Maintaining their genetic distance: little evidence for introgression between widely hybridising species of Geum with contrasting mating systems

Within the plant kingdom many genera contain sister lineages with contrasting outcrossing and inbreeding mating systems that are known to hybridise. The evolutionary fate of these sister lineages is likely to be influenced by the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing G. urbanum, sister species that hybridise in contemporary populations. We generated and used a draft genome of G. urbanum to develop dd-RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the species diverged 2-3 Mya, and that historical gene flow between them was extremely low (1 migrant every 25 generations). Comparison of genetic divergence between species in sympatry and allopatry, together with an analysis of allele frequencies in potential parental and hybrid populations, provided no evidence of contemporary introgression in sympatric populations. Cluster and species specific marker analyses revealed that, apart from four early generation hybrids, individuals in sympatric populations fell into two genetically distinct groups that corresponded exactly to their morphological species classification with maximum individual admixture estimates of only 1 -3%. However, we did observe joint segregation of four putatively introgressed SNPs across two scaffolds in the G. urbanum population that was associated with significant morphological variation, interpreted as tentative evidence for rare, recent interspecific gene flow. Overall, our results indicate that despite the presence of hybrids in contemporary populations, genetic exchange between G. rivale and G. urbanum has been extremely limited throughout their evolutionary history.

在植物界中，诸多属内存在具有迥异异交、自交交配系统的姊妹支系，且已知这些支系间可发生杂交。这些姊妹支系的演化命运，大概率会受其基因交流程度的影响。我们对异交的紫萼路边青（Geum rivale）与自交的城镇路边青（G. urbanum）这一对姊妹种间的基因流进行了测定，这两个物种在当代种群中可发生杂交。我们组装并应用城镇路边青（G. urbanum）的基因组草图，开发出可在两个物种中实现有效分型的dd-RAD数据。对异域种群的RAD数据进行溯祖分析后发现，这两个物种的分化时间为200万至300万年前，且二者间的历史基因流水平极低（每25代仅1个迁移个体）。通过比较同域与异域分布种群间的物种遗传分化，并结合对潜在亲本种群及杂交种群的等位基因频率分析，未发现同域种群中存在当代基因渐渗的证据。聚类分析与物种特异性标记分析结果显示，除4个早期世代杂交个体外，同域种群中的所有个体均可划分为两个遗传上截然不同的类群，且完全匹配其形态学物种鉴定结果，单个个体的最大基因混合比例仅为1%~3%。不过，我们在城镇路边青（G. urbanum）种群中观察到，4个疑似渐渗的单核苷酸多态性（SNPs）在两个基因组支架上存在共分离现象，且该现象与显著的形态变异相关，这被视为罕见、近期发生种间基因流的初步证据。综上，我们的研究结果表明，尽管当代种群中存在杂交个体，但紫萼路边青（Geum rivale）与城镇路边青（G. urbanum）之间的遗传交流在其整个演化历史中始终极为有限。