Data from: The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex

The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system-related traits, and leaf shape between Mimulus laciniatus and a sympatric population of its close relative M. guttatus. These three traits are probably involved in M. laciniatus’ adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them ‘magic traits’. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next-generation sequencing, we generate dense SNP markers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to few QTL of large effect including a highly pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in other Mimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects.

自现代综合进化论（modern synthesis）确立以来，局部适应的遗传架构一直是进化生物学家的核心研究议题。除费希尔（Fisher）、木村资生（Kimura）与奥尔（Orr）提出的关于适应性突变效应大小的经典理论外，近期的理论还针对持续基因流场景下的局部适应遗传架构展开了探讨。该理论预测，当种群间存在显著基因流时，局部适应主要应通过大效应突变，或是小效应位点的紧密连锁簇来实现。本研究聚焦于裂叶沟酸浆（Mimulus laciniatus）与其近缘物种黄花沟酸浆（Mimulus guttatus）的同域种群间，在开花时间、交配系统相关性状以及叶形上的分化遗传架构。上述三类性状很可能参与了裂叶沟酸浆对干燥裸露花岗岩露头生境的适应过程。开花时间与交配系统的差异同时也是生殖隔离屏障，因此属于“神奇性状（magic traits）”。该种群中的表型杂种为近期基因流提供了实证证据。借助下一代测序（next-generation sequencing）技术，我们构建了全基因组高密度单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记图谱，并对调控开花时间、花大小及叶形的数量性状位点（QTL）进行定位。研究发现，三类性状的种间分化均由少量大效应QTL导致，其中包含8号染色体上一个高度多效性的QTL。该QTL区域包含多效性候选基因TCP4，且在其他沟酸浆属物种中已被证实与生态重要表型相关。本研究结果与前述理论一致，表明存在基因流的局部适应与生殖隔离，可由少数兼具大效应与多效性的位点所驱动。