Data from: SNP genotyping identifies new signatures of selection in a deep sample of West African P. falciparum malaria parasites

We used a high density SNP array to genotype 75 P. falciparum isolates recently collected from Senegal and The Gambia in order to search for signals of selection in this malaria endemic region. We found little geographic or temporal stratification of the genetic diversity among the sampled parasites. Through application of the iHS and REHH haplotype-based tests for positive selection, we found evidence of recent selective sweeps at a known drug resistance locus, at several known antigenic loci, and at several genomic regions not previously identified as sites of recent selection. We discuss the value of deep population-specific genomic analyses for identifying selection signals within sampled endemic populations of parasites, which may correspond to local selection pressures such as distinctive therapeutic regimes or mosquito vectors. senegambia_genotype_dataPlasmodium falciparum isolates from Senegal and The Gambia, some DNA directly drawn and some from culture-adapted parasites; only single infections included. SNP calling was as described in (Van Tyne, et al. 2011): Parasite DNA was hybridized to a P. falciparum Affymetrix array containing 74,656 SNP markers and genotypes called using the BRLMM-P algorithm. SNPs were validated by comparing array genotypes with Sanger sequencing genotypes for 17 reference strains (Van Tyne, et al. 2011); perfect concordance was required, as was a minimum 80% call rate. Genomic positions and translations are based on the PlasmoDB v5.0 assembly and annotation.