ArticleMalaria journal2016
Exceptionally long-range haplotypes in Plasmodium falciparum chromosome 6 maintained in an endemic African population.
Article in Malaria journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Low nucleotide diversity of the Plasmodium falciparum AP2-EXP2 gene among clinical samples from Ghana.Parasites & vectors · 2024Article
- A paradoxical population structure ofbioRxiv : the preprint server for biology · 2023Article
- Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species.PLoS genetics · 2022Article
- Order within chaos: Harnessing Plasmodium falciparum var gene extreme polymorphism for malaria epidemiology.PLoS genetics · 2021Article
- Evolutionary analysis of the most polymorphic gene family inWellcome open research · 2019Article
- Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development.Scientific reports · 2018Article
- Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia.Scientific reports · 2018Article
- Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens.PLoS genetics · 2018Article
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Authors and funding
8 authors.
Funding
Abstract
backgroundPrevious genome-wide analyses of single nucleotide variation in Plasmodium falciparum identified evidence of an extended haplotype region on chromosome 6 in West Africa, suggesting recent positive selection. Such a pattern is not seen in samples from East Africa or South East Asia, so it could be marking a selective process specific to West Africa. Analyses of the haplotype structure in samples taken at different times could give clues to possible causes of selection.
methodsThis study investigates chromosome 6 extended haplotypes in The Gambia by analysing alleles at multiple microsatellite loci using genome sequence data previously obtained from clinical isolates collected in 2008, followed by genotyping of 13 loci in 439 isolates from 1984, 1991, 2008 and 2014. Temporal changes in haplotype structure and frequencies were determined.
resultsA region of high linkage disequilibrium spanning over 170 kilobases (kb) was identified with both NGS and laboratory determined microsatellite alleles. Multiple long haplotypes were found in all temporal populations from The Gambia. Two of the haplotypes were detected in samples from 1984 and 1991. The frequency of long-range haplotypes increased in 2008 and 2014 populations. There was higher Fst between older and more recent populations at loci in proximity to genes involved in drug metabolism pathways.
conclusionsThe occurrence of several long haplotypes at intermediate frequencies suggests an unusual mode of selection in chromosome 6, possibly combined with recombination suppression on specific haplotypes. Such selection apparently occurred before the emergence of known anti-malarial drug resistance alleles, and could be due to effects of other drugs or unknown processes that have long been operating in this endemic region.
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