Fig. 4

Per scaffold difference in heterozygosity and genome coverage between male and female mantled howler monkeys, with scaffold lengths indicated by symbol colour and/or size (top row in A and B) or plotted on the y-axis (bottom row in A and B). Genome coverage was calculated for three different mismatch filtering stringencies of mapped reads (left, mid, right panels: strict (0 mismatches), intermediate (≤ 2 mismatches) and no filtering (“unfiltered”)). The left-side panels show three separate clusters of scaffolds, corresponding to the expected patterns of autosomes, and sex chromosome regions of low and high differentiation, respectively. (A) This plot was generated through the pipeline directly, with the findZX option (i.e., not using a synteny-species reference genome). (B) The underlying data in this plot is identical to Fig. 4a but coloured differently to facilitate interpretation of Fig. 4a (see Main text). In this plot, the data points are coloured blue if the scaffolds aligned to the human X chromosome and red if the scaffolds aligned to the sex-linked region of chromosome 3 (134–178 Mb; Fig. 3). All other scaffolds are coloured grey. The silhouette was downloaded from phylopic.org