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（Pleistocene）期间，热带森林在冰期与间冰期分别经历了反复的碎片化与扩张过程。针对这类反复森林碎片化驱动热带类群地理分异的效应，学界已开展了充分的研究。然而，关于该过程促成异域物种形成的频率，目前仍知之甚少：一方面，反复二次接触过程中的重复基因流可能会抑制物种分化；另一方面，在存在基因流的背景下，更新世时期的物种形成在多大程度上源自生态特化，相关认知仍较为匮乏。本研究聚焦于东南亚森林特有、亲缘关系密切的3种按蚊——隶属于按蚊达氏种复合体（Anopheles dirus species complex），通过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模式。研究采用隔离与迁移（Isolation with Migration）模型，对2个线粒体基因、3个核基因以及11个微卫星（microsatellites）的序列数据进行了分析。研究结果显示，尽管存在从斯氏按蚊（An. scanloni）向达氏按蚊（An. dirus）的单向核基因流，斯氏按蚊仍完成了物种分化。这种不对称的基因流，可能源于斯氏按蚊对石灰岩喀斯特生境的独特演化适应，使其在同域分布区域相比达氏按蚊具备更高的适合度。线粒体基因渐渗（mitochondrial introgression）通过距今约6.2万年前的一次选择性清除（selective sweep）事件，使得达氏按蚊的单倍型完全被拜氏按蚊（An. baimaii）的单倍型所取代。研究推断，拜氏按蚊与达氏按蚊的物种形成过程，在更新世的大部分时期均以异域分化为主。二者仅在近10万年内才出现二次接触与双向基因流，此时异域物种形成的过程已基本完成。