Data from: Genomic analyses of three malaria vectors reveals extensive shared polymorphism but contrasting population histories

Anopheles gambiae s.l. are important malaria vectors, but little is known about their genomic variation in the wild. Here we present inter- and intra- species analysis of genome-wide RADseq data, in three Anopheles gambiae s.l. species collected from East Africa. The mosquitoes fall into three genotypic clusters representing described species (An. gambiae, An. arabiensis, and An. merus) with no evidence of cryptic breeding units. An. merus is the most divergent of the three species, supporting a recent new phylogeny based on chromosomal inversions. Even though the species clusters are well separated, there is extensive shared polymorphism, particularly between An. gambiae and An. arabiensis. Divergence between An. gambiae and An. arabiensis does not vary across the autosomes, but is higher in X-linked inversions than elsewhere on X or on the autosomes, consistent with the suggestion that this inversion (or a gene within it) is important in reproductive isolation between the species. The 2La/2L+a inversion shows no more evidence of introgression between An. gambiae and An. arabiensis than the rest of the autosomes. Population differentiation within An. gambiae and An. arabiensis is weak over ~190-270km, implying no strong barriers to dispersal. Analysis of Tajima's D and the allele frequency spectrum is consistent with modest population increases in An. arabiensis and An. merus, but a more complex demographic history of expansion followed by contraction in An. gambiae. Although they are less than 200km apart, the two An. gambiae populations show evidence of different demographic histories.广义冈比亚按蚊（Anopheles gambiae sensu lato, An. gambiae s.l.）是一类重要的疟疾传播媒介，但其野生种群的基因组变异特征尚未得到充分研究。本研究针对从东非采集的3种广义冈比亚按蚊物种，开展了全基因组限制性位点相关DNA测序（Restriction-site Associated DNA sequencing, RADseq）数据的种间与种内分析。所采集的蚊虫可划分为3个基因型聚类，分别对应已正式描述的3个物种：冈比亚按蚊（An. gambiae）、阿拉伯按蚊（An. arabiensis）与迷走按蚊（An. merus），未发现存在隐蔽繁殖单元的证据。其中迷走按蚊是3个物种中分化程度最高的类群，这一结果支持了近期基于染色体倒位构建的新系统发育框架。尽管各物种聚类间界限清晰，但存在广泛的共享多态性，尤以冈比亚按蚊与阿拉伯按蚊之间最为显著。冈比亚按蚊与阿拉伯按蚊的基因组分化程度在常染色体上无显著差异，但X染色体连锁的倒位区域的分化水平显著高于X染色体其余区域或常染色体区域，这与“该倒位（或其内部的功能基因）在物种间生殖隔离中发挥关键作用”的推测相一致。2La/2L+a染色体倒位在冈比亚按蚊与阿拉伯按蚊之间的基因渐渗证据，并未显著多于其余常染色体区域。在约190~270公里的地理尺度下，冈比亚按蚊与阿拉伯按蚊内部的种群分化程度均较弱，表明二者不存在较强的种群扩散障碍。对Tajima's D检验与等位基因频率谱的分析结果显示，阿拉伯按蚊与迷走按蚊的种群规模呈现适度扩张，而冈比亚按蚊的种群历史更为复杂，表现为扩张后发生收缩的动态过程。尽管两个冈比亚按蚊种群的地理间距不足200公里，但二者却展现出了截然不同的种群历史特征。