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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.

Santpere G, Carnero-Montoro E, Petit N, Serra F, Hvilsom C, Rambla J, Heredia-Genestar JM, Halligan DL, Dopazo H, Navarro A, Bosch E - Genome Biol Evol (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain.

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Fraction of substitutions due to positive selection: alpha (α) values. Alpha (α) values per genomic element and pathway. Significance values are obtained as explained in the text. Values for the 2.5% and 97.5% thresholds are indicated.
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evv082-F2: Fraction of substitutions due to positive selection: alpha (α) values. Alpha (α) values per genomic element and pathway. Significance values are obtained as explained in the text. Values for the 2.5% and 97.5% thresholds are indicated.

Mentions: We first focused on coding regions of the Complement and the Actin pathway and found them to present significantly higher α and ωα values in Complement (figs. 2 and 3, supplementary table S10, Supplementary Material online). The use of each pathway’s 4-fold sites as neutral reference rendered consistent results with the use of the concatenation of all 4-fold sites: The complement pathway always presents significantly higher values of α and ωα, with the single exception of the comparison of ωα between the Actin and Complement pathways, which is not significant. However, the confidence intervals for both estimates when using this neutral reference were in general wider, probably due to the lower number of sites. Therefore, adding to our previous biological knowledge on these pathways, the results of GSSA enrichment analysis and our estimates on adaptive evolution, in what follows we will consider the Actin and Complement pathways as reference sets for purifying and positive selection, using them to benchmark the CDS of other gene sets.Fig. 2.—


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 JM, Halligan DL, Dopazo H, Navarro A, Bosch E - Genome Biol Evol (2015)

Fraction of substitutions due to positive selection: alpha (α) values. Alpha (α) values per genomic element and pathway. Significance values are obtained as explained in the text. Values for the 2.5% and 97.5% thresholds are indicated.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494068&req=5

evv082-F2: Fraction of substitutions due to positive selection: alpha (α) values. Alpha (α) values per genomic element and pathway. Significance values are obtained as explained in the text. Values for the 2.5% and 97.5% thresholds are indicated.
Mentions: We first focused on coding regions of the Complement and the Actin pathway and found them to present significantly higher α and ωα values in Complement (figs. 2 and 3, supplementary table S10, Supplementary Material online). The use of each pathway’s 4-fold sites as neutral reference rendered consistent results with the use of the concatenation of all 4-fold sites: The complement pathway always presents significantly higher values of α and ωα, with the single exception of the comparison of ωα between the Actin and Complement pathways, which is not significant. However, the confidence intervals for both estimates when using this neutral reference were in general wider, probably due to the lower number of sites. Therefore, adding to our previous biological knowledge on these pathways, the results of GSSA enrichment analysis and our estimates on adaptive evolution, in what follows we will consider the Actin and Complement pathways as reference sets for purifying and positive selection, using them to benchmark the CDS of other gene sets.Fig. 2.—

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain.

Show MeSH
Related in: MedlinePlus