Fig. 4

Comparing the number of mutations on divergent Y chromosomes to non-divergent Y chromosomes for different maximum human-chimp sequence divergence filters (lower x-axis). The upper x-axis represents the average number of positions (in Mb) used for each comparison. The colors correspond to the three divergent Y chromosomes (A00, A0a1, and B-M181). The shaded area indicates the divergence filters that minimize the branch length variation while maximizing the proportion of the Y chromosome available for further analysis. The error bars denote 95% CIs computed by resampling branch lengths from a Poisson distribution