Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Détails

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Etat: Public
Version: Final published version
ID Serval
serval:BIB_D31F50F1E1CF
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
Périodique
Genome Biology and Evolution
Auteur(s)
Boeckmann B., Marcet-Houben M., Rees J.A., Forslund K., Huerta-Cepas J., Muffato M., Yilmaz P., Xenarios I., Bork P., Lewis S.E., Gabaldón T.
Collaborateur(s)
Quest for Orthologs Species Tree Working Group
ISSN
1759-6653 (Electronic)
ISSN-L
1759-6653
Statut éditorial
Publié
Date de publication
2015
Peer-reviewed
Oui
Volume
7
Numéro
7
Pages
1988-1999
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Résumé
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.
Mots-clé
Tree of Life, species tree, gene tree support
Pubmed
Web of science
Open Access
Oui
Création de la notice
20/08/2015 12:15
Dernière modification de la notice
20/08/2019 15:53
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