Fig. 3.

Effects of selection based on heteroplasmy allele frequencies (Top row) and their branch-specific changes (Bottom row). (A) Allele frequency distribution for 32 pathogenic vs. 280 nonpathogenic heteroplasmies. (B) Allele frequency distribution for 77 synonymous vs. 123 nonsynonymous heteroplasmies. See SI Appendix, Table S5 for summary statistics. (C) Observed differences in branch length between pathogenic and nonpathogenic heteroplasmies (vertical black lines) and permuted null distributions of the differences (violin plots). P values for each comparison are listed on the right. The colors of the violin plots correspond to branches in Fig. 1A. (D) Like (C) but for synonymous and nonsynonymous mutations.