New measures of topological stability in phylogenetic trees - Taking taxon composition into account.

Dirk Krüger,Andrea Gargas

doi:10.6026/97320630001327

Abstract

In phylogenetic trees the addition and removal of taxa has large effects on tree topology, hence measures of branch support and tree stability should account for taxonomic composition. Currently no comprehensive system of composition-dependent parameters exists in any cladistic or phenetic strategy. We introduce several values and indices based on a modification of the original jackknife resampling. Their advantage is a complete evaluation and optimization of taxon composition in phylogenetic data. While related to the Jackknife Monophyly Index (JMI), our system of support measures expands beyond parsimony analyses, and includes indices estimating support for the entire phylogenetic tree based on individual branch supports.

Highlights

Phylogenetics relies on statistical measures of tree robustness, branching topology, and of the data consistency
The scores where converted to distance values by dividing BLAST scores by the maximum BLAST score in the matrix, and subtracting that value from 1
The introduced measures of tree support are related to Jackknifing across taxa (JAT)

Summary

Background

Phylogenetics relies on statistical measures of tree robustness, branching topology, and of the data consistency. [10] Given that taxon sampling is important, measures of branch stability should include this aspect as well as those relying on character resampling This has been taken up by Siddall [11] who invented a parameter called Jackknife Monophyly Index (JMI). Siddall’s estimator was introduced for parsimony analyses We take his approach a step further, which brings about a family of new values of support for tree branches, and overall tree stability. The JAT values are In large data sets, neither increasing taxon number nor gene assigned on the corresponding branches of the total number [8] may allow inference of the true tree, tree solution of the data set, the one where all taxa are so that researchers will still have to rely on resampling included. Support and the JAG support of a given internal branch, with iJATxJAG the overall support index of the total tree

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