中国鲚属鱼类进化关系及刀鲚、凤鲚的分子系统地理学研究
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摘要
本研究采用形态学、线粒体DNA和AFLP三种方法，分析了中国鲚属（Coilia）鱼类的系统发育关系和种间的分类地位，并探讨了湖鲚和短颌鲚的物种有效性。同时以刀鲚（C. nasus）和凤鲚（C. mystus）为研究对象，通过线粒体DNA和ISSR标记技术，探讨了中国长江流域以及西北太平洋刀鲚群体的系统地理格局；以形态学分析、线粒体DNA和AFLP技术探讨了中国沿海凤鲚群体的遗传结构差异和地理分布格局。
1.中国鲚属鱼类的系统发育研究
（1）通过形态学方法探讨了5种鲚属鱼类的系统发育关系和种间的分类地位。聚类分析结果表明湖鲚、短颌鲚与刀鲚的亲缘关系紧密，而与凤鲚和七丝鲚亲缘关系较远。聚类分析、主成分分析的结果及分节特征的分布频率显示刀鲚、湖鲚与短颌鲚间亲缘关系较近，可能为同一物种。
（2）利用线粒体DNA的COI、ND5和Cytb基因片段进行序列联合分析，研究了中国鲚属鱼类的系统发育关系。短颌鲚、刀鲚、湖鲚的个体间遗传距离非常接近于这三者的种间遗传距离；而短颌鲚、刀鲚与湖鲚的Fst值也显著低于这三者与七丝鲚（Coilia grayi）和凤鲚的Fst值。在NJ、MP和BI法构建的系统发育树中，刀鲚、短颌鲚和湖鲚未能各自形成单系群。刀鲚、短颌鲚与湖鲚的AMOVA分析结果显示种间的分子差异仅占9.76%，且统计检验不显著。Fst值变化范围和AMOVA分析的统计检验结果表明短颌鲚、刀鲚与湖鲚之间无显著的遗传分化。因此，短颌鲚和湖鲚应为刀鲚的不同生态型种群，而不能作为独立的种。
（3）应用AFLP分子标记技术对5种鲚属鱼类的系统发育关系进行了分析。结果显示：刀鲚、短颌鲚和湖鲚的种间平均遗传距离和基因分化系数明显低于它们与七丝鲚和凤鲚间的比较结果。将短颌鲚与湖鲚被视作刀鲚的种群，对刀鲚、七丝鲚与凤鲚来进行AMOVA分析的结果显示分子差异主要属于种间差异，且统计检验结果显著。NJ系统发育树与UPGMA系统树的结果也显示出湖鲚、短颌鲚与刀鲚的亲缘关系紧密，而与凤鲚和七丝鲚亲缘关系较远。据此推测短颌鲚、湖鲚与刀鲚应属于同一个种。
2.刀鲚的分子系统地理学研究
（1）利用线粒体DNA控制区片段及Cytb片段对刀鲚的11个群体进行了分析，基于BI法构建的系统发育树中，刀鲚群体113个控制区单倍型聚为3个类群。中性检验的结果都表明三个类群都经历过群体扩张。根据贝叶斯系统发育树划分为三个组群进行AMOVA分析的结果显示三个组群间存在显著的遗传结构。更新世冰期导致长江河流湖泊的隔离可能使刀鲚分化出的淡水生态型。更新世冰期晚期，日本海的剧烈波动以及有明海的特殊地理环境可能是日本刀鲚群体发生隔离的重要原因。此外，刀鲚洄游的生活史特性也影响3个类群在地理上的分布频率。
（2）基于ISSR分子标记开展了西北太平洋刀鲚种群遗传结构及其地理分布格局研究。UPGMA系统树与PCA分析的结果显示日本有明海群体与中国群体间呈现显著的遗传分化。STRUCTURE分析结果表明刀鲚5个群体应分为2个遗传上不同的组群；AMOVA分析的结果也表明了两组群间存在显著的遗传差异。基因流结果显示刀鲚的日本有明海群体与中国群体间的基因交流受到限制，而中国群体间的基因交流频繁。更新世晚期日本海平面的剧烈波动导致的栖息地隔离，以及较强的海洋环流可能限制了中日群体间刀鲚的基因交流，刀鲚的栖息地和生活史特征导致的基因同质可能是中国群体间基因交流频繁的重要原因。
（3）应用ISSR分子标记对长江流域刀鲚种群遗传结构及其地理分布格局进行了研究。STRUCTURE分析结果表明刀鲚的5个群体应分为2个遗传上不同的组群。AMOVA分析的结果也表明了两组群间存在显著的遗传差异。刀鲚群体UPGMA系统树中，安庆、天鹅洲和赤壁群体大部分个体聚为一支，镇江与太湖群体聚为另一支。本研究结果表明刀鲚群体间存在显著的遗传分化。长江河流湖泊的隔离可能使刀鲚分化出淡水生态型，并且这种分化可能与更新世的气候波动有关。
3.凤鲚群体的形态学、遗传学研究
