Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements.
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.
Affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain.Show MeSH
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Mentions: A complete list of genes included in each of the five datasets under study is presented in supplementary table S2, Supplementary Material online. Their corresponding CDS, introns, and regulatory regions were specifically sequenced with an Illumina Hiseq2000 instrument after enrichment with two custom Agilent SureSelect kits in 20 central chimpanzee individuals (supplementary table S1, Supplementary Material online) to an average depth of 72X (see Materials and Methods and supplementary tables S3 and S4, Supplementary Material online). A total of 79,650 SNPs (with a Ti/Tv ratio = 2.29) were identified in a total callable length of 8,599,335 bp (see Materials and Methods). Next, we calculated measures of polymorphism and human–chimpanzee divergence for all five-gene datasets and five differentiated genomic regions (fig. 1 and supplementary table S6, Supplementary Material online): CDS, introns, promoters, CNC, and UTRs.Fig. 1.—
Affiliation: Departament de Ciències Experimentals i la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Barcelona, Spain.