Data from: Prominent intra-specific genetic divergence within Anopheles gambiae sibling species triggered by habitat discontinuities across a riverine landscape

The Anopheles gambiae complex of mosquitoes includes malaria vectors at different stages of speciation, whose study enables a better understanding of how adaptation to divergent environmental conditions leads to evolution of reproductive isolation. We investigated the population genetic structure of closely-related sympatric taxa that have recently been proposed as separate species (An. coluzzii and An. gambiae), sampled from diverse habitats along the Gambia River in West Africa. We characterised putatively neutral microsatellite loci as well as chromosomal inversion polymorphisms known to be associated with ecological adaptation. The results revealed strong ecologically-associated population subdivisions within both species. Microsatellite loci at chromosome-3L revealed a clear differentiation between coastal and inland populations, which in An. coluzzii is reinforced by a peculiar inversion polymorphism pattern, supporting the hypothesis of genetic divergence driven by adaptation to the coastal habitat. Striking genetic differences, compatible with a strong reduction of gene-flow, were observed between An. gambiae populations west and east of an extensively rice-cultivated region exclusively occupied by An. coluzzii. Notably, this ‘intra-specific’ differentiation was higher than that observed between the two species and involved also the centromeric region of chromosome-X which has previously been considered a marker of speciation within this complex, suggesting that the two populations may be at an advanced stage of reproductive isolation triggered by human-made habitat fragmentation. These results confirm ongoing ecological speciation within these most important Afro-tropical malaria vectors and raise new questions on the possible effect of this process in malaria transmission.

冈比亚按蚊复合体（Anopheles gambiae complex）包含处于不同物种形成阶段的疟疾传播媒介，对其开展研究可助力深入解析：针对差异化环境条件的适应性演化如何推动生殖隔离的形成。本研究针对近期被提议为独立物种的近缘同域类群——科卢齐按蚊（An. coluzzii）与冈比亚按蚊（An. gambiae）——展开种群遗传结构分析，样本采集自西非冈比亚河沿岸的多样生境。研究人员对假定的中性微卫星位点（microsatellite loci）以及已知与生态适应相关的染色体倒位多态性（chromosomal inversion polymorphisms）进行了分型表征。

研究结果显示，两个物种内部均存在显著的生态关联型种群分化。3L染色体上的微卫星位点可清晰区分沿海与内陆种群；在科卢齐按蚊中，这一分化模式得到了特殊倒位多态性特征的强化，该结果支持“针对沿海生境的适应性演化驱动了遗传分化”的假说。值得注意的是，在被科卢齐按蚊独占的大面积水稻种植区的东西两侧，冈比亚按蚊种群间出现了与基因流（gene flow）大幅降低相符的显著遗传差异。尤为关键的是，这种“种内”分化程度高于两个物种之间的分化，且涉及X染色体着丝粒区域——该区域此前被视为该复合体内物种形成的标志性位点，这表明两个种群或许正处于由人为栖息地破碎化触发的生殖隔离高级阶段。

本研究结果证实，这些至关重要的非洲热带疟疾媒介内部正持续发生生态物种形成过程，同时也为该过程对疟疾传播的潜在影响提出了新的科学问题。