BIOINFORMATICS doi:10.1093/bioinformatics/btu461 Point estimates in phylogenetic reconstructions

Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc methods such as the derivation of a consensus tree makeup for the ill-definition of the usual concepts of posterior mean, while bootstrap methods mitigate the absence of a sound concept of variance. Yielding satisfactory results with suffi-ciently concentrated posterior distributions, such methods fall short of providing a faithful summary of posterior distributions if the data do not offer compelling evidence for a single topology. Results: Building upon previous work of Billera et al., summary stat-istics such as sample mean, median and variance are defined as the geometric median, Frechet mean and variance, respectively. Their computation is enabled by recently published works, and embeds an algorithm for computing shortest paths in the space of trees. Studying the phylogeny of a set of plants, where several tree topolo-gies occur in the posterior sample, the posterior mean balances cor-rectly the contributions from the different topologies, where a consensus tree would be biased. Comparisons of the posterior mean, median and consensus trees with the ground truth using simu-lated data also reveals the benefits of a sound averaging method when reconstructing phylogenetic trees. Availability and implementation: We provide two independent im-plementations of the algorithm for computing Frechet means, geomet-ric medians and variances in the space of phylogenetic trees