（1）对中国沿海的5个凤鲚群体进行了形态学研究。聚类分析表明凤鲚的宁波群体与其他群体间差异显著。单因子方差分析也显示出宁波群体与其他的凤鲚群体之间存在差异。与其他凤鲚群体相比，宁波群体在上下鳃耙数和脊椎骨数等分节特征的分布频率上均存在明显差异。栖息地环境可能导致不同凤鲚群体适应了不同的地理环境，从而限制了不同凤鲚群体的扩散区域，最终导致凤鲚群体形态特征上出现差异。
（2）基于线粒体控制区、Cytb及COI片段序列开展了凤鲚的分子系统地理学研究。结果显示分布于中国沿岸的5个凤鲚群体分化为南北两个世系。基于细胞色素b计算的两个种的分化时间约为390万年，分化事件发生于上新世中期；基于COI基因片段序列得出的凤鲚两个世系间净遗传距离为5.6%，超过了COI基因DNA条形码鉴别不同物种2~3%的遗传距离阈值，这表明凤鲚的群体中可能存在一个隐蔽种，凤鲚的南北两个世系应为两个不同的物种。在更新世的末次冰盛期以后，随着海平面的升高，凤鲚的栖息地可能也发生了扩张。因此，群体数量的增长和栖息地的扩大可能是导致凤鲚mtDNA多态性模式的原因。
（3）应用ISSR分子标记对分布于中国沿岸4个凤鲚群体遗传多样性进行了研究。STRUCTURE分析结果表明4个群体应分为2个遗传上不同的组群；AMOVA分析的结果显示两组群间的遗传差异显著。UPGMA系统树显示上海凤鲚群体单独聚为一支，而温州、厦门和大亚湾群体聚为另一支。研究结果显示，长江型凤鲚群体与其他凤鲚群体间存在较大的遗传分化并且缺乏基因交流。凤鲚南北两类群在地理上为异域分布，这可能与其产卵场的不同、以及栖息水域的温度、盐度等环境因子有关。
In the present study, morphological, mitochondrial DNA sequence and AFLP markerswere used for the phylogenetic and taxonomic analysis of Coilia in China. Thevalidity of naming species of C. brachygnathus and C. nasus taihuensis wasinvestigated. To elucidate the phylogeographic pattern of C. nasus, mitochondrialDNA sequence and ISSR markers were used to study the sample of C. nasus inYangtze River and Northwestern Pacific. To assess the genetic structure of C. mystus,we also examined the sample along the coastal regions of China by usingmorphological, mitochondrial DNA sequence and ISSR markers.
1The phylogenetic and taxonomic analysis of Coilia in China:
(1) The phylogeny and taxonomy of Coilia was studied by the morphological analysisin China. The results from the cluster analysis showed a close relationship among C.brachygnathus, C. nasus taihuensis, and C. nasus. C. brachygnathus and C. nasustaihuensis should be synonymized with C. nasus based on the results from the thecluster analysis, principal component analysis and the frequency distribution of themeristic characters in Coilia species.
