Journal article
Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
Genome biology, Vol.15(6), pp.R88-R88
2014
DOI: 10.1186/gb-2014-15-6-r88
PMCID: PMC4197830
PMID: 24980144
Abstract
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 with 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 identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.
Details
- Title: Subtitle
- Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
- Creators
- Vincenza Colonna - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UKQasim Ayub - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UKYuan Chen - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UKLuca Pagani - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UKPierre Luisi - Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia 08003, SpainMarc Pybus - Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia 08003, SpainErik Garrison - Department of Biology, Boston College, Chestnut Hill, MA 02467, USAYali Xue - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UKChris Tyler-Smith - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK1000 Genomes Project Consortium
- Contributors
- Jacob J Michaelson (Contributor) - University of Iowa, Roy J. Carver Department of Biomedical Engineering
- Resource Type
- Journal article
- Publication Details
- Genome biology, Vol.15(6), pp.R88-R88
- DOI
- 10.1186/gb-2014-15-6-r88
- PMID
- 24980144
- PMCID
- PMC4197830
- NLM abbreviation
- Genome Biol
- ISSN
- 1474-7596
- eISSN
- 1474-760X
- Publisher
- BioMed Central
- Language
- English
- Date published
- 2014
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Communication Sciences and Disorders; Psychiatry; Iowa Neuroscience Institute
- Record Identifier
- 9984070832002771
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