A Statistical Test for Clades in Phylogenies

We investigated testing the likelihood of a phylogenetic tree by comparison to its subtree pruning and regrafting (SPR) neighbors, with or without re-optimizing branch lengths. This is inspired by aspects of Bayesian significance tests, and the use of SPRs for heuristically finding maximum likelihood trees. Through a number of simulations with the Jukes-Cantor model on various topologies, it is observed that the SPR tests are informative, and reasonably fast compared to searching for the maximum likelihood tree. This suggests that the SPR tests would be a useful addition to the suite of existing statistical tests, for identifying potential inaccuracies of inferred topologies.