Abstract
BackgroundThe identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodological reliance on accurate gene trees, which are difficult to obtain for duplicated genes.ResultsIn this work, we detected exons with an accumulation of high-quality nucleotide differences between the human assembly and shotgun sequencing reads from single human and macaque individuals. Comparing the observed rates of nucleotide differences between coding exons and their flanking intronic sequences with a likelihood-ratio test, we identified 74 exons with evidence for rapid coding sequence evolution during the evolution of humans and Old World monkeys. Fifty-five percent of rapidly evolving exons were either partially or totally duplicated, which is a significant enrichment of the 6% rate observed across all human coding exons.ConclusionsOur results provide a more comprehensive view of the action of selection upon segmental duplications, which are the most complex regions of our genomes. In light of these findings, we suggest that segmental duplications could be subjected to rapid evolution more frequently than previously thought.
Highlights
The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species
We demonstrate the feasibility of our approach by testing its ability to distinguish between distinct evolutionary signatures in a set of genes whose selective histories have been determined using other methods
Approach We have applied an assembly-free approach for genomewide screening for patterns of rapid evolution on single genes or gene families (Materials and methods; Figure 1)
Summary
The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Segmental duplications (SDs) are highly identical low copy number repeated genomic fragments ranging in size from one to hundreds of kilobases. They are important genomic features in the evolution of primates and humans for several reasons. A mutational active set of duplicated sequences, termed ‘core duplicons’, are enriched for gene sequences and associated with many genomic disorders characterized by recurrent, highly deleterious. Positive selection may outweigh the deleterious effects of duplication events in gene dosage or in creating disease labile genomic regions [16,17,18,19]. The extent of positive selection within duplicated regions remains an open question
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
