title: Point estimates in phylogenetic reconstructions.
abstract: BACKGROUND
  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 sufficiently 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 statistics such as sample mean, median and variance are defined as the geometric median, Fréchet 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 topologies occur in the posterior sample, the posterior mean balances correctly 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 simulated data also reveals the benefits of a sound averaging method when reconstructing phylogenetic trees.
  
  
  METHODS
  We provide two independent implementations of the algorithm for computing Fréchet means, geometric medians and variances in the space of phylogenetic trees. TFBayes: https://github.com/pbenner/tfbayes, TrAP: https://github.com/bacak/TrAP.
authors.affiliation: Max-Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany and Isthmus SARL, 75002 Paris, France.
authors.forename: Philipp
authors.initials: P
authors.lastname: Benner
authors.affiliation: Max-Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany and Isthmus SARL, 75002 Paris, France.
authors.forename: Miroslav
authors.initials: M
authors.lastname: Bačák
authors.affiliation: Max-Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany and Isthmus SARL, 75002 Paris, France Max-Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany and Isthmus SARL, 75002 Paris, France.
authors.forename: Pierre-Yves
authors.initials: PY
authors.lastname: Bourguignon
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D015233:Models, Statistical; D010802:Phylogeny