Data from: The last bastion? X-chromosome genotyping of Anopheles gambiae species-pair males from a hybrid zone reveals complex recombination within the major candidate ‘genomic island of speciation'

Speciation with gene flow may be aided by reduced recombination helping to build linkage between genes involved in the early stages of reproductive isolation. Reduced recombination on chromosome-X has been implicated in speciation within the Anopheles gambiae complex, species of which represent the major Afrotropical malaria vectors. The most recently diverged, morphologically-indistinguishable, species-pair, An. gambiae and An. coluzzii, ubiquitously display a ‘genomic island of divergence’ spanning over 4Mb from chromosome-X centromere, which represents a particularly promising candidate region for reproductive isolation genes, in addition to containing the diagnostic markers used to distinguish the species. Very low recombination makes the island intractable for experimental recombination studies, but an extreme hybrid zone in Guinea Bissau offers the opportunity for natural investigation of X-island recombination. SNP-analysis of chromosome-X hemizygous males revealed: (i) strong divergence in the X-island despite a lack of autosomal divergence; (ii) individuals with multiple-recombinant genotypes, including likely double crossovers and localized gene conversion; (iii) recombination-driven discontinuity both within and between the molecular species markers, suggesting that the utility of the diagnostics is undermined under high hybridization. The largely-, but incompletely-protected nature of the X-centromeric genomic island is consistent with a primary candidate area for accumulation of adaptive variants driving speciation with gene flow, whilst permitting some selective shuffling and removal of genetic variation.

存在基因流的物种形成过程，可借由重组率降低得以推进——重组率降低有助于建立生殖隔离早期阶段所涉及基因间的连锁关联。X染色体（chromosome-X）上的重组率降低，曾被证实与冈比亚按蚊复合体（Anopheles gambiae complex）内的物种形成过程相关，该复合体的物种均为非洲热带地区主要的疟疾传播媒介。
最晚分化、形态上无法区分的物种对——冈比亚按蚊（An. gambiae）与科卢齐按蚊（An. coluzzii）——普遍存在一段从X染色体（chromosome-X）着丝粒区域延伸超过4Mb的“分化基因组岛（genomic island of divergence）”；该区域不仅是生殖隔离基因极具潜力的候选区域，还包含用于区分这两个物种的诊断性分子标记。
该基因组岛区域重组率极低，使得实验性重组研究难以开展，但几内亚比绍境内的极端杂交带为研究X染色体分化基因组岛的重组提供了天然的研究契机。对X染色体半合子雄性个体的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分析显示：(1) 尽管常染色体未出现遗传分化，但X染色体分化基因组岛区域存在显著遗传分化；(2) 部分个体携带多重重组基因型，包括疑似的双交换与局部基因转换事件；(3) 物种诊断性分子标记内部及标记间均存在由重组介导的遗传间断现象，表明在高杂交压力下，这些诊断标记的应用价值会受到削弱。
X染色体着丝粒区分化基因组岛整体上受到保护但并不完全，这一特性符合在存在基因流的物种形成过程中，适应性变异积累的核心候选区域特征，同时也允许一定程度的选择性洗牌与遗传变异清除。