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 similitudes between the selective forces acting upon the coding and non-coding regions of five different sets of genes defined according to functional and evolutionary criteria: i) two reference gene sets presenting accelerated and slow rates of protein evolution (the Complement and Actin pathways), ii) a set of genes with evidence of accelerated evolution in at least one of their introns; and iii) 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 DFE-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 genomics elements (UTRs, promoters and conserved non-coding sequences (CNS)). Our results suggest that (i) DFE-alpha method successfully helps distinguishing different scenarios of accelerated divergence (adaptation or relaxed selective constraints); and (ii) the adaptive history of coding and non-coding sequences within the gene sets analyzed may transcur independently.