A simple polytomy resolver for dated phylogenies

Abstract

Summary1. Unresolved nodes in phylogenetic trees (polytomies) have long been recognized for their influences on specific phylogenetic metrics such as topological imbalance measures, diversification rate analysis and measures of phylogenetic diversity. However, no rigorously tested, biologically appropriate method has been proposed for overcoming the effects of this phylogenetic uncertainty. 2. Here, we present a simple approach to polytomy resolution, using biologically relevant models of diversification. Using the powerful and highly customizable phylogenetic inference and analysis software beast and r, we present a semi-automated 'polytomy resolver' capable of providing a distribution of tree topologies and branch lengths under specified biological models. 3. Utilizing both simulated and empirical data sets, we explore the effects and characteristics of this approach on two widely used phylogenetic tree statistics, Pybus' gamma (c) and Colless' normalized tree imbalance (I c ). Using simulated pure birth trees, we find no evidence of bias in either estimate using our resolver. Applying our approach to a recently published Cetacean phylogeny, we observed the expected small positive bias in c and decrease in I c . 4. We further test the effect of polytomy resolution on diversification rate analysis using the Cetacean phylogeny. We demonstrate that using a birth-death model to resolve the Cetacean tree with 20%, 40% and 60% of random nodes collapsed to polytomies gave qualitatively similar patterns regarding the tempo and mode of diversification as the same analyses on the original, fully resolved phylogeny. 5. Finally, we applied the birth-death polytomy resolution approach to a large (>5000 tips), but unresolved, supertree of extant mammals. We report a distribution of fully resolved model-based trees, which should be useful for many future analysis of the mammalian supertree.

Ecology and mode-of-life explain lifespan variation in birds and mammals

“…We extracted 500 bird trees from the posterior distribution of a recent bird phylogeny generated under a Bayesian inference framework [31], and used the 10 000 mammal trees constructed by Kuhn et al [32]. Each individual mammal tree comprises one resolution of the polytomies of a previously published supertree [33].…”

Investing in evolutionary history: implementing a phylogenetic approach for mammal conservation

“…For the new list, we calculated ED scores for each of 1000 supertrees, each of which was resolved using Bayesian methods described in Kuhn et al [59]. These fully resolved supertrees represent the pseudo-posterior distribution of the underlying mammalian phylogeny.…”

Eusociality but not fossoriality drives longevity in small mammals

“…To carry out this analysis, I use the same approach as previously [3,4]. I selected a distribution of 25 randomly chosen trees from Kuhn et al [4] and treated them as equivalent to a Bayesian posterior distribution of trees.…”

“…I selected a distribution of 25 randomly chosen trees from Kuhn et al [4] and treated them as equivalent to a Bayesian posterior distribution of trees. I used the data collated by Williams and Shattuck [1] and log 10 transformed both maximum longevity and body mass before mean centring and expressing the data in units of standard deviation.…”