近些年来，由于过度捕捞和环境衰退等原因，鲚属（Coilia）鱼类的资源遭到了严重的破坏，其中以刀鲚（Coilia nasus）最为显著，价格已涨至天价。迄今，部分鲚属鱼类的确切分类仍存在较大争议，如湖鲚（C. nasus taihuensis）的亚种地位；日本刀鲚和我国刀鲚是否为同种异名等。遗传多样性是生物多样性的重要层次，也是物种进化潜能的保证。因此研究鲚属之间的遗传关系，同时研究其遗传多样性特征将有利于鲚属物种的保护和管理。本文以刀鲚（包括陆封湖鲚和我国、日本采集的刀鲚）、凤鲚（C. mystus）、七丝鲚（C. grayii）为研究对象，利用分子生物学和生物信息学方法：首次将凤鲚中的基因间内转录1区（ITS1）序列和细胞色素b（Cyt b）基因序列进行了比较研究（遗传多样性和遗传关系分析）；联合采用线粒体（mtDNA）Cyt b基因序列和线粒体控制区（D-loop）序列对日本刀鲚、湖鲚和刀鲚进行了遗传关系研究，并分析了日本刀鲚的遗传多样性；结合Cyt b基因序列和D-loop序列对鲚属鱼类早期生活个体（鱼卵、仔幼鱼）进行遗传多样性分析，探索了鲚属早期生活个体的物种分子生物学判别潜力。主要的研究内容和结果如下： 1）比较分析了分子标记核DNA 基因间内转录1区（ITS1）序列和细胞色素b（Cyt b）基因序列在凤鲚遗传多样性分析和凤鲚与其它鲚属鱼类（以刀鲚为例）间亲缘关系研究中的特征。结果显示其ITS1序列的GC含量（71.19%）显著高于Cyt b基因序列（42.96%），ITS1序列的单倍型多样性（0.900）和核苷酸多样性（0.00997±0.00413）也显著高于Cyt b基因序列（0.400/0.000369±0.000469）。基于ITS1序列所得的凤鲚与刀鲚间的最大似然（MCL）和Kimura双参数（K2P）遗传距离可明确区分这两种鲚属鱼类，与Cyt b基因序列的结果相一致。通过最大似然法（ML）和非加权分组平均法（UPGMA）所构建的系统树发现，凤鲚和刀鲚分别形成独立的分支。本研究显示ITS1序列与Cyt b基因序列所得结果一致性较好，可考虑将ITS1序列作为凤鲚的遗传多样性分析及其与其它鲚属鱼类间亲缘关系研究中有效的分子标记。 2）利用Cyt b基因序列和D-loop序列对日本刀鲚、湖鲚和刀鲚进行分类学鉴定分析，同时对日本有明海六角川所采刀鲚群体进行遗传多样性分析。结果表明：基于Cyt b基因序列和D-loop序列日本刀鲚群体核苷酸多样性分别为0.003257±0.00042和0.006135±0.00050，与我国刀鲚群体的遗传多样性相比均偏低。基于Cyt b基因序列和D-loop序列，日本刀鲚群体和刀鲚群体间的种群分化指数（Fst）和基因交流值（Nm）分别为0.36111/0.44和0.54983/0.16，协同Tajima’D和Fu’s Fs中性检验和核苷酸不配对分析的结果，推断日本刀鲚和我国刀鲚群体间出现过种群扩张，扩张时间约在更新世末期的8.0~12.6万年前，受到更新世末期海平面升降的影响。基于两种序列得出日本刀鲚与刀鲚间的K2P平均遗传距离分别为0.0059293±0.0015225和0.0119264±0.0025281；湖鲚与刀鲚间的K2P平均遗传距离分别为0.00360±0.00090和0.00423±0.00085，与前人的研究相比得出该遗传距离均属于种内个体间的遗传距离水平。基于两种序列构建的ML树（以凤鲚作为外类群），日本刀鲚、我国刀鲚和湖鲚均不具单系性，三者共同构成一个单系，协同分子方差分析（AMOVA）和亲缘关系图，均说明了日本刀鲚、湖鲚与刀鲚群体属同种。 3）基于1022bp左右的Cyt b基因序列，对七丝鲚进行遗传多样性分析，结果显示其核苷酸多样性（0.00274±0.00092）略低于刀鲚群体，推测其遗传多样性可能已受到不利的影响。同时通过Cyt b基因序列和D-loop序列分析研究了七丝鲚、刀鲚和凤鲚三者间的遗传关系，计算所得的平均K2P遗传距离和邻接法（NJ）所构建的系统树显示，凤鲚较为原始，七丝鲚与刀鲚构成姐妹群，处于较进化的位置，支持率为100%（Cyt b）和97%（D-loop）。推测鲚属的进化方式为：刀鲚和七丝鲚可能是凤鲚在演化过程中分别适应寒冷和温暖气候而分化出的物种。 4）使用mtDNA Cyt b基因序列和D-loop序列作为分子标记，基于1022bp和1322bp左右的序列分析了鲚属早期生活个体的遗传多样性，并分析了刀鲚、湖鲚、七丝鲚及凤鲚成鱼之间的遗传关系。结果显示鲚属早期生活个体的遗传多样性均偏低（Cyt b：0.00235~0.00319；D-loop：0.00297~0.01070）；不同种群成鱼间平均K2P遗传距离和基于K2P模型构建的两种序列的NJ分子系统树均显示，湖鲚和刀鲚不能形成独立的分支，而是混合聚在一起形成一个分支；七丝鲚和凤鲚则形成另外两个分支。基于K2P模型构建的NJ分子系统树中，刀鲚仔幼鱼、湖鲚稚鱼、刀鲚鱼卵与刀鲚成鱼、湖鲚成鱼聚为一类，凤鲚鱼卵与凤鲚成鱼聚为一支。由此可见，Cyt b基因序列和D-loop序列作为分子标记可以准确判别外形上具有相似性的刀鲚和凤鲚的早期生活个体，但该法尚不能判别刀鲚和湖鲚的早期生活个体。

To date, the Coilia resources have decreased sharply due to the impacts of overfishing, environment destruction and pollution. And the situation is the most striking on the estuarine tapertail anchovy, C. nasus, which has been sold at a whopping price recently. For Coilia fish, it still has been debated on the molecular genetic differences and species classification, e.g., the validities of sub-species status of land-locked estuarine tapertail anchovy (C. nasus taihuensis), the classification for the estuarine tapertail anchovy distributed in China and Japan (Coilia nasus is suggested as the accepted scientific name for the anchovy from both China and Japan), respectively. Genetic diversity is an important level of biological diversity and the guarantee of potential evolution. Therefore, the