(2) To elucidate the phylogeny and taxonomy of Coilia, mitochondrial COI, ND5andCytb fragment were used for the combined analysis. C. brachygnathus, C. nasustaihuensis, and C. nasus did not form three separate monophyletic groups in the NJ,MP and BI trees. The average intraspecific genetic distance within C. brachygnathus,C. nasus, and C. nasus taihuensis approximates to their interspecific genetic distance.The mean pairwise Fst value obtained from C. brachygnathus, C. nasus, and C. nasus taihuensis comparisons was significantly lower than the mean pairwise Fst valueobtained between these species and the species of C. grayii and C. mystuscomparisons. Results of the AMOVA revealed that9.76%of the total molecularvariance can be attributed to the significant differences among species. The studyshowed no significant difference among C. brachygnathus, C. nasus, and C. nasustaihuensis. C. brachygnathus and C. nasus taihuensis should therefore besynonymized with C. nasus.
(3) AFLP analysis was applied to study the phylogeny and taxonomy of Coilia inChina. The Gst value and the interspecific genetic distance among C. brachygnathus,C. nasus, and C. nasus taihuensis were significantly lower than those of Gst value andinterspecific genetic distance which were obtained between these species and thespecies of C. grayii and C. mystus. If C. brachygnathus and C. nasus taihuensis wereregarded as populations of C. nasus to investigate the genetic structures of the threespecies, C. nasus, C. grayii and C. mystus, most of the variance (P=0.00) was foundamong species and a small amount within species. In the neighbor-joining tree andUPGMA dendrogram, a close relationship was indicated among C. brachygnathus, C.nasus taihuensis, and C. nasus. Therefore, C. brachygnathus and C. nasus taihuensisshould be synonymized with C. nasus.
2Molecular Phylogeography of C. nasus:
(1) To elucidate the phylogeographic pattern of C. nasus, mitochondrial DNAsequences were used to study the sample of C. nasus in Yangtze River andNorthwestern Pacific. The BI tree constructed using the complete data set of113mitochondrial control region haplotypes identified three distinct lineages. The FStestsof three lineages were negative and highly significant, which indicated populationexpansion. Analyses of molecular variance and the population statistic Fst alsorevealed significant genetic structure among three lineages. As the base levels oferosion and ground water levels were lower as well, rivers in upland areas could formdeeply incised river valleys during the last Pleistocene glaciation. We conclude thatfreshwater populations of C. nasus could thereby have become isolated in the lakes ofYangtze River, resulting in a separate lineage observed in the mitochondrial genome. Strong genetic break was found between the Sea of Japan and the China Seapopulations, likely reflecting isolation of Ariake Bay in the Northwestern Pacificduring the late Pleistocene. A hypothetical scenario to explain the observedphylogeographic pattern is that genetic differentiation and homogeneity may beattributed to habitat and life-history characteristics.
(2) Northwestern Pacific provides unique scenarios for studying the roles ofgeography and ecology in driving population divergence and speciation. Toinvestigate geographical patterns of genetic variation in the Japanese grenadieranchovy using ISSR markers we collected individuals from five locations throughouttheir distribution in the Northwest Pacific. Analyses of molecular variance showedthat genetic differentiation among groups is relatively high. Bayesian analysis of ISSRdata also revealed significant population structuring between Chinese and Japaneselocations. Phylogenetic reconstructions show reciprocal monophyly in populationsbetween China and the Ariake Bay of Japan. We conclude that the present-dayphylogeographic pattern is the result of genetic isolation between Japanese andChinese populations in the Northwestern Pacific following the glacial retreat, and thatlife-history traits and ecology may play a pivotal role in shaping the realizedgeographical distribution pattern of this species.
(3) To investigate the phylogeographic pattern of C. nasus, ISSR markers were usedto study the sample of C. nasus in Yangtze River. Bayesian analysis of ISSR datarevealed significant population structuring between freshwater and anadromouspopulations (K=2). Analyses of molecular variance also revealed that geneticdifferentiation among groups is relatively high. Phylogenetic reconstructions showtwo distinct lineages in Yangtze River. We conclude that the present-dayphylogeographic pattern is the result of genetic isolation between freshwater andanadromous populations in Yangtze River during the last Pleistocene glaciation, andthat life-history traits and ecology may play a pivotal role in shaping the realizedgeographical distribution pattern of this species.
