title: Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements.
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.
authors.affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Santpere
authors.affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain.
authors.forename: Elena
authors.initials: E
authors.lastname: Carnero-Montoro
authors.affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain.
authors.forename: Natalia
authors.initials: N
authors.lastname: Petit
authors.affiliation: Structural Genomics Team, Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain.
authors.forename: François
authors.initials: F
authors.lastname: Serra
authors.affiliation: Research and Conservation, Copenhagen Zoo, Frederiksberg, Denmark.
authors.forename: Christina
authors.initials: C
authors.lastname: Hvilsom
authors.affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Rambla
authors.affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain.
authors.forename: Jose Maria
authors.initials: JM
authors.lastname: Heredia-Genestar
authors.affiliation: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Halligan
authors.affiliation: Biomedical Genomics & Evolution Laboratory, Departamento de Ecología, Genética y Evolución, IEGEBA (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina.
authors.forename: Hernan
authors.initials: H
authors.lastname: Dopazo
authors.affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain National Institute for Bioinformatics (INB), PRBB, Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), PRBB, Barcelona, Spain Center for Genomic Regulation (CRG), PRBB, Barcelona, Spain arcadi.navarro@upf.edu elena.bosch@upf.edu.
authors.forename: Arcadi
authors.initials: A
authors.lastname: Navarro
authors.affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain arcadi.navarro@upf.edu elena.bosch@upf.edu.
authors.forename: Elena
authors.initials: E
authors.lastname: Bosch
mesh_terms: D000199:Actins / Q000235:genetics; D000818:Animals; D003165:Complement System Proteins / Q000235:genetics; D019143:Evolution, Molecular; D005796:Genes; D006801:Humans; D007438:Introns; D009154:Mutation; D016366:Open Reading Frames; D002679:Pan troglodytes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D012641:Selection, Genetic; D020506:Untranslated Regions
chemical_list: D000199:Actins; D020506:Untranslated Regions; D003165:Complement System Proteins
keywords: Alzheimer; Parkinson; biochemical pathways; chimpanzee; distribution of fitness effects; fraction of adaptive substitution (α) and adaptive substitution rate (ωα); natural selection