南岭山地是我国生物多样性中心及特有中心，也是植物重要的避难所。喀斯特洞穴是该区域常见的特殊生境，空间及生态隔离明显，植物特有性强。因局部环境的特殊性及稳定性，喀斯特洞穴在生物进化中可能起着微避难所（microrefugia）的作用。探究洞穴植物的谱系地理格局及环境适应性机制，对南岭地区特殊生境的物种保护具有重要意义。本研究以南岭喀斯特洞穴特有濒危植物报春苣苔（Primulina tabacum）为例，拟基于高通量测序及近缘种参考基因组，综合叶绿体基因组及核基因组水平分析，探查该物种的谱系地理格局及进化历史；结合不同居群环境因子，采用生态位模拟鉴定其微避难所；检测居群遗传变异及遗传分化格局，阐明距离隔离及环境隔离的影响；整合基因组扫描及SNP-环境关联分析，揭示该物种环境适应性遗传基础；为该类特殊生境的濒危物种保护提供科学依据，并为揭示我国南岭地区物种多样性及特有性的进化及维持机制奠定基础。

Nanling mountain area has long been recognized as one of the important biodiversity hotspots with high floristic richness and species endemism. Nanling mountain area is also considered one of the important refugia for plants in China. Karst cave is a popular kind of special habitat in this area. Cave-associated plant species are highly endemic with severely geographical and ecological isolation. Given the particularity and stability of local environment, karst cave habitats might have played important roles as microrefugia during the long-term evolution process of biodiversity. Uncovering the phylogeographic structure and mechanisms of environment adaptation of cave-associated species is very important for conservation of endangered species within such special habitat. In the present study, Primulina tabacum, a typically endangered plant endemic to Nanling karst caves, will be selected as a case study to examine phylogeographic sturcture and environmental adaptation of plants in Nanling mountain area. The phylogeographic structure of P. tabacum will be examined at both choloroplastic and genomic levels based on next-generation sequencing technologies and the reference genome of closely realted species. Together with environmental factors, we will identify the potential microrefugia for this species with the ecological niche modeling and test the hypothesis of “karst caves as microrefugia”. Genetic diversity and population genetic structure of P. tabacum will be examined and the relative effect of isolation by distance (IBD) and isolation by environment (IBE) on genetic differentiation will be quantitativly evaluated. Both genomic scanning and SNP-environment association analysis will be performed to uncover the genetic basis for envirenmental adaptation of this species. The results will provide important information for better conservation management of endangered species in such special habitat, and the study overall will be important for understanding the long-term evolutionary mechanisms of species diversity and endemism in Nanling mountain area.