Uncovering Hidden Phylogenetic Consensus

Abstract. Many of the steps in phylogenetic reconstruction can be confounded by “rogue” taxa, taxa that cannot be placed with assurance anywhere within the tree—whose location within the tree, in fact, varies with almost any choice of algorithm or parameters. Phylogenetic consensus methods, in particular, are known to suffer from this problem. In this paper we provide a novel framework in which to define and identify rogue taxa. In this framework, we formulate a bicriterion optimization problem that models the net increase in useful information present in the consensus tree when certain taxa are removed from the input data. We also provide an effective greedy heuristic to identify a subset of rogue taxa and use it in a series of experiments, using both pathological examples described in the literature and a collection of large biological datasets. As the presence of rogue taxa in a set of bootstrap replicates can lead to deceivingly poor support values, we propose a procedure ...

• Type: Conference
• Year: 2010
• Where: ISBRA
• Authors: Nicholas D. Pattengale, Krister M. Swenson, Bernard M. E. Moret
• Keywords: Bioinformatics, Certain Taxa, ISBRA 2010, Phylogenetic Consensus Methods, Rogue Taxa