Data from: Inter-specific gene flow dynamics during the Pleistocene-dated speciation of forest-dependent mosquitoes in Southeast Asia

Tropical forests have undergone repeated fragmentation and expansion during Pleistocene glacial and interglacial periods, respectively. The effects of this repeated forest fragmentation in driving vicariance in tropical taxa have been well studied. However, relatively little is known about how often this process results in allopatric speciation, since it may be inhibited by recurrent gene flow during repeated secondary contact, or to what extent Pleistocene-dated speciation results from ecological specialisation in the face of gene flow. Here, divergence times and gene flow between three closely-related mosquito species of the Anopheles dirus species complex endemic to the forests of Southeast Asia, are inferred using coalescent based Bayesian analysis. An Isolation with Migration model is applied to sequences of two mitochondrial and three nuclear genes, and 11 microsatellites. The divergence of An. scanloni has occurred despite unidirectional nuclear gene flow from this species into An. dirus. The inferred asymmetric gene flow may result from the unique evolutionary adaptation of An. scanloni to limestone karst habitat, and therefore the fitness advantage of this species over An. dirus in regions of sympatry. Mitochondrial introgression has led to the complete replacement of An. dirus haplotypes with those of An. baimaii through a recent (~62 kya) selective sweep. Speciation of An. baimaii and An. dirus is inferred to have involved allopatric divergence throughout much of the Pleistocene. Secondary contact and bidirectional gene flow has occurred only within the last 100,000 years, by which time the process of allopatric speciation seems to have been largely completed.更新世冰期与间冰期期间，热带森林经历了反复的破碎化与扩张。这类反复的森林破碎化推动热带类群发生异域分化（vicariance）的效应已得到充分研究。然而，该过程促成异域成种（allopatric speciation）的频率仍鲜为人知——这可能是因为反复二次接触过程中会出现反复的基因流，进而抑制成种；或是因为在基因流存在的情况下，更新世时期的成种事件在多大程度上源于生态特化。 本研究针对东南亚森林特有、亲缘关系紧密的3种按蚊，隶属于德里按蚊物种复合体（Anopheles dirus species complex），利用基于溯祖理论的贝叶斯分析，推断了它们的分化时间与基因流水平。研究采用隔离与迁移模型（Isolation with Migration model），分析了2个线粒体基因、3个核基因以及11个微卫星位点的序列数据。 尽管斯坎隆按蚊存在向德里按蚊的单向核基因流，但该物种仍完成了分化。推测这种不对称基因流可能源于斯坎隆按蚊对石灰岩喀斯特生境的独特进化适应，使其在同域分布区域相比德里按蚊具备更高的适合度优势。 线粒体基因渐渗通过一次约6.2万年前的选择性清除事件，使得德里按蚊的单倍型完全被白氏按蚊的单倍型所替代。研究推断，白氏按蚊与德里按蚊的成种过程在更新世的大部分时期均处于异域分化状态，仅在近10万年内才出现二次接触与双向基因流；此时异域成种过程已基本完成。