A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations

We report a study of genome-wide, dense SNP (∼ 900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasi...

Full description

Saved in:
Bibliographic Details
Published in:PLoS genetics 2015-03, Vol.11 (3), p.e1005052-e1005052
Main Authors: Chimusa, Emile R, Meintjies, Ayton, Tchanga, Milaine, Mulder, Nicola, Seoighe, Cathal, Seioghe, Cathal, Soodyall, Himla, Ramesar, Rajkumar
Format: Article
Language:English
Subjects:
Africa, Southern
Biodiversity
Disease
DNA Copy Number Variations - genetics
Gene loci
Genealogy
Genetic diversity
Genetic recombination
Genetic Variation
Genetics, Population
Genome, Human
Genome-Wide Association Study
Genomes
Genotype & phenotype
Haplotypes
Haplotypes - genetics
HIV
Human immunodeficiency virus
Humans
Identification and classification
Influenza
Linkage Disequilibrium
Migration
Mitochondrial DNA
Polymorphism, Single Nucleotide - genetics
Population
Population genetics
Recombination, Genetic
Selection, Genetic
Single nucleotide polymorphisms
Studies
Tuberculosis
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:We report a study of genome-wide, dense SNP (∼ 900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1005052