Appendix 2.

Nested statistical design for Clade B in Fig. 4 (a—f) and Clade C (g—j) for NCA. Bars indicate mutations inferred using parsimony and zeroes indicate inferred (but unobserved) intermediate haplotypes. The tree structure is based on Fig. 4, but is unrooted. The original haplotypes (numbers corresponding to Fig. 4) are shown in a (Clade B) and g (Clade C), along with the corresponding (and numbered) 1-step clades. Successively higher nested clades are shown and numbered in b—f and h—j.