: 0.0001 ‘***’, 0.001 ‘**’, 0.01 ‘*’. Data show for liver (A, B, C) and spleen (D, E, F).</p

Gene ontology enrichment analysis (GO) of shared expressed balanced genes on the Z chromosome.

Gene ontology enrichment analysis (GO) of shared expressed balanced genes on the Z chromosome.</p

Sex-specific CpG methylation divergence genome-wide.

Differentially methylated features (genes or CpG islands) were identified with a beta-binomial regression using methylation counts implemented with a general experimental design framework in DSS. FDR-corrected -log10(p-values) for sex divergence are plotted along the bottom first and third panels for liver and spleen, respectively, with the dashed line indicating FDR-corrected significance (0.05). Bootstrap sampling log2(F/M) values are shown along bottom second and fourth panels. (TIFF)</p

Correlations between sex-specific DNA methylation divergence.

(log2(F/M)) and expression (log2(F/M)) across both tissues for both CpG islands and directly over gene bodies for Z-linked transcripts. CpG island expression level was determined as the expression level of the closest genomic transcript. Spearman’s rho is written for each facet, and for each dosage compensation state (dosage balanced, or unbalanced, as identified from expression data). (TIFF)</p

Number of mapped reads after filtering steps described in the methods section.

The libaries were down-sampled to the library with the lowest number of reads. The normalization factor indicates whichi proportion of original reads was kept. Data is shown seperately for liver and spleen. (XLSX)</p

F:m peak ratios.

Pvalues correspond to Wilcoxon test comparing peak heights between females and males. NA correspond to those peaks where the peak number was less than three. (XLSX)</p

Identification of the pseudo-autosomal region (PAR) on the Z chromosome of the European crow.

(A) F:m DNA sequencing coverage along the Z chromosome. (B) heterozygosity levels across the Z chromosome in females (light blue) and males (gray). A drop in both measures after 688 kb defines the end of the PAR. (C) One Mb of Z chromosome alignment between the flycatcher and the European crow. Lines between the Z represent orthologous regions found between the two species. Red: protein coding genes. Blue: non-coding regions. The vertical red dashed line marks the end of the PAR region in the European crow in all panels.</p

Patterns of dosage effects for gene expression, chromatin accessibility (peak height) and 5mC methylation shown for 27 autosomes and the Z chromosome.

The two leftmost columns show f:m ratios of genes by chromosome for liver and spleen, respectively, with the Z chromosome highlighted in color. Horizontal red dashed lines indicate an equal f:m ratio. Boxes encompass the interquartile range across genes, whiskers extend to 1.5 x the interquartile range. The two rightmost columns show Z-chromosomal to autosomal (Z:A) model estimate ratios separately for females (Zf:AAf, light shading) and males (ZZm:AAm, dark shading). Here, red vertical lines mark a ratio of Z:A = 0.5 and blue vertical lines mark a ratio of Z:A = 1. Bars in dot plots represent 95% confidence intervals of parameter estimates of statistical models controlling for co-variates drawn from 10,000 bootstraps (S2A–S2C Table). (A) Log2(f:m) gene expression, (B) log2(f:m) ATAC-seq peak height in the regulatory region of a gene and (C) f:m 5mC methylation percentages in CpG islands. Consult Table 1 for model-based estimates and confidence intervals for AAf:AAm, ZZm:AAm, Zf:AAf and Zf:ZZm ratios. Additional results from statistical analyses including other regions of the gene can be found in S2 Table.</p