study of the genetic relationship among the Coilia species will facilitate the protection and management of these commecial fish. In the present study, we investigated the genetic relationship of C. nasus (include C. nasus taihuensis and the estuarine tapertail anchovy collected in China and Japan), C. mystus and C. grayii by means of molecular biological and bioinformatics approaches on a comparative study of the internal transcribed spacer-1 (ITS1) sequence and Cytochrome b (Cyt b) gene sequence in Coilia mystus; a re-confirmation of the taxonomic relationship among C. nasus from China and Japan, as well as the C. nasus taihuensis using the two sequences (Cyt b gene and Mitochondrial DNA (mtDNA) control region (D-loop) sequences); and an analysis on the genetic diversity of eggs and juveniles of Coilia fishes to assesse the potential of species identification using the sequences of Cyt b gene and D-loop sequences. The main results were summarized as follows: 1) Through comparison with Cyt b gene sequence, we presented the first investigation to reveal ITS1 sequence characteristics and its potential utilization for genetic diversity and phylogenetic relationship measurements for this species and other Coilia fish. The results indicated that the GC content of ITS1 sequence (71.19%) was higher than Cyt b gene sequence (42.96%). Also, the haplotype and nucleotide diversity of ITS1 sequence (0.900/0.00997±0.00413) were higher than those of Cyt b gene sequence (0.400/0.000369±0.000469). Both maximum composite likelihood (MCL) and kimura-2-parameter (K2P) genetic distances of ITS1 were at interspecies level between C. mystus and C. nasus, which were coincident with those of Cyt b gene sequences. The maximum-likelihood (ML) and unweights pair method with arithmetic means (UPGMA) trees constructed with ITS1 sequences and Cyt b gene sequences suggested that C. mystus and C. nasus formed the separate monophyletic groups, respectively. Hence, it was concluded that ITS1 sequence could be used as a good genetic marker for genetic diversity and phylogenetic relationship measurements for C. mystus and other Coilia species (e.g. C. nasus). 2) We used Cyt b gene and D-loop sequences to re-confirm the taxonomic relationship of estuarine tapertail anchovies (C. nasus) from China and Japan, and, C. nasus taihuensis from the Taihu Lake of China. The results suggested that the nucleotide diversity of C. nasus from the river mouth of Rokkaku-gawa in Inner Ariake bay of Japan was lower than those of C. nasus from the waters of China in some previous studies, based on Cyt b gene (0.003257±0.00042) and D-loop sequences (0.006135±0.00050). All results of the high level of population differentiation index (Fst) values (Cyt b 0.36111/D-loop 0.54983) and low gene exchange value (Nm) (Cyt b 0.44/D-loop 0.16), as well as the Tajima’D and Fu’s Fs neutrality tests implied that a late Pleistocene population expansion might be occurred between C. nasus from Japan and C. nasus