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Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

Brigitte Boeckmann, David Dylus, Sebastien Moretti, Adrian Altenhoff, Clément-Marie Train, Evgenia Kriventseva, Lydie Bougueleret, Ioannis Xenarios, Eyal Privman, Toni Gabaldon, Christophe Dessimoz
doi: https://doi.org/10.1101/181966
Brigitte Boeckmann
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
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David Dylus
2Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
3Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
4SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Sebastien Moretti
5Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
6Evolutionary Bioinformatics group, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Adrian Altenhoff
7Department of Computer Science, ETH Zurich, Zurich, Switzerland
8SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
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Clément-Marie Train
2Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
4SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Evgenia Kriventseva
9Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
10SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
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Lydie Bougueleret
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
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Ioannis Xenarios
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
5Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
11University of Geneva, Department of Biochemistry, Geneva, Switzerland
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Eyal Privman
12Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
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Toni Gabaldon
13Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology1, Barcelona, Spain.
14Universitat Pompeu Fabra (UPF), Barcelona, Spain
15Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Christophe Dessimoz
2Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
3Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
4SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
16Department of Genetics Evolution and Environment, University College London, London, United Kingdom
17Department of Computer Science, University College London, London, United Kingdom
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Abstract

Medium to large phylogenetic gene trees constructed from datasets of different species density and taxonomic range are rarely topologically consistent because of missing phylogenetic signal, non-phylogenetic signal and error. In this study, we first use simulations to show that taxon sampling unequally affects nodes in a gene tree, which likely contributes to controversial conclusions from taxon sampling experiments and contradicting species phylogenies such as for the boreoeutherians. Hence, because it is unlikely that a large gene tree can be reconstructed correctly based on a single optimized dataset, we take a two-step approach for the construction of model gene trees. First, stable and unstable clades are identified by comparing phylogenetic trees inferred from multiple datasets and data types (nucleotide, amino acid, codon) from the same gene family. Subsequently, data subsets are optimized for the analysis of individual uncertain clades. Results are summarized in form of a model tree that illustrates the evolutionary relationship of gene loci. A case study shows how a seemingly complex gene phylogeny becomes increasingly consistent with the reference species tree by attentive taxon sampling and subtree analysis. The procedure is progressively introduced to SwissTree (http://swisstree.vital-it.ch), a resource of high confidence model gene (locus) trees. Finally we demonstrate the usefulness of SwissTree for orthology benchmarking.

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Posted September 05, 2017.
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Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree
Brigitte Boeckmann, David Dylus, Sebastien Moretti, Adrian Altenhoff, Clément-Marie Train, Evgenia Kriventseva, Lydie Bougueleret, Ioannis Xenarios, Eyal Privman, Toni Gabaldon, Christophe Dessimoz
bioRxiv 181966; doi: https://doi.org/10.1101/181966
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Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree
Brigitte Boeckmann, David Dylus, Sebastien Moretti, Adrian Altenhoff, Clément-Marie Train, Evgenia Kriventseva, Lydie Bougueleret, Ioannis Xenarios, Eyal Privman, Toni Gabaldon, Christophe Dessimoz
bioRxiv 181966; doi: https://doi.org/10.1101/181966

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