Supplemental Material for Lichilín et al., 2022

<strong>File S2</strong> This file contains large figures representing heatmaps with sample clustering of individual genotypes at SNPs located in the the previously described LG05, LG18 and LG13 sex- determining region in <em>A. burtoni</em> (Böhne et al. 2016; Roberts et al. 2016). Genotypes in blue are heterozygous, in black homozygous reference, and in grey homozygous alternative. <strong>HeatmapXYRegionLG05HetBlueNaWhite.pdf</strong> Heatmap clustering for genotypes on the previously described XY sex-determining region on LG05. <strong>HeatmapXYRegionLG18HetBlueNaWhite.pdf</strong> Heatmap clustering for genotypes on the previously described XY sex-determining region on LG18. <strong>HeatmapZWRegionHetBlueNaWhite.pdf</strong> Heatmap clustering for genotypes on the previously described ZW sex-determining region on LG13. <br> <strong>File S3</strong> This file contains large figures investigating sex differences in genome coverage. <strong>Female_Assemblies.pdf</strong> Coverage 10Kb window visualization for each population and chromosome for female assemblies. Each page shows the mapping coverage for each chromosome within a population. The figures are sorted accordingly to chromosome numbers (columns) first showing the four identified sex chromosomes in <em>A. burtoni</em> LG05/ 14, LG13 and LG18, and then numerically sorted; rows correspond to species. X-axis: chromosomal positions; y-axis: log2 normalized- median coverage. Red lines and dots = female coverage, blue lines and dots = male coverage. yellow lines = windows in the upper 99% quantile of male-female coverage ratio and with normalized-median coverage above 0.25 in females. <strong>Male_Assemblies.pdf</strong> Coverage 10Kb window visualization for each population and chromosome for male assemblies. Each page shows the mapping coverage for each chromosome within a population. The figures are sorted accordingly to chromosome numbers (columns) first showing the four identified sex chromosomes in <em>A. burtoni</em> LG05/ 14, LG13 and LG18, and then numerically sorted; rows correspond to species. X-axis: chromosomal positions; y-axis: log2 normalized- median coverage. Red lines and dots = female coverage, blue lines and dots = male coverage. yellow lines = windows in the upper 99% quantile of male-female coverage ratio and with normalized-median coverage above 0.25 in males. <br> <strong>File S4</strong> This file contains large figures representing sex-specific genome sequence analyses. <strong>Female-specific_regions_in_Scaffolds.pdf</strong> Scaffolds with female-specific regions of at least 500bp length. Each separate sheet shows the scaffolds found in each population. The right-hand side labels show the assigned scaffold name. Red = female median coverage normalized by overall median depth for the corresponding population across the <em>de novo</em> assembled genome, blue = male median coverage normalized by overall median depth for the corresponding population across the <em>de novo</em> assembled genome. <strong>Male-specific_regions_in_Scaffolds.pdf</strong> Scaffolds with male-specific regions of at least 500bp length. Each separate sheet shows the scaffolds found in each population. The right-hand side labels show the assigned scaffold name. Red = female median coverage normalized by overall median depth for the corresponding population across the <em>de novo</em> assembled genome, blue = male median coverage normalized by overall median depth for the corresponding population across the <em>de novo</em> assembled genome.