Accelerated exon evolution within primate segmental duplications.
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.
Belen
B
Lorente-Galdos
Jonathan
J
Bleyhl
Gabriel
G
Santpere
Laura
L
Vives
Oscar
O
Ramírez
Jessica
J
Hernandez
Roger
R
Anglada
Gregory M
GM
Cooper
Arcadi
A
Navarro
Evan E
EE
Eichler
Tomas
T
Marques-Bonet
D000818:Animals; D019143:Evolution, Molecular; D005091:Exons; D020440:Gene Duplication; D015894:Genome, Human; D006801:Humans; D011323:Primates / Q000235:genetics*