Data from: The genetic architecture of local adaptation and reproductive isolation in sympatry in 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 likely 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 same QTL region is involved in ecologically important photoperiod differences 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（modern synthesis）提出以来，局部适应的遗传架构始终是进化生物学家的核心研究议题。除费希尔（Fisher）、木村资生（Kimura）与奥尔（Orr）关于适应性突变效应大小的经典理论外，近期理论还探讨了持续基因流（gene flow）背景下局部适应的遗传架构。该理论预测，若种群间存在显著基因流，局部适应主要应通过大效应突变，或是紧密连锁的小效应位点簇来实现。本研究针对裂叶沟酸浆（Mimulus laciniatus）与其近缘物种黄花沟酸浆（Mimulus guttatus）的同域种群，探究了三者在开花时间、交配系统相关性状以及叶片形状上的分化遗传架构。这三类性状很可能参与了裂叶沟酸浆对干燥裸露的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构成生殖隔离障碍（reproductive isolating barriers），因此这类性状被称为“魔力性状（magic traits）”。该种群中的表型杂种为近期基因流提供了佐证。本研究利用下一代测序（next generation sequencing）技术生成了全基因组范围内的高密度单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，并对与开花时间、花大小及叶片形状相关的数量性状位点（quantitative trait loci, QTLs）进行了定位分析。研究发现，三个性状的种间分化均由少数大效应QTL所致，其中包括8号染色体上一个具有高度多效性的QTL。该QTL区域在其他沟酸浆属物种中，同样参与调控具有生态重要性的光周期差异（photoperiod differences）。本研究结果与相关理论相符，即存在基因流的局部适应与生殖隔离，应由少数兼具大效应与多效性的位点所介导。