Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

By Nicolas Lartillot, H. Brinkmann, Hervé Philippe. BMC Evolutionary Biology, 2007

595 citations recorded by the source corpus.

BackgroundThanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees. However, high statistical support does not imply that the tree is accurate. Systematic errors, such as the Long Branch Attraction (LBA) artefact, can be misleading, in particular when the taxon sampling is poor, or the outgroup is distant. In an otherwise consistent probabilistic framework, systematic errors in genome-wide analyses can be traced back to model mis-specification problems, which suggests that better models of sequence evolution should be devised, that would be more robust to tree reconstruction artefacts, even under the most challenging conditions.MethodsWe focus on a well characterized LBA artefact analyzed in a previous phylogenomic study of the metazoan tree, in which two fast-evolving animal phyla, nematodes and platyhelminths, emerge either at the base of all other Bilateria, or within protostomes, depending on the outgroup. We use this artefactual result as a case study for comparing the robustness of two alternative models: a standard, site-homogeneous model, based on an empirical matrix of amino-acid replacement (WAG), and a site-heterogeneous mixture model (CAT). In parallel, we propose a posterior predictive test, allowing one to measure how well a model acknowledges sequence saturation.ResultsAdopting a Bayesian framework, we show that the LBA artefact observed under WAG disappears when the site-heterogeneous model CAT is used. Using cross-validation, we further demonstrate that CAT has a better statistical fit than WAG on this data set. Finally, using our statistical goodness-of-fit test, we show that CAT, but not WAG, correctly accounts for the overall level of saturation, and that this is due to a better estimation of site-specific amino-acid preferences.ConclusionThe CAT model appears to be more robust than WAG against LBA artefacts, essentially because it correctly anticipates the high probability of convergences and reversions implied by the small effective size of the amino-acid alphabet at each site of the alignment. More generally, our results provide strong evidence that site-specificities in the substitution process need be accounted for in order to obtain more reliable phylogenetic trees.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2c8718808e5a337cdae9a2e2c5f0c093e7a3d2ec

Citations in the corpus

• Empirical profile mixture models for phylogenetic reconstruction (2008, unknown): “multiple substitutions), making it more robust to phylogenetic artifacts ( Lartillot et al., 2007 ).”
• Detecting and overcoming systematic errors in genome-scale phylogenies. (2007, unknown): “Another kind of model violation that may result in phylogenetic artefacts is the heterogeneity of the amino acid replacement process across sites (Baurain et al., 2006; Koshi and Goldstein, 2001; Lartillot et al., 2006; Lartillot and Philippe, 2004; Pagel and Meade, 2004).”
• Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, unknown): “To explore this on real data, here we present two contrasting examples of suboptimal metazoan phylogenies from the set of proteins previously considered by Lartillot et al. (2007).”
• Taxon sampling and the accuracy of phylogenetic analyses (2008, unknown): “…of model assumptions (e.g., not accurately modeling multiple substitutions), finding a better-fitting model could solve the problem (Olsen, 1987; Whelan & Goldman, 2001; Lartillot & Philippe, 2004; Anderson & Swofford, 2004; Delsuc et al., 2005; Baurain et al., 2007; Lartillot et al., 2007).”
• The Phylogeny and Evolution of Ants (2014, unknown): “…data to reduce the likelihood of phylogenetic artifacts (Lemmon & Lemmon 2013), ( b ) employ models that better capture process heterogeneity (Lartillot et al. 2007, & www annualreviews.org Ant Phylogeny and Evolution 31 Deans 2010), and ( c ) sample a sufficiently representative diversity of…”
• Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1 (2010, unknown): “To address these and other concerns, in the near future we plan to increase taxon sampling in Poales several-fold, and to explore additional analytical techniques (e.g., Lartillot et al., 2007) that may be less sensitive to long-branch attraction.”
• Phylogenomics revives traditional views on deep animal relationships. (2009, unknown): “3, which has been shown in some contexts to be less prone to LBA artifacts than other models [13, 15].”
• PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. (2013, unknown): “…are observed between the trees inferred under homogeneous and mixture models (Supplementary Figs S4 and S5), confirming previous observations collected across several examples of large-scale reconstruction using amino acid data (Lartillot et al. 2007; Philippe et al. 2009, 2011a, 2011b).”