RT Journal Article
SR Electronic
T1 Human genomic regions with exceptionally high or low levels of population differentiation identified from 911 whole-genome sequences
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 005462
DO 10.1101/005462
A1 Vincenza Colonna
A1 Qasim Ayub
A1 Yuan Chen
A1 Luca Pagani
A1 Pierre Luisi
A1 Marc Pybus
A1 Erik Garrison
A1 Yali Xue
A1 Chris Tyler-Smith
A1 The 1000 Genomes Project Consortium
YR 2014
UL http://biorxiv.org/content/early/2014/05/23/005462.abstract
AB Background Population differentiation has proved to be effective for identifying loci under geographically-localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes.Results We demonstrate that while sites of low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively.Conclusions We have identified known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.