Quest for orthologs entails quest for tree of life: in search of the gene stream

Boeckmann, Brigitte; Marcet Houben, Marina; Rees, Jonathan A.; Forslund, Kristoffer; Huerta Cepas, Jaime; Muffato, Matthieu; Yilmaz, Pelin; Xenarios, Ioannis; Bork, Peer; Lewis, Suzanna E.; Gabaldón Estevan, Juan Antonio, 1973-; Quest for Orthologs Species Tree Working Group

Quest for orthologs entails quest for tree of life: in search of the gene stream

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dc.contributor.author Boeckmann, Brigitteca
dc.contributor.author Marcet Houben, Marinaca
dc.contributor.author Rees, Jonathan A.ca
dc.contributor.author Forslund, Kristofferca
dc.contributor.author Huerta Cepas, Jaimeca
dc.contributor.author Muffato, Matthieuca
dc.contributor.author Yilmaz, Pelinca
dc.contributor.author Xenarios, Ioannisca
dc.contributor.author Bork, Peerca
dc.contributor.author Lewis, Suzanna E.ca
dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
dc.contributor.author Quest for Orthologs Species Tree Working Groupca
dc.date.accessioned 2015-11-12T15:27:54Z
dc.date.available 2015-11-12T15:27:54Z
dc.date.issued 2015
dc.description.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.ca
dc.description.sponsorship This work was supported by the Swiss Federal Government through the Federal Office of Education and/nScience (B.B.). Funding for open access charge: Swiss Institute of Bioinformatics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. T.G. group research is funded in part by a grant from the Spanish ministry of Economy and Competitiveness (BIO2012-37161), a Grant from the Qatar National Research Fund (NPRP 5-298-3-086), and a grant from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC (grant agreement no. ERC-2012-StG-310325). M.M. acknowledges support from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory.en
dc.format.mimetype application/pdfca
dc.identifier.citation Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M et al. Quest for orthologs entails quest for tree of life: in search of the gene stream. Genome Biol Evol. 2015;7(7):1988-99. DOI: 10.1093/gbe/evv121ca
dc.identifier.doi http://dx.doi.org/10.1093/gbe/evv121
dc.identifier.issn 1759-6653
dc.identifier.uri http://hdl.handle.net/10230/25073
dc.language.iso engca
dc.publisher Oxford University Pressca
dc.relation.ispartof Genome biology and evolution. 2015;7(7):1988-99
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/310325
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2012-37161
dc.rights © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.ca
dc.rights.accessRights info:eu-repo/semantics/openAccessca
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/ca
dc.subject.keyword Tree of Life
dc.subject.keyword Species tree
dc.subject.keyword Gene tree support
dc.subject.other Evolució (Biologia)ca
dc.subject.other Genèticaca
dc.title Quest for orthologs entails quest for tree of life: in search of the gene streamca
dc.type info:eu-repo/semantics/articleca
dc.type.version info:eu-repo/semantics/publishedVersionca

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