from China (0.80~1.26 million years ago), and climatic oscillations during the Pleistocene Ice Ages might contributed to the great difference between them. The average K2P genetic distances between C. nasus from Japan and China (Cyt b 0.0059293±0.0015225/D-loop 0.0119264±0.0025281) and the distances between C. nasus taihuensis and C. nasus of China (Cyt b: 0.00360±0.00090; D-loop: 0.00423±0.00085) were at the intraspecies level. The ML trees of Cyt b gene and D-loop sequences (C. mystus as outgroup) indicated that C. nasus from Japan, and C. nasus taihuensis and C. nasus from China failed to form monophyletic class and could not be separated clearly. Moreover, the corresponding analyses of molecular variance (AMOVA) and median-joining network figures could reveal that C. nasus from Japan, C. nasus taihuensis and C. nasus from China could be reconfirmed as a same species. 3) It was believed that the nucleotide diversity of C. grayii (0.00274±0.00092) was lower than that of C. nasus and the diversity of C. grayii might be destroyed, based on the analysis of ca. 1022 bp Cyt b gene sequences. In addition, both sequences of Cyt b gene and D-loop were studied for the genetic relationship among C. grayii, C. nasus and C. mystus. The results of average K2P genetic distance and neighbour-joining (NJ) molecular dendrogram indicated that C. mystus should be the most primitive among the three valid species of Coilia, while C. grayii and C. mystus seemed to be more derived and were believed to be the sister groups [the bootstrap values were 100 (Cyt b) and 97 (D-loop), respectively]. Therefore, the proposed evaluation model will probably be that the C. nasus and C. grayii are the species diverged from C. mystus for adaptation to cold and warm living environment, respectively. 4) Based on about 1022bp and 1322bp sequences, nucleotide sequences of Cyt b and D-loop segments of mtDNA were studied in order to develop some species identification approaches of molecular biology and bioinformatics for eggs and larvae of Coilia fishes. The genetic diversity of eggs and juveniles of Coilia fish seemed to be low (Cyt b: 0.00235~0.00319; D-loop: 0.00297~0.01070). The average K2P genetic distance and NJ molecular dendrogram of the Cyt b gene and D-loop sequence showed the anchovies of C. nasus and C. nasus taihuensis mixed into a cluster, and those of C mystus and C. grayii formed another two clusters. According to the above reference information, nucleotide sequences of Cyt b and D-loop of Coilia eggs and juveniles were analyzed. NJ molecular dendrogram showed that all the eggs and juveniles of C. nasus, adults of C. nasus and juveniles C. nasus taihuensis clustered together, while the eggs of C. mystus and adults of C. mystus formed a separate cluster. Thus, the eggs and juveniles of C. nasus and C. mystus could be identified by means of Cyt b and D-loop sequence analysis. However, this approach could not identify the eggs and juveniles of C. nasus and C. nasus taihuensis.