3Phylogeography of C. mystus:
(1) To investigate the genetic difference of C. mystus by the morphological analysis we collected individuals from five locations throughout their distribution alongChinese coastal waters. The results from the cluster analysis showed strong geneticbreak between Ningbo and the other populations. There were significant differencesbetween Ningbo and the other populations based on the results from the clusteranalysis, principal component analysis and the frequency distribution of the meristicand gill rakers characters in populations of C. mystus. Local populations may besufficiently locally adapted to the particular habitat to limit the dispersal amongpopulations of C. mystus. Habitat and life-history differences may play a pivotal rolein shaping morphological characteristics of this species.
(2) To elucidate the phylogeographic pattern of C. mystus, mitochondrial DNAsequences were used to study the sample of C. mystus along Chinese coastal waters.The NJ tree constructed with mtDNA sequences identified two distinct lineages. Thecytochrome b and control region data suggests a divergence time of3.9MY betweenthe two lineages, indicating isolation in the middle Pliocene. A highest geneticdistance for COI gene was found between two lineages (5.6%). According to thebarcoding approach, species could be identified based on a ‘barcoding gap’ betweenintra-and interspecific genetic distances by using a threshold value of23%forspecies delimitation. The study indicated the presence of cryptic species within thepopulations of C. mystus. The neutrality tests indicated population expansion in thetwo lineages. Population range expansion must have occurred after the last glacialmaximum. Range contractions and expansions played a central role in shaping thegenetic diversity of the two lineages of C. mystus.
(3) To investigate the phylogeographic pattern, ISSR markers were used to study thesample of C. mystus along Chinese coastal waters. Bayesian analysis of ISSR datarevealed significant population structuring between northern and southern groups(K=2). Analyses of molecular variance also revealed that genetic differentiationamong groups is relatively high. Phylogenetic reconstructions show reciprocalmonophyly in populations between northern (SH) and southern (NB, XM and DB)groups. The results showed strong genetic break northern and southern populations.Local populations may be sufficiently locally adapted to the particular habitat to limit the dispersal among populations of C. mystus. Life-history traits and ecology mayplay a pivotal role in shaping the realized geographical distribution pattern of thisspecies.
1.中国鲚属鱼类的系统发育研究
