title: Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection.
abstract: Assessing the robustness of an inferred phylogeny is an important element of phylogenetics. This is typically done with measures of stabilities at the internal branches and the variation of the positions of the leaf nodes. The bootstrap support for branches in maximum parsimony, distance and maximum likelihood estimation, or posterior probabilities in Bayesian inference, measure the uncertainty about a branch due to the sampling of the sites from genes or sampling genes from genomes. However, these measures do not reveal how taxon sampling affects branch support and the effects of taxon sampling on the estimated phylogeny. An internal branch in a phylogenetic tree can be viewed as a split that separates the taxa into two nonempty complementary subsets. We develop several split-specific measures of stability determined from bootstrap support for quartets. These include BPtaxon_split (average bootstrap percentage [BP] for all quartets involving a taxon within a split), BPsplit (BPtaxon_split averaged over taxa), BPtaxon (BPtaxon_split averaged over splits) and RBIC-taxon (average BP over all splits after removing a taxon). We also develop a pruned-tree distance metric. Application of our measures to empirical and simulated data illustrate that existing measures of overall stability can fail to detect taxa that are the primary source of a split-specific instability. Moreover, we show that the use of many reduced sets of quartets is important in being able to detect the influence of joint sets of taxa rather than individual taxa. These new measures are valuable diagnostic tools to guide taxon sampling in phylogenetic experimental design.
authors: Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Canada. Electronic address: huaichun.wang@dal.ca.
authors: Huai-Chun
authors: HC
authors: Wang
authors: Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Canada.
authors: Edward
authors: E
authors: Susko
authors: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Canada; Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Canada.
authors: Andrew J
authors: AJ
authors: Roger
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D016013:Likelihood Functions; D010802:Phylogeny
keywords: Bootstrap support; Phylogenetic stability; Split; Taxon influence; Taxon sampling