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）诞生以来，局部适应的遗传架构始终是进化生物学家的核心研究方向。除费希尔（Fisher）、木村资生（Kimura）与奥尔（Orr）提出的适应性突变效应大小经典理论外，新近的理论聚焦于持续存在基因流情境下的局部适应遗传架构。该理论预测，若种群间存在显著基因流，局部适应主要通过大效应突变，或是由多个小效应位点紧密连锁形成的簇来完成。本研究以裂叶猴面花（*Mimulus laciniatus*）与其近缘物种、同域分布的小花猴面花（*Mimulus guttatus*）种群为研究对象，探究二者在开花时间、交配系统相关性状以及叶形上的分化遗传架构。上述三类性状大概率与裂叶猴面花适应干燥、裸露的花岗岩露头生境密切相关。其中，开花时间与交配系统的差异同时构成生殖隔离屏障，因此这类性状被称为“神奇性状（magic traits）”。该种群中出现的表型杂种为近期存在基因流提供了直接证据。本研究借助下一代测序技术，在全基因组范围内开发了高密度单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，并对与开花时间、花大小及叶形相关的数量性状位点（Quantitative Trait Locus, QTL）进行定位。研究发现，三类性状的种间分化均由少数大效应QTL驱动，其中8号染色体上存在一个具有高度多效性的QTL。该QTL区域包含多效性候选基因TCP4，且在其他猴面花属物种中，该区域与具有重要生态意义的表型调控相关。本研究结果与前述理论一致，表明在存在基因流的情况下，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介导。