Fig. 3.

—Identification of undifferentiated ZW region. (A) Coverage and proportion of ZW SNPs on each scaffold. Scaffolds below the horizontal red dashed line are defined as Z-specific based on their log₂(female:male) coverage ratio. Autosomal scaffolds are above the horizontal red dashed line and to the left of the vertical red dashed line. Young Z scaffolds are above the horizontal red dashed line and to the right of the vertical dashed line, and are defined by having >20% of the SNPs consistent with ZW-inheritance. The number of transcripts in each category is given in parentheses. (B) The proportion of sex-chromosome consistent SNPs in the RNA data that are also consistent in the DNA sequencing data set. Only SNPs on scaffolds with >20% of SNPs supporting a ZW karyotype in the RNA data set (putative young ZW strata) were considered. *** denotes a significant enrichment in the proportion of ZW-consistent SNPs in the RNA that were also ZW-consistent in the DNA, compared with the same proportion for all SNPs identified in the RNA (P < 2.2×10⁻¹⁶).