洞穴植物报春苣苔谱系地理及适应性的基因组水平解析

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.

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。

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。探究洞穴植物的谱系地理格局、进化历史及环境适应性机制，对南岭地区特殊生境的物种保护具有重要意义。本研究以分布于特殊生境的报春苣苔为研究对象，基于简化基因组测序进行了系统的保育基因组学研究。研究结果显示，地理隔离和环境隔离均促进了该物种的群体遗传分化。冗余分析显示气候环境、地理隔离对群体基因组SNP变异解析度分别为38.85%和12.46%，共达51.31%，表明环境适应性在促进群体分化中可能起着更重要的作用。共160个可能受到歧化选择的异常位点，其中125个分布在被注释基因的编码区内，暗示大部分受选择位点可能与基因功能有关。避难所分析支持喀斯特洞穴是该物种的潜在避难所的研究假设；其在末次盛冰期的分布主要在广西和湖南两省喀斯特地区交界处，且其适合度较低。末次盛冰期后的全新世中期，报春苣苔向北部和东部地区扩张，但核心适生区不变。未来不同碳浓度排放情况下适生区分布模拟表明，未来报春苣苔的适生区分布范围会大幅度缩小，且碳排放浓度越高，其适生区范围越小，暗示该物种对温度升高尤为敏感，在未来全球气候变化下野外种群及个体数量可能会急剧减少，面临更大的生存压力及灭绝风险。此外，基于重测序数据的交配系统演化比较分析表明，报春苣苔群体存在一个自交率梯度，即低自交、混合交配和高自交组群。高自交群体遗传多样性降低、遗传负荷显著增高，暗示自交率升高可能导致物种的适应性潜力下降。这些研究结果为我们更好地理解南岭山地生物多样性形成进化机制及其对气候变化的响应提供了重要信息，并为进一步制定特殊生境物种保护措施提供了新的启示。