Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics.

Wasiu A Akanni,Mark Wilkinson,Christopher J Creevey,Davide Pisani,Peter G Foster

doi:10.1098/rsos.140436

Abstract

Since their advent, supertrees have been increasingly used in large-scale evolutionary studies requiring a phylogenetic framework and substantial efforts have been devoted to developing a wide variety of supertree methods (SMs). Recent advances in supertree theory have allowed the implementation of maximum likelihood (ML) and Bayesian SMs, based on using an exponential distribution to model incongruence between input trees and the supertree. Such approaches are expected to have advantages over commonly used non-parametric SMs, e.g. matrix representation with parsimony (MRP). We investigated new implementations of ML and Bayesian SMs and compared these with some currently available alternative approaches. Comparisons include hypothetical examples previously used to investigate biases of SMs with respect to input tree shape and size, and empirical studies based either on trees harvested from the literature or on trees inferred from phylogenomic scale data. Our results provide no evidence of size or shape biases and demonstrate that the Bayesian method is a viable alternative to MRP and other non-parametric methods. Computation of input tree likelihoods allows the adoption of standard tests of tree topologies (e.g. the approximately unbiased test). The Bayesian approach is particularly useful in providing support values for supertree clades in the form of posterior probabilities.

Highlights

Supertrees [1] are phylogenies that are built by combining the information contained in a set of input trees
Wilkinson et al [15] used two conflicting input trees of different shapes to show that matrix representations with parsimony (MRP) and other liberal supertree methods (SMs) suffer from input tree shape biases due to objective functions based on unusual asymmetric measures
The MRP analysis of the same dataset returned 77 parsimonious trees, most similar supertree (MSS) found 42 supertrees, RF found 26 supertrees and in each case the supertrees returned are a subset of the 79 supertrees that minimize the sum of the supertree–input tree RF distances and their strict consensus is identical to the MR(-) supertree

Summary

Introduction

Supertrees [1] are phylogenies that are built by combining the information contained in a set of input trees. Different supertree methods (SMs) offer alternative ways to amalgamate input tree information. Most liberal SMs are somewhat ad hoc and many lack seemingly desirable properties or have seemingly undesirable ones [2,14] including biases with respect to input tree size [6] and shape [15]. These SMs, especially MRP, have been used to build supertrees for many animal, plant and microbial taxa These SMs, especially MRP, have been used to build supertrees for many animal, plant and microbial taxa (e.g. [16,17,18]) either from partially overlapping phylogenies extracted from the literature (e.g. [8,19,20]) or from trees generated de novo including large sets of gene trees in phylogenomic studies (e.g. [10,21,22])

Methods

Results

Discussion

Conclusion