（1）通过形态学方法探讨了5种鲚属鱼类的系统发育关系和种间的分类地位。聚类分析结果表明湖鲚、短颌鲚与刀鲚的亲缘关系紧密，而与凤鲚和七丝鲚亲缘关系较远。聚类分析、主成分分析的结果及分节特征的分布频率显示刀鲚、湖鲚与短颌鲚间亲缘关系较近，可能为同一物种。
（2）利用线粒体DNA的COI、ND5和Cytb基因片段进行序列联合分析，研究了中国鲚属鱼类的系统发育关系。短颌鲚、刀鲚、湖鲚的个体间遗传距离非常接近于这三者的种间遗传距离；而短颌鲚、刀鲚与湖鲚的Fst值也显著低于这三者与七丝鲚（Coilia grayi）和凤鲚的Fst值。在NJ、MP和BI法构建的系统发育树中，刀鲚、短颌鲚和湖鲚未能各自形成单系群。刀鲚、短颌鲚与湖鲚的AMOVA分析结果显示种间的分子差异仅占9.76%，且统计检验不显著。Fst值变化范围和AMOVA分析的统计检验结果表明短颌鲚、刀鲚与湖鲚之间无显著的遗传分化。因此，短颌鲚和湖鲚应为刀鲚的不同生态型种群，而不能作为独立的种。
（3）应用AFLP分子标记技术对5种鲚属鱼类的系统发育关系进行了分析。结果显示：刀鲚、短颌鲚和湖鲚的种间平均遗传距离和基因分化系数明显低于它们与七丝鲚和凤鲚间的比较结果。将短颌鲚与湖鲚被视作刀鲚的种群，对刀鲚、七丝鲚与凤鲚来进行AMOVA分析的结果显示分子差异主要属于种间差异，且统计检验结果显著。NJ系统发育树与UPGMA系统树的结果也显示出湖鲚、短颌鲚与刀鲚的亲缘关系紧密，而与凤鲚和七丝鲚亲缘关系较远。据此推测短颌鲚、湖鲚与刀鲚应属于同一个种。
2.刀鲚的分子系统地理学研究
（1）利用线粒体DNA控制区片段及Cytb片段对刀鲚的11个群体进行了分析，基于BI法构建的系统发育树中，刀鲚群体113个控制区单倍型聚为3个类群。中性检验的结果都表明三个类群都经历过群体扩张。根据贝叶斯系统发育树划分为三个组群进行AMOVA分析的结果显示三个组群间存在显著的遗传结构。更新世冰期导致长江河流湖泊的隔离可能使刀鲚分化出的淡水生态型。更新世冰期晚期，日本海的剧烈波动以及有明海的特殊地理环境可能是日本刀鲚群体发生隔离的重要原因。此外，刀鲚洄游的生活史特性也影响3个类群在地理上的分布频率。
（2）基于ISSR分子标记开展了西北太平洋刀鲚种群遗传结构及其地理分布格局研究。UPGMA系统树与PCA分析的结果显示日本有明海群体与中国群体间呈现显著的遗传分化。STRUCTURE分析结果表明刀鲚5个群体应分为2个遗传上不同的组群；AMOVA分析的结果也表明了两组群间存在显著的遗传差异。基因流结果显示刀鲚的日本有明海群体与中国群体间的基因交流受到限制，而中国群体间的基因交流频繁。更新世晚期日本海平面的剧烈波动导致的栖息地隔离，以及较强的海洋环流可能限制了中日群体间刀鲚的基因交流，刀鲚的栖息地和生活史特征导致的基因同质可能是中国群体间基因交流频繁的重要原因。
（3）应用ISSR分子标记对长江流域刀鲚种群遗传结构及其地理分布格局进行了研究。STRUCTURE分析结果表明刀鲚的5个群体应分为2个遗传上不同的组群。AMOVA分析的结果也表明了两组群间存在显著的遗传差异。刀鲚群体UPGMA系统树中，安庆、天鹅洲和赤壁群体大部分个体聚为一支，镇江与太湖群体聚为另一支。本研究结果表明刀鲚群体间存在显著的遗传分化。长江河流湖泊的隔离可能使刀鲚分化出淡水生态型，并且这种分化可能与更新世的气候波动有关。
3.凤鲚群体的形态学、遗传学研究
（1）对中国沿海的5个凤鲚群体进行了形态学研究。聚类分析表明凤鲚的宁波群体与其他群体间差异显著。单因子方差分析也显示出宁波群体与其他的凤鲚群体之间存在差异。与其他凤鲚群体相比，宁波群体在上下鳃耙数和脊椎骨数等分节特征的分布频率上均存在明显差异。栖息地环境可能导致不同凤鲚群体适应了不同的地理环境，从而限制了不同凤鲚群体的扩散区域，最终导致凤鲚群体形态特征上出现差异。
（2）基于线粒体控制区、Cytb及COI片段序列开展了凤鲚的分子系统地理学研究。结果显示分布于中国沿岸的5个凤鲚群体分化为南北两个世系。基于细胞色素b计算的两个种的分化时间约为390万年，分化事件发生于上新世中期；基于COI基因片段序列得出的凤鲚两个世系间净遗传距离为5.6%，超过了COI基因DNA条形码鉴别不同物种2~3%的遗传距离阈值，这表明凤鲚的群体中可能存在一个隐蔽种，凤鲚的南北两个世系应为两个不同的物种。在更新世的末次冰盛期以后，随着海平面的升高，凤鲚的栖息地可能也发生了扩张。因此，群体数量的增长和栖息地的扩大可能是导致凤鲚mtDNA多态性模式的原因。
（3）应用ISSR分子标记对分布于中国沿岸4个凤鲚群体遗传多样性进行了研究。STRUCTURE分析结果表明4个群体应分为2个遗传上不同的组群；AMOVA分析的结果显示两组群间的遗传差异显著。UPGMA系统树显示上海凤鲚群体单独聚为一支，而温州、厦门和大亚湾群体聚为另一支。研究结果显示，长江型凤鲚群体与其他凤鲚群体间存在较大的遗传分化并且缺乏基因交流。凤鲚南北两类群在地理上为异域分布，这可能与其产卵场的不同、以及栖息水域的温度、盐度等环境因子有关。
In the present study, morphological, mitochondrial DNA sequence and AFLP markerswere used for the phylogenetic and taxonomic analysis of Coilia in China. Thevalidity of naming species of C. brachygnathus and C. nasus taihuensis wasinvestigated. To elucidate the phylogeographic pattern of C. nasus, mitochondrialDNA sequence and ISSR markers were used to study the sample of C. nasus inYangtze River and Northwestern Pacific. To assess the genetic structure of C. mystus,we also examined the sample along the coastal regions of China by usingmorphological, mitochondrial DNA sequence and ISSR markers.
