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Accelerated exon evolution within primate segmental duplications

Belen Lorente-Galdos12, Jonathan Bleyhl3, Gabriel Santpere1, Laura Vives3, Oscar Ramírez1, Jessica Hernandez1, Roger Anglada1, Gregory M Cooper3, Arcadi Navarro124, Evan E Eichler35 and Tomas Marques-Bonet14*

Author affiliations

1 IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain

2 National Institute for Bioinformatics (INB), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain

3 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA

4 Institucio Catalana de Recerca i Estudis Avançats (ICREA), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain

5 Howard Hughes Medical Institute, Seattle, Washington 98195, USA

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Citation and License

Genome Biology 2013, 14:R9  doi:10.1186/gb-2013-14-1-r9

Published: 29 January 2013

Abstract

Background

The 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.

Results

In 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.

Conclusions

Our 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.