Localizing FST outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow

Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence-with-gene-flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing FST outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between-population recombination and gene exchange are reduced over large ‘divergence hitchhiking’ (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in geno...在同域分布条件下维持表型分化的种群，通常呈现基因组分化的镶嵌模式，这需要与之匹配的基因组隔离（即基因流降低）。然而，除了选择在着丝粒或倒位区域附近产生的传统局部效应以及重组率降低之外，能够满足伴随基因流的分化所需的基因组隔离机制，迄今几乎未得到探索。我们通过将野生豌豆蚜宿主宗的全基因组扫描所得的FST异常值，定位至关键性状的数量性状位点（Quantitative Trait Locus, QTL）图谱上，以此检验如下假说：在大片段的"分歧搭车效应（divergence hitchhiking, DH）"区域内，种群间的重组与基因交流均受到抑制。正如分歧搭车效应假说所预期的那样，我们的图谱证实，数量性状位点与分化标记在多个大片段基因组区域中聚集分布。在分歧搭车效应模型下，相较于基因组区域内的非异常值标记，这些区域内的非异常值标记应表现出基因交流降低的特征...