极危物种五针白皮松基因组遗传多样性及其种群动态历史研究

The mechanisms of species endangering and extinct have always been the focus of conservation biology. Genetic diversity is an important indicator that can mirror species evolutionary potential and defense ability to environmental changes, and the loss of genetic diversity easily triggers the reducing of adaptation and fitness, even the endangered or extinction for many species on earth. So, accurate assessment of genetic diversity is crucial for understanding the levels of genetic variation and informing the conservation strategies for endangered species. However, for most of the studies concerning conservation biology of endangered species, historical factors (such as climate changes and human activities), that are assumed to be responsible for reducing the genetic diversity and population sizes in their long evolutionary history, are almost unascertained, but it could be worked out through the simulations of demographic history. Pinus squamata X. W. Li, discovered in the northeastern corner of Yunnan, China in 1992, is one of the critically endangered conifers in the world with a small population (two subpopulations) and only 32 individuals in the wild. Because of its rareness and endangered status, it was listed as a first-class protected plant by the Chinese government. While successful strategies for the conservation of an endangered species must include an understanding of the levels and distribution of genetic diversity. Unfortunately, due to the poor informativeness of molecular markers and simple analytical methods used in previous studies, almost no genetic variation was detected in the natural population of P. squamata, let alone the cause of its population decrease that can be concluded by the simulation of population demographic history. Therefore, to find out the historical factors that induced the population decline of P. squamata, its widespread congener P. bungeana, be native to north, northwest and southwest China, will be used as a reference in this project. Then we will compare their genetic variation across the whole genome based on the high-throughput sequencing (genotyping by sequencing, GBS) and demographic histories inferred and simulated by coalescence-based methods, such as fastsimcoal2 and PSMC. We believe that the results from this project would not only have important implications for the conservation of P. squamata, but also provide new insights concerning the conservation of other endangered species with extremely small populations.

深度解析濒危物种基因组水平遗传多样性，既可评估其进化的潜力，也可推测影响其有效种群大小和遗传多样性水平的历史因素，从而全面解答濒危物种的濒危机制。五针白皮松是世界上最濒危的裸子植物之一，具有极高的保护价值。但是，由于极小的自然群体，加上前人所采用的研究方法和数据类型的限制，几乎没有检测到群体遗传变异，同时也未对其种群动态历史进行追溯，使其保护遗传学研究一直停滞不前。本项目拟采用高通量简化基因组测序技术，检测五针白皮松基因组水平的遗传变异，并与其近缘广布种白皮松进行比较，评估其进化的潜力；随后采用先进的基于溯祖理论的统计模拟分析方法，比较两个物种的种群动态历史，找到五针白皮松种群衰退的历史原因，为其科学保护提供坚实的理论依据。本项目不仅对极危物种五针白皮松的保护有重要意义，也将为极小种群物种的保护遗传学研究提供新的研究思路。

深度解析影响濒危物种进化命运的关键因素，如基因组遗传多样性、种群历史动态、基因组突变负荷，以及历史生态位变迁等，可全面解析濒危物种的濒危机制，也可准确预测其未来的进化潜力，为濒危物种科学合理的保护提供建议。五针白皮松是世界上最濒危的裸子植物之一，具有极高的研究和保护价值。但是，由于极小的自然群体，加上前人所采用的研究方法和数据类型的限制，几乎没有检测到群体遗传变异，同时也未从多个角度对其濒危原因和进化潜力进行研究，使其保护遗传学研究一直停滞不前。本项目以五针白皮松，及其近缘濒危物种白皮松和西藏白皮松为研究对象，通过群体转录组测序和低深度全基因组测序获得的SNP数据，对影响其进化命运的关键因素进行物种间的比较分析。研究结果显示：1）三种濒危物种五针白皮松、白皮松和西藏白皮松具有不同水平的基因组遗传多样性，前两者的遗传多样性极低，而后者的相对较高，且遗传多样性的高低与其濒危等级并无直接关联。2）三个物种均经历了严重的历史瓶颈事件，且与重大地质和气候事件相关联；在群体瓶颈之后，前者发生了明显群体扩张，而后两者的有效群体大小保持在一个较低的水平。3）三个物种的基因组累积和清除突变负荷的模式也不同，白皮松基因组累积的纯合衍生有害突变相对较少，且有害突变的选择性清除能力相对较强，西藏白皮松累积了较高水平的杂合突变负荷，选择性清除能力相对较弱，而白皮松不但累积了相对较高水平的有害突变，同时选择性清除能力也较弱。4）白皮松的历史潜在分布区随气候变化发生了轻微的波动，且在未来的气候环境下，其分布区将会发生显著的扩张。综上结果表明，五针白皮松、白皮松和西藏白皮松具有截然不同的进化命运，且未来的进化潜力也不同，这些结果将为三种濒危物种的科学合理保护提供重要建议。