基因组冲突、限制性基因流与自然选择能够强化群体的生殖隔离并最终导致新物种的形成，然而它们是如何次第或共同作用驱动物种分化与生态适应的，具体机制仍不清楚。具备异域-同域地理分布模式和倍性变化的地黄属为从属水平探讨物种形成过程中多因子综合作用机理提供了非常宝贵的契机。在前期研究种间关系与地理遗传变异的基础上，本项目利用转录组和简化基因组测序（SLAF-seq）技术，比较各物种对之间基因流水平、选择作用强度等方面的遗传变异规律，阐明物种详尽的群体进化历史，揭示物种分化与生态适应的遗传基础、研究种内可能存在的地理隔离与局地适应，探讨冲突式成种、突变式成种与生态成种等成种模型在地黄属存在的可能性与相互关系。这些研究能够拓展我们对于物种形成理论的认识，具有重要的科学价值；同时本项目的研究成果也为著名中药地黄的品种改良与野生植物资源的开发利用提供线索。

Reproduction isolation is the basis of species maintenance and could arise from intragenomic conflict, limited gene flow and natural selection. But little is known about how such factors drive population divergence and speciation. Rehmannia becomes good materials for speciation study due to its complexity involving sympatric / allopatric diploid and polyploid species. In previous studies, phylogeography and population genetics methods were used to elucidate the geographic genetic variation among natural populations. But the driving force in the procedure of speciation in Rehmannia remains unclear. In this project, transcriptome sequencing and specific-locus amplified fragment sequencing（SLAF-seq) will be used to compare the genomic structure, gene flow and selection level between species pairs. Our aims are: (1) to elucidate the evolutionary history of Rehmannia. (2) to know the patterns of the genomic organization. (3) to screen genes possibly experienced with selection and local adaptation. (4) to understand the concepts of conflictual speciation, mutation-order speciation and ecological speciation. The results will not only help to understand the speciation mechanism of Rehmannia, but also benefit the development, utilization, and breeding improvement of R. glutinosa, the famous Chinese traditional medicine herb.