Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements
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 pr...
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todo:paper_17596653_v7_n6_p1490_Santpere2023-10-03T16:32:47Z Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements Santpere, G. Carnero-Montoro, E. Petit, N. Serra, F. Hvilsom, C. Rambla, J. Heredia-Genestar, J.M. Halligan, D.L. Dopazo, H. Navarro, A. Bosch, E. Alzheimer Biochemical pathways Chimpanzee Distribution of fitness effects Fraction of adaptive substitution (α) and adaptive substitution rate (ωa) Natural selection Parkinson actin complement untranslated region animal gene genetic selection genetics human intron molecular evolution mutation open reading frame Pan troglodytes promoter region single nucleotide polymorphism untranslated region Actins Animals Complement System Proteins Evolution, Molecular Genes Humans Introns Mutation Open Reading Frames Pan troglodytes Polymorphism, Single Nucleotide Promoter Regions, Genetic Selection, Genetic Untranslated Regions 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. © The Author(s) 2015. Fil:Dopazo, H. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_17596653_v7_n6_p1490_Santpere |
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Universidad de Buenos Aires |
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I-28 |
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R-134 |
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Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Alzheimer Biochemical pathways Chimpanzee Distribution of fitness effects Fraction of adaptive substitution (α) and adaptive substitution rate (ωa) Natural selection Parkinson actin complement untranslated region animal gene genetic selection genetics human intron molecular evolution mutation open reading frame Pan troglodytes promoter region single nucleotide polymorphism untranslated region Actins Animals Complement System Proteins Evolution, Molecular Genes Humans Introns Mutation Open Reading Frames Pan troglodytes Polymorphism, Single Nucleotide Promoter Regions, Genetic Selection, Genetic Untranslated Regions |
| spellingShingle |
Alzheimer Biochemical pathways Chimpanzee Distribution of fitness effects Fraction of adaptive substitution (α) and adaptive substitution rate (ωa) Natural selection Parkinson actin complement untranslated region animal gene genetic selection genetics human intron molecular evolution mutation open reading frame Pan troglodytes promoter region single nucleotide polymorphism untranslated region Actins Animals Complement System Proteins Evolution, Molecular Genes Humans Introns Mutation Open Reading Frames Pan troglodytes Polymorphism, Single Nucleotide Promoter Regions, Genetic Selection, Genetic Untranslated Regions Santpere, G. Carnero-Montoro, E. Petit, N. Serra, F. Hvilsom, C. Rambla, J. Heredia-Genestar, J.M. Halligan, D.L. Dopazo, H. Navarro, A. Bosch, E. Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements |
| topic_facet |
Alzheimer Biochemical pathways Chimpanzee Distribution of fitness effects Fraction of adaptive substitution (α) and adaptive substitution rate (ωa) Natural selection Parkinson actin complement untranslated region animal gene genetic selection genetics human intron molecular evolution mutation open reading frame Pan troglodytes promoter region single nucleotide polymorphism untranslated region Actins Animals Complement System Proteins Evolution, Molecular Genes Humans Introns Mutation Open Reading Frames Pan troglodytes Polymorphism, Single Nucleotide Promoter Regions, Genetic Selection, Genetic Untranslated Regions |
| description |
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. © The Author(s) 2015. |
| format |
JOUR |
| author |
Santpere, G. Carnero-Montoro, E. Petit, N. Serra, F. Hvilsom, C. Rambla, J. Heredia-Genestar, J.M. Halligan, D.L. Dopazo, H. Navarro, A. Bosch, E. |
| author_facet |
Santpere, G. Carnero-Montoro, E. Petit, N. Serra, F. Hvilsom, C. Rambla, J. Heredia-Genestar, J.M. Halligan, D.L. Dopazo, H. Navarro, A. Bosch, E. |
| author_sort |
Santpere, G. |
| title |
Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements |
| title_short |
Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements |
| title_full |
Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements |
| title_fullStr |
Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements |
| title_full_unstemmed |
Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements |
| title_sort |
analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements |
| url |
http://hdl.handle.net/20.500.12110/paper_17596653_v7_n6_p1490_Santpere |
| work_keys_str_mv |
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