A phylogenomics approach for selecting robust sets of phylogenetic markers

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• dc.contributor.author Capella Gutiérrez, Salvador Jesús, 1985-
• dc.contributor.author Kauff, Frank
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
• dc.date.accessioned 2023-11-21T06:47:26Z
• dc.date.available 2023-11-21T06:47:26Z
• dc.date.issued 2014
• dc.description Includes supplementary materials for the online appendix.
• dc.description.abstract Reconstructing the evolutionary relationships of species is a major goal in biology. Despite the increasing number of completely sequenced genomes, a large number of phylogenetic projects rely on targeted sequencing and analysis of a relatively small sample of marker genes. The selection of these phylogenetic markers should ideally be based on accurate predictions of their combined, rather than individual, potential to accurately resolve the phylogeny of interest. Here we present and validate a new phylogenomics strategy to efficiently select a minimal set of stable markers able to reconstruct the underlying species phylogeny. In contrast to previous approaches, our methodology does not only rely on the ability of individual genes to reconstruct a known phylogeny, but it also explores the combined power of sets of concatenated genes to accurately infer phylogenetic relationships of species not previously analyzed. We applied our approach to two broad sets of cyanobacterial and ascomycetous fungal species, and provide two minimal sets of six and four genes, respectively, necessary to fully resolve the target phylogenies. This approach paves the way for the informed selection of phylogenetic markers in the effort of reconstructing the tree of life.
• dc.description.sponsorship Spanish ministry of science and innovation [BIO2012-37161 towards T.G. group research (in part)] and Qatar National Research Fund [NPRP 5-298-3-086]. Funding for open access charge: Core funding from the group of the corresponding author.
• dc.format.mimetype application/pdf
• dc.identifier.citation Capella-Gutierrez S, Kauff F, Gabaldón T. A phylogenomics approach for selecting robust sets of phylogenetic markers. Nucleic Acids Research. 2014 Apr 1;42(7):e54. DOI: 10.1093/nar/gku071
• dc.identifier.doi http://dx.doi.org/10.1093/nar/gku071
• dc.identifier.issn 0305-1048
• dc.identifier.uri http://hdl.handle.net/10230/58335
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Nucleic Acids Research. 2014 Apr 1;42(7):e54
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2012-37161
• dc.rights © The Author(s) 2014. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/3.0/
• dc.subject.other Biologia
• dc.subject.other Genomes
• dc.subject.other Filogènia -- Aspectes moleculars
• dc.title A phylogenomics approach for selecting robust sets of phylogenetic markers
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion