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.

本研究采用高密度单核苷酸多态性阵列（SNP array）对近期从塞内加尔及冈比亚采集的75株恶性疟原虫（P. falciparum）分离株进行基因分型，以探寻该疟疾流行区域内的选择信号。研究发现，所采样的疟原虫群体的遗传多样性几乎不存在显著的地理或时间分层现象。通过应用基于单倍型的整合单倍型得分（iHS）与相对延伸单倍型纯合性（REHH）正向选择检验方法，我们在已知的耐药基因座、多个已知抗原基因座以及此前未被鉴定为近期选择位点的数个基因组区域中，发现了近期发生选择性清除事件的证据。本研究还探讨了群体特异性深度基因组分析的应用价值，该方法可用于在所采样的寄生虫流行群体中识别选择信号，而此类信号或与当地特有的选择压力相关，例如差异化的治疗方案或蚊虫媒介类型。