1The phylogenetic and taxonomic analysis of Coilia in China:
(1) The phylogeny and taxonomy of Coilia was studied by the morphological analysisin China. The results from the cluster analysis showed a close relationship among C.brachygnathus, C. nasus taihuensis, and C. nasus. C. brachygnathus and C. nasustaihuensis should be synonymized with C. nasus based on the results from the thecluster analysis, principal component analysis and the frequency distribution of themeristic characters in Coilia species.
(2) To elucidate the phylogeny and taxonomy of Coilia, mitochondrial COI, ND5andCytb fragment were used for the combined analysis. C. brachygnathus, C. nasustaihuensis, and C. nasus did not form three separate monophyletic groups in the NJ,MP and BI trees. The average intraspecific genetic distance within C. brachygnathus,C. nasus, and C. nasus taihuensis approximates to their interspecific genetic distance.The mean pairwise Fst value obtained from C. brachygnathus, C. nasus, and C. nasus taihuensis comparisons was significantly lower than the mean pairwise Fst valueobtained between these species and the species of C. grayii and C. mystuscomparisons. Results of the AMOVA revealed that9.76%of the total molecularvariance can be attributed to the significant differences among species. The studyshowed no significant difference among C. brachygnathus, C. nasus, and C. nasustaihuensis. C. brachygnathus and C. nasus taihuensis should therefore besynonymized with C. nasus.
(3) AFLP analysis was applied to study the phylogeny and taxonomy of Coilia inChina. The Gst value and the interspecific genetic distance among C. brachygnathus,C. nasus, and C. nasus taihuensis were significantly lower than those of Gst value andinterspecific genetic distance which were obtained between these species and thespecies of C. grayii and C. mystus. If C. brachygnathus and C. nasus taihuensis wereregarded as populations of C. nasus to investigate the genetic structures of the threespecies, C. nasus, C. grayii and C. mystus, most of the variance (P=0.00) was foundamong species and a small amount within species. In the neighbor-joining tree andUPGMA dendrogram, a close relationship was indicated among C. brachygnathus, C.nasus taihuensis, and C. nasus. Therefore, C. brachygnathus and C. nasus taihuensisshould be synonymized with C. nasus.
2Molecular Phylogeography of C. nasus:
(1) To elucidate the phylogeographic pattern of C. nasus, mitochondrial DNAsequences were used to study the sample of C. nasus in Yangtze River andNorthwestern Pacific. The BI tree constructed using the complete data set of113mitochondrial control region haplotypes identified three distinct lineages. The FStestsof three lineages were negative and highly significant, which indicated populationexpansion. Analyses of molecular variance and the population statistic Fst alsorevealed significant genetic structure among three lineages. As the base levels oferosion and ground water levels were lower as well, rivers in upland areas could formdeeply incised river valleys during the last Pleistocene glaciation. We conclude thatfreshwater populations of C. nasus could thereby have become isolated in the lakes ofYangtze River, resulting in a separate lineage observed in the mitochondrial genome. Strong genetic break was found between the Sea of Japan and the China Seapopulations, likely reflecting isolation of Ariake Bay in the Northwestern Pacificduring the late Pleistocene. A hypothetical scenario to explain the observedphylogeographic pattern is that genetic differentiation and homogeneity may beattributed to habitat and life-history characteristics.
