title: Detecting and overcoming systematic errors in genome-scale phylogenies.
abstract: Genome-scale data sets result in an enhanced resolution of the phylogenetic inference by reducing stochastic errors. However, there is also an increase of systematic errors due to model violations, which can lead to erroneous phylogenies. Here, we explore the impact of systematic errors on the resolution of the eukaryotic phylogeny using a data set of 143 nuclear-encoded proteins from 37 species. The initial observation was that, despite the impressive amount of data, some branches had no significant statistical support. To demonstrate that this lack of resolution is due to a mutual annihilation of phylogenetic and nonphylogenetic signals, we created a series of data sets with slightly different taxon sampling. As expected, these data sets yielded strongly supported but mutually exclusive trees, thus confirming the presence of conflicting phylogenetic and nonphylogenetic signals in the original data set. To decide on the correct tree, we applied several methods expected to reduce the impact of some kinds of systematic error. Briefly, we show that (i) removing fast-evolving positions, (ii) recoding amino acids into functional categories, and (iii) using a site-heterogeneous mixture model (CAT) are three effective means of increasing the ratio of phylogenetic to nonphylogenetic signal. Finally, our results allow us to formulate guidelines for detecting and overcoming phylogenetic artefacts in genome-scale phylogenetic analyses.
authors.affiliation: Canadian Institute for Advanced Research, Centre Robert Cedergren, Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec, H3T 1J4, Canada.
authors.forename: Naiara
authors.initials: N
authors.lastname: Rodríguez-Ezpeleta
authors.forename: Henner
authors.initials: H
authors.lastname: Brinkmann
authors.forename: Béatrice
authors.initials: B
authors.lastname: Roure
authors.forename: Nicolas
authors.initials: N
authors.lastname: Lartillot
authors.forename: B Franz
authors.initials: BF
authors.lastname: Lang
authors.forename: Hervé
authors.initials: H
authors.lastname: Philippe
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002965:Classification / Q000379:methods*; D019295:Computational Biology; D019143:Evolution, Molecular; D016678:Genome; D010802:Phylogeny; D025341:Principal Component Analysis; D015983:Selection Bias