Fig. 5

Schematic overview of the methods used to identify the Z-chromosome in a scaffold assembled genome. The golden eagle genome referred to in the dark grey box represents the reference in which we are attempting to identify scaffolds belonging to the Z-chromosome. The golden eagle genome in the black bar is the genome with known chromosomes, used to identify which scaffolds in the dark grey boxed genome probably belong to Z-chromosome (and autosomes) – to use as a reference. The light grey boxes are the four approaches we tested to find the scaffolds belonging to the Z-chromosome: 1) Depth: analysis of difference in sequencing depth between scaffolds in a high depth whole genome sequenced white-tailed eagle female. 2) Heterozygosity: analysis of the difference in heterozygosity per scaffold a high depth whole genome sequenced white-tailed eagle male and female. 3) LASTZ: mapping of the golden eagle reference genome to the chicken genome using LASTZ. 4) SNP-loadings: analysis of SNP-loadings for principal components splitting the sexes, in 133 RADseq white-tailed eagle individuals