Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
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.
Type
Journal articleSubject
1000 Genomes Project ConsortiumHumans
Sequence Analysis, DNA
Gene Frequency
Genetic Drift
Polymorphism, Single Nucleotide
Genome, Human
INDEL Mutation
Selection, Genetic
Permalink
https://hdl.handle.net/10161/19161Published Version (Please cite this version)
10.1186/gb-2014-15-6-r88Publication Info
Colonna, Vincenza; Ayub, Qasim; Chen, Yuan; Pagani, Luca; Luisi, Pierre; Pybus, Marc;
... McVean, Gil A (2014). Human genomic regions with exceptionally high levels of population differentiation
identified from 911 whole-genome sequences. Genome biology, 15(6). pp. R88. 10.1186/gb-2014-15-6-r88. Retrieved from https://hdl.handle.net/10161/19161.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
Collections
More Info
Show full item record
Articles written by Duke faculty are made available through the campus open access policy. For more information see: Duke Open Access Policy
Rights for Collection: Scholarly Articles
Works are deposited here by their authors, and represent their research and opinions, not that of Duke University. Some materials and descriptions may include offensive content. More info
Related items
Showing items related by title, author, creator, and subject.
-
2011 18 August Mark Guyer-Jane Peterson interview
Unknown author (2011-08-18)Mark Guyer and Jane Peterson, in-person interview with Kathryn Maxson and Robert Cook-Deegan, conducted in Rockville, MD (NIH campus), 18 August 2011. Mark Guyer and Jane Peterson were grants program officers at the NIH ... -
A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh, Kerstin; Garber, Manuel; Zuk, Or; Lin, Michael F; Parker, Brian J; Washietl, Stefan; Kheradpour, Pouya; ... (89 authors) (Nature, 2011-10-12)The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome ... -
An Exploration into Fern Genome Space.
Wolf, PG; Sessa, EB; Marchant, DB; Li, F; Rothfels, CJ; Sigel, EM; Gitzendanner, MA; ... (10 authors) (Genome Biol Evol, 2015-08-26)Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, ...