
(A) The distribution of fragment lengths supporting each of the four states. A geometric distribution (full line) is fitted to the observed distribution. (B) Examples of an alignment supporting the alternative [(H,O),C] genealogy. The top of the figure shows the posterior probability of being in the basic state (HC1) or in each of the three alternative states (HC2, HO, or CO). The bottom of the figure indicates informative sites and singletons.











