Fig. 3.

Frequentist non-parametric p-values where the null distribution was approximated by reshuffling columns of a subset of the sequences. On the left we have the distribution of the test statistics for the “original” sequences simulated under IO (blue) or under UCA (red), while the right show their associated p-values. At the top the test statistic is the maximum likelihood tree length under the common ancestry hypothesis, and at the bottom the statistic is the difference in average similarity within each group and between one group and the other