Statistics for Phylogenetic Trees in the Presence of Stickiness

TL;DR

This paper investigates the statistical properties and computational challenges of the Fréchet mean in phylogenetic tree space, especially under the influence of stickiness, and introduces new methods and hypothesis tests for analyzing such trees.

Contribution

It presents novel methods for identifying edges in the Fréchet mean, explores the impact of stickiness on asymptotics, and develops hypothesis tests for tree data with complex topologies.

Findings

New algorithms for edge identification in Fréchet means

Demonstration of stickiness effects in biological and medical data

Hypothesis tests robust to the presence of stickiness

Abstract

Samples of phylogenetic trees arise in a variety of evolutionary and biomedical applications, and the Fr\'echet mean in Billera-Holmes-Vogtmann tree space is a summary tree shown to have advantages over other mean or consensus trees. However, use of the Fr\'echet mean raises computational and statistical issues which we explore in this paper. The Fr\'echet sample mean is known often to contain fewer internal edges than the trees in the sample, and in this circumstance calculating the mean by iterative schemes can be problematic due to slow convergence. We present new methods for identifying edges which must lie in the Fr\'echet sample mean and apply these to a data set of gene trees relating organisms from the apicomplexa which cause a variety of parasitic infections. When a sample of trees contains a significant level of heterogeneity in the branching patterns, or topologies, displayed by the trees then the Fr\'echet mean is often a star tree, lacking any internal edges. Not only in this situation, the population Fr\'echet mean is affected by a non-Euclidean phenomenon called stickness which impacts upon asymptotics, and we examine two data sets for which the mean tree is a star tree. The first consists of trees representing the physical shape of artery structures in a sample of medical images of human brains in which the branching patterns are very diverse. The second consists of gene trees from a population of baboons in which there is evidence of substantial hybridization. We develop hypothesis tests which work in the presence of stickiness. The first is a test for the presence of a given edge in the Fr\'echet population mean; the second is a two-sample test for differences in two distributions which share the same sticky population mean.