Data from: Chromosome arm specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus

Chromosomal inversions facilitate local adaptation of beneficial mutations and modulate genetic polymorphism, but the extent of their effects within the genome is still insufficiently understood. The genome of Anopheles funestus, a malaria mosquito endemic to sub-Saharan Africa, contains an impressive number of paracentric polymorphic inversions, which are unevenly distributed among chromosomes and provide an excellent framework for investigating the genomic impacts of chromosomal rearrangements. Here we present results of a fine-scale analysis of genetic variation within the genome of two weakly differentiated populations of Anopheles funestus inhabiting contrasting moisture conditions in Cameroon. Using population genomic analyses, we found that genetic divergence between the two populations is centered on regions of the genome corresponding to three inversions, which are characterized by high values of FST, absolute sequence divergence and fixed differences. Importantly, in contrast to the 2L chromosome arm, which is collinear, nucleotide diversity is significantly reduced along the entire length of three autosome arms bearing multiple overlapping chromosomal rearrangements. These findings support the idea that interactions between reduced recombination and natural selection within inversions contribute to sculpt nucleotide polymorphism across chromosomes in An. funestus.

染色体倒位（chromosomal inversions）可促进有益突变的本地适应，并调控遗传多态性，但目前学界对其在基因组内的影响范围仍缺乏足够认知。作为撒哈拉以南非洲特有的疟疾媒介蚊，斯氏按蚊（Anopheles funestus）的基因组中存在大量臂内多态性倒位，这类倒位在染色体间分布不均，为研究染色体重排的基因组效应提供了极佳的研究框架。本研究对喀麦隆境内两种栖息于湿度迥异生境、遗传分化程度较低的斯氏按蚊种群的基因组遗传变异开展了高精度分析，现将研究结果报道如下。通过群体基因组学分析，我们发现两个种群间的遗传分化主要集中在对应三种倒位的基因组区域，这些区域表现出较高的FST值、绝对序列分化度以及固定差异位点。值得注意的是，与共线性的2L染色体臂不同，携带多处重叠染色体重排的三条常染色体臂的全序列范围内，核苷酸多态性均显著降低。上述研究结果支持这一假说：倒位区域内重组率降低与自然选择之间的相互作用，共同塑造了斯氏按蚊全染色体的核苷酸多态性分布格局。