石爬鮡属鱼类局域适应的分子基础研究

Local adaptation, as an important aspect of species’ adaptation to their habitats, plays an important role in shaping species diversity, contributing to the maintenance of genetic variation, facilitating species range expansion and promotion of ecological speciation. In the previous studies, we found that there may exist local adaptation or be in the process of speciation in the Euchiloglanis fish species, a species complex belonging to the Sisoridae in Siluriformes, which is distributed in the drainages among Hengduan Mountains in Eastern Tibetan Plateau. Therefore, in this project, using this species complex as a model, we will combine the theory and methods of morphology, ecology, evolutionary genomics, bioinformatics and statistics together, trying to investigate the molecular basis of local adaptation of Euchiloglanis fish species in the river system of Hengduan Mountains, and pave the way for further research in species’ adaptation and evolution under the extreme environmental conditions of the Tibetan Plateau. Specific studies include: 1) collecting data for such as altitude and water current at each sampling location; 2) measurements and analyses of fish body shape and gill raker morphology based on traditional morphological methods as well as geometric morphometric methods; 3) diet analysis based on stomach and gut content identification combined with contents’ DNA barcoding analysis; 4) genome-wide population genetic analysis based on RAD-seq data; and 5) tests for local selection by searching for increased population differentiation using FST-based outlier analysis, and tests for associations between SNP loci, morphometric traits and environmental variables.

局域适应，作为生物适应环境的重要方面，在生物多样性塑造、物种遗传变异维持、物种分布范围扩张以及促进生态物种形成方面起着重要作用。本项目以我们最新研究发现可能存在局域适应的、局限分布于青藏高原横断山区水系的石爬鮡属鱼类为研究对象，运用形态学、生态学、演化基因组学、生物信息学以及统计学等多学科的理论与方法，试图探明石爬鮡属鱼类在青藏高原横断山区水系局域适应的分子基础，为进一步探讨青藏高原极端环境下物种的适应与演化奠定基础。具体研究内容包括：1）样品采样点海拔高度与水流速度等环境因子数据的采集；2）基于传统形态学与几何形态测量法的表型特征分析；3）基于胃肠内含物鉴定结合DNA条形码数据的食性分析；4）基于RAD测序数据的基因组水平群体遗传分析；5）基于FST的遗传分化离群分析以及环境因子、表型特征与SNP位点间的相关性分析。

石爬鮡属隶属于辐鳍鱼纲、鲇形目、鮡科，是在高山峡谷、陡坡急流的环境中营底栖生活、无洄游的淡水鱼类。分布于横断山区长江上游水系的3种石爬鮡由于在形态上极其相似、在分子水平上分歧小，该属物种在成种时间上并不长且有可能还正处在成种过程中，彼此间可能还存在一定的基因交流。因此，横断山区分布的石爬鮡属鱼类是研究局域适应以及物种形成的理想模型。.基于此，本项目以分布于横断山区的石爬鮡属鱼类为研究对象，从多变量形态度量学、几何形态学、谱系地理学以及群体基因组学的角度，探讨了其局域适应及物种形成的分子基础。首先，对8个不同群体共233尾样本，选取11个解剖学坐标点以及52个可量性状对其进行多变量形态度量分析；同时选取与多变量形态度量对应的8个群体共226尾样本，基于20个标定点（背面观）和17个标定点（腹面观）对其进行了几何形态学分析。其次，基于线粒体cytb基因序列以及10个微卫星分子标记对石爬鮡进行了遗传分化和谱系地理学分析。最后，利用RAD测序技术，对9个群体213尾石爬鮡以及3尾中华鮡进行了高通量测序，共获得226.52 Gb过滤数据以及6,606个SNP位点，基于这些SNPs或SNPs所在的RAD-tags进行了系统发育、聚类、基因流、物种界定以及分子功能注释分析。.本项目采用逐步深入的方式解析了石爬鮡属鱼类在局域适应及物种形成过程中的分子基础。首先采用多变量形态度量学与几何形态学方法分析了石爬鮡的形态分化；其次基于线粒体cytb基因序列与多态性微卫星分子标记分析了石爬鮡的遗传分化；最后基于全基因组扫描的RAD测序技术分析了石爬鮡在局域适应及物种形成过程中与表型变异相关的关键遗传改变。这为横断山区物种多样性的成因与适应性演化机制研究提供了资料与范例。