Data from: Selfish evolution of cytonuclear hybrid incompatibility in (Mimulus)

Intraspecific co-evolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in (Mimulus). In hybrids between Iron Mountain (IM) (M. guttatus x M. nasutus), two tightly linked <i>M. guttatus</i> alleles (<i>Rf</i>1/<i>Rf</i>2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the <i>Rf</i> alleles experienced strong selection in the presence of IM-CMS. Using whole genome sequences, we compared patterns of population-genetic variation in (Rf) at IM to a neighboring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the <i>Rf</i> region shows elevated <i>F</i>_ST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at CP, suggesting a recent sweep in the presence of IM-CMS. In both populations, <i>Rf</i>2 exhibited lower polymorphism than other regions, but the low diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility.自私遗传元件（selfish genetic elements）与抑制因子之间的种内协同进化，或可推动种间杂交不亲和性状的演化，但目前该过程的相关证据仍较为罕见。本研究利用基因组数据，检验沟酸浆属（Mimulus）核质互作杂交雄性不育演化的两种备选模型。在由铁山种群（Iron Mountain, IM，亲本为斑点沟酸浆Mimulus guttatus与小花沟酸浆Mimulus nasutus的杂交组合）产生的杂种后代中，两个紧密连锁的斑点沟酸浆来源的恢复等位基因（Restorer of fertility, Rf1/Rf2），均可通过抑制本地线粒体雄性不育基因（IM-CMS）恢复雄性育性。与杂交不亲和位点演化的中性进化模型不同，自私进化理论预测，Rf等位基因在IM-CMS存在的背景下曾经历强烈的定向选择。本研究借助全基因组测序数据，对比了IM种群与邻近不含IM-CMS的CP对照种群中Rf区域的群体遗传变异模式。与IM种群中IM-CMS存在背景下的局部选择效应相符，Rf区域在IM种群中呈现出升高的种群分化指数（Fixation Index, FST）值、显著的局部连锁不平衡水平以及独特的单倍型结构，而在CP种群中则无此特征，这暗示在IM-CMS存在的背景下，该区域曾发生过一次近期选择性清除。在两个种群中，Rf2的多态性水平均低于其他基因组区域，但CP与IM种群中呈现低多态性的异常区域并不一致。本研究结果验证了植物中普遍存在核质冲突的理论预测，并为一类常见杂交不亲和性状的演化提供了群体遗传机制。