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Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements

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dc.contributor.author Santpere Baró, Gabriel, 1981-
dc.contributor.author Carnero-Montoro, Elena, 1985-
dc.contributor.author Petit, Natalia
dc.contributor.author Serra, François
dc.contributor.author Hvilsom, Christina
dc.contributor.author Rambla de Argila, Jordi
dc.contributor.author Heredia Genestar, José María, 1985-
dc.contributor.author Halligan, Daniel L.
dc.contributor.author Dopazo, Hernán
dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-
dc.contributor.author Bosch Fusté, Elena
dc.date.accessioned 2015-11-12T14:47:18Z
dc.date.available 2015-11-12T14:47:18Z
dc.date.issued 2015
dc.identifier.citation Santpere G, Carnero-Montoro E, Petit N, Serra F, Hvilsom C, Rambla J et al. Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements. Genome Biol Evol. 2015;7(6):1490-505. DOI: 10.1093/gbe/evv082
dc.identifier.issn 1759-6653
dc.identifier.uri http://hdl.handle.net/10230/25071
dc.description.abstract We set out to investigate potential differences and similarities between the selective forces acting upon the coding and noncoding regions of five different sets of genes defined according to functional and evolutionary criteria: 1) two reference gene sets presenting accelerated and slow rates of protein evolution (the Complement and Actin pathways); 2) a set of genes with evidence of accelerated evolution in at least one of their introns; and 3) two gene sets related to neurological function (Parkinson's and Alzheimer's diseases). To that effect, we combine human-chimpanzee divergence patterns with polymorphism data obtained from target resequencing 20 central chimpanzees, our closest relatives with largest long-term effective population size. By using the distribution of fitness effect-alpha extension of the McDonald-Kreitman test, we reproduce inferences of rates of evolution previously based only on divergence data on both coding and intronic sequences and also obtain inferences for other classes of genomic elements (untranslated regions, promoters, and conserved noncoding sequences). Our results suggest that 1) the distribution of fitness effect-alpha method successfully helps distinguishing different scenarios of accelerated divergence (adaptation or relaxed selective constraints) and 2) the adaptive history of coding and noncoding sequences within the gene sets analyzed is decoupled.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Genome biology and evolution. 2015;7(6):1490-505
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 License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Alzheimer
dc.subject.other Parkinson
dc.subject.other Ximpanzés -- Genètica
dc.subject.other Parkinson, Malaltia de -- Aspectes genètics
dc.subject.other Alzheimer, Malaltia d' -- Aspectes genètics
dc.title Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/gbe/evv082
dc.subject.keyword Chimpanzee
dc.subject.keyword Biochemical pathways
dc.subject.keyword Natural selection
dc.subject.keyword Distribution of fitness effects
dc.subject.keyword Fraction of adaptive subsubstitution (a) and adaptive substitution rate (oa)
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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