Fig. 1

Sex-linked genomic regions of varying stages of differentiation can be detected through differences in genome coverage and heterozygosity between WGS reads of males and females aligned to a homogametic (XX/ZZ) reference genome. Reads are coloured according to chromosome origin (“autosomal”, “X/Z-linked” or “Y/W-linked”). Genome coverage is calculated as the number of WGS reads aligning to a specific genomic region. The black bars within the WGS reads represent genetic variants compared to the reference allele (i.e., heterozygous sites). (A) Genome coverage and heterozygosity is expected to be similar between sexes on autosomes. (B) Sex chromosomes of low differentiation are characterized by higher heterozygosity in the heterogametic sex. They often display equal genome coverage between sexes when allowing mismatching reads to map to the reference genome but pronounced coverage differences when restricting the number of allowed mismatches. (C,D) Highly differentiated sex chromosomes are expected to have either equal genome covera ge between sexes when allowing mismatches, or lower genome coverage in the heterogametic sex if the sequence divergence is large enough to prevent successful alignment of reads to the reference genome. When restricting the allowed number of mismatches, we expect significantly lower genome coverage in the heterogametic sex. If the genomic region has a completely degenerated sex-limited chromosome copy, we expect lower genome coverage in the heterogametic sex regardless of the number of allowed mismatches. Highly differentiated sex chromosomes will have either (C) very high or (D) lower heterozygosity in the heterogametic sex depending on mapping success, level of Y/W degeneration, and level of genetic variation on X/Z