title: Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
abstract: Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287) and by Huerta-Cepas et al. (Huerta-Cepas J, Marcet-Houben M, Gabaldon T. 2014. A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:223) Our study reveals that each species tree suggests a different phylogeny: 87 of the 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes, we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species_tree) that can serve different benchmarking purposes.
authors.affiliation: Swiss-Prot, Swiss Institute of Bioinformatics, Geneva, Switzerland brigitte.boeckmann@isb-sib.ch.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Boeckmann
authors.affiliation: Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Marina
authors.initials: M
authors.lastname: Marcet-Houben
authors.affiliation: US National Evolutionary Synthesis Center, Duke University, Durham, NC.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Rees
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Forslund
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Muffato
authors.affiliation: Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
authors.forename: Pelin
authors.initials: P
authors.lastname: Yilmaz
authors.affiliation: Swiss-Prot, Swiss Institute of Bioinformatics, Geneva, Switzerland Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit, University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.affiliation: Genomics Division, Lawrence Berkeley National Lab, Berkeley.
authors.forename: Suzanna E
authors.initials: SE
authors.lastname: Lewis
authors.affiliation: Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats, Barcelona, Spain.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D056890:Eukaryota / Q000145:classification / Q000235:genetics; D005796:Genes; D010802:Phylogeny
keywords: Tree of Life; gene tree support; species tree