Data from: Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group

Ongoing speciation in most African malaria vectors gives rise to cryptic populations, which differ remarkably in their behaviour, ecology and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is crucial for effective disease control because heterogeneity within species contribute to variability in malaria cases and allow fractions of vector populations to escape control efforts. To examine the population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group — a large taxonomic group that diverged ~3Myr ago. Using 4343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.

绝大多数非洲疟疾媒介正处于持续的物种形成进程中，由此产生了诸多隐存种群，这些种群在行为、生态学特征以及传播疟原虫的能力上存在显著差异。了解蚊子的种群结构及其遗传分化的驱动因素，对于有效开展疾病防控至关重要——因为物种内的异质性会导致疟疾发病情况出现波动，还会使得部分媒介种群得以逃脱防控措施的压制。为了探究种群结构以及近期大规模防控干预措施可能带来的影响，我们针对隶属于尼利按蚊组（Anopheles nili group）的蚊子展开了基因组分化模式研究——该类群是一个分化于约300万年前的大型分类学类群。我们利用4343个单核苷酸多态性（single nucleotide polymorphisms, SNPs）标记，在适应中非雨林不同生境的多个分化种群之间，检测到了以高FST值为特征的显著种群结构。由于形态学、核糖体DNA与单核苷酸多态性标记之间存在不一致性，这与不完全谱系分选或种间基因流的特征相符，因此对尼利按蚊组内的隐存物种进行界定颇具挑战。在推定物种的基因组中，极高比例的基因座处于固定状态（FST=1），这表明生态和/或生殖隔离是通过对大量基因的强选择作用得以维持的。