(2) Northwestern Pacific provides unique scenarios for studying the roles ofgeography and ecology in driving population divergence and speciation. Toinvestigate geographical patterns of genetic variation in the Japanese grenadieranchovy using ISSR markers we collected individuals from five locations throughouttheir distribution in the Northwest Pacific. Analyses of molecular variance showedthat genetic differentiation among groups is relatively high. Bayesian analysis of ISSRdata also revealed significant population structuring between Chinese and Japaneselocations. Phylogenetic reconstructions show reciprocal monophyly in populationsbetween China and the Ariake Bay of Japan. We conclude that the present-dayphylogeographic pattern is the result of genetic isolation between Japanese andChinese populations in the Northwestern Pacific following the glacial retreat, and thatlife-history traits and ecology may play a pivotal role in shaping the realizedgeographical distribution pattern of this species.
(3) To investigate the phylogeographic pattern of C. nasus, ISSR markers were usedto study the sample of C. nasus in Yangtze River. Bayesian analysis of ISSR datarevealed significant population structuring between freshwater and anadromouspopulations (K=2). Analyses of molecular variance also revealed that geneticdifferentiation among groups is relatively high. Phylogenetic reconstructions showtwo distinct lineages in Yangtze River. We conclude that the present-dayphylogeographic pattern is the result of genetic isolation between freshwater andanadromous populations in Yangtze River during the last Pleistocene glaciation, andthat life-history traits and ecology may play a pivotal role in shaping the realizedgeographical distribution pattern of this species.
3Phylogeography of C. mystus:
(1) To investigate the genetic difference of C. mystus by the morphological analysis we collected individuals from five locations throughout their distribution alongChinese coastal waters. The results from the cluster analysis showed strong geneticbreak between Ningbo and the other populations. There were significant differencesbetween Ningbo and the other populations based on the results from the clusteranalysis, principal component analysis and the frequency distribution of the meristicand gill rakers characters in populations of C. mystus. Local populations may besufficiently locally adapted to the particular habitat to limit the dispersal amongpopulations of C. mystus. Habitat and life-history differences may play a pivotal rolein shaping morphological characteristics of this species.
(2) To elucidate the phylogeographic pattern of C. mystus, mitochondrial DNAsequences were used to study the sample of C. mystus along Chinese coastal waters.The NJ tree constructed with mtDNA sequences identified two distinct lineages. Thecytochrome b and control region data suggests a divergence time of3.9MY betweenthe two lineages, indicating isolation in the middle Pliocene. A highest geneticdistance for COI gene was found between two lineages (5.6%). According to thebarcoding approach, species could be identified based on a ‘barcoding gap’ betweenintra-and interspecific genetic distances by using a threshold value of23%forspecies delimitation. The study indicated the presence of cryptic species within thepopulations of C. mystus. The neutrality tests indicated population expansion in thetwo lineages. Population range expansion must have occurred after the last glacialmaximum. Range contractions and expansions played a central role in shaping thegenetic diversity of the two lineages of C. mystus.
(3) To investigate the phylogeographic pattern, ISSR markers were used to study thesample of C. mystus along Chinese coastal waters. Bayesian analysis of ISSR datarevealed significant population structuring between northern and southern groups(K=2). Analyses of molecular variance also revealed that genetic differentiationamong groups is relatively high. Phylogenetic reconstructions show reciprocalmonophyly in populations between northern (SH) and southern (NB, XM and DB)groups. The results showed strong genetic break northern and southern populations.Local populations may be sufficiently locally adapted to the particular habitat to limit the dispersal among populations of C. mystus. Life-history traits and ecology mayplay a pivotal role in shaping the realized geographical distribution pattern of thisspecies.
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