基于线粒体全基因组的中国石首鱼科分子系统发生学研究

The Sciaenidae fishes live in marine, brackish and freshwater habitats along the Atlantic, Indian and Pacific coasts. China has the highest number of species in this family and knowledge about the Sciaenidae fishes' phylogenetic relationships and evolution adds to our understanding of biodiversity. To study the origin, patterns, and process of evolutionary diverfication of Sciaenidae fishes, it is needed to perform a comprehensive phylogenetic analysis of Sciaenidae fishes inferred from the complete mitochondrial genome sequences and more than 22 species, representing almost of recognized Sciaenidae fishes of China. Firstly, the complete mitochondrial genome sequences of Sciaenidae fishes will be determined and characterized. Then, the sequences will be aligned by using the Muscle algorithm, chi-square test for homogeneity of base composition and saturation of substitution analyzes will be conducted to exclude the unstable region and heterogeneity sites to generate the unambiguous aligned sequences data matrix. Secondly, the data matrix was divided into different partitions based on different models of evolution (e.g. stems and loops, codon positions). Best model of nucleotide evolution will be selected for each partition. Bayesian analysis and RAML analyses will be performed to reconstruct the phylogeny of Sciaenidae fishes by applying the best-fit models and their specified parameters estimates to each data partition and sub-sequently incorporating this into a single ML tree search. One and two-side Kishino-Hasegawa test, Shimodaira-Hasegawa test, and Approximation Unbiased test will be conducted to compare the alternative topologies. Finally, nonparametric (PL and NPRS) and parametric (Bayesian, clock3 and IR models) method will be performed to estimate the divergence times of Sciaenidae species based on the calibration information and geological data with aim to reconstruct the evolutionary scenario of Sciaenidae fishes of China and its reason behind.

为厘清中国石首鱼科各支系物种系统发育关系及探索其物种的起源演化历史与机制。本项目拟测定该类群各属种线粒体全序列并基于计算分子进化手段开展全面的中国石首鱼科分子系统发生学研究。首先获得各物种线粒体全序列，在解析与比较各物种线粒体基因组序列组成与结构特征的基础上，利用不同类型的线粒体单基因、多基因、全基因组变异结合不同分区策略的贝叶斯法与分区最大似然法进行分子系统树的构建与拓扑结构比较检验，明确中国石首鱼科物种系统发育关系。其次，以所获得的稳健可信的中国石首鱼科系统进化树为基础，结合石首鱼类群化石资料，基于参数法与非参数法及多模型策略的分子钟标定技术估计物种分歧时间表，联合化石资料与物种分歧对应的地质地史状况，综合探索中国石首鱼科物种起源演化历史和机制。

石首鱼类隶属于鲈形目，鲈亚目，石首鱼科，我国共有17属30种，居世界首位。石首鱼种类繁多且大多数种类具有显著的种属地理分布局限性，是研究鱼类系统进化发生关系、起源和进化的良好材料。但是，一方面基于形态特征的系统发育研究在物种明确、属的范围等方面有较多分歧，另一方面分子系统学的研究类群较少、物种代表性不够全面，科内系统关系尚无明确定论。脱氧核糖核酸序列作为遗传信息的载体相比形态特征能更客观和本质地反应系统发育关系。线粒体全序列已广泛应用于动物类群系统发生与起源演化研究并取得了诸多重大研究成果。为厘清中国石首鱼科各支系物种系统发育关系以及探索其物种的起源演化历史与机制，本项目对有代表性的石首鱼的完整线粒体序列进行了扩增，结合公开数据库中的其他石首鱼线粒体全序列，利用不同类型的线粒体单基因、多基因、全基因组变异结合不同分区策略的贝叶斯法与分区最大似然法进行分子系统树的构建与拓扑结构比较检验，明确了中国石首鱼科物种系统发育关系，估计了物种分歧时间表，探索了中国石首鱼科物种起源演化历史和机制。