Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream
| Autor: | 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 |
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| Přispěvatelé: | Quest for Orthologs Species Tree Working Group |
| Rok vydání: | 2015 |
| Předmět: |
0106 biological sciences
Gene tree support 010603 evolutionary biology 01 natural sciences Genome 03 medical and health sciences Tree of Life species tree gene tree support Phylogenetics Genetics Clade Phylogeny Ecology Evolution Behavior and Systematics 030304 developmental biology 0303 health sciences Bacteria biology Phylogenetic tree Eukaryota Ribosomal RNA biology.organism_classification 16S ribosomal RNA Archaea Laurasiatheria Genes Cardiovascular and Metabolic Diseases Evolutionary biology Taxonomy (biology) Species tree Genètica Research Article Evolució (Biologia) |
| Zdroj: | Genome Biology and Evolution Genome Biology and Evolution, vol. 7, no. 7, pp. 1988-1999 Recercat. Dipósit de la Recerca de Catalunya instname |
| ISSN: | 1759-6653 |
| Popis: | 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. 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. |
| Databáze: | OpenAIRE |
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