东海鮸鱼群体遗传多样性与11种石首鱼分子系统学研究
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摘要
石首鱼是重要的经济鱼类，中国有石首鱼类17属30种。由于过度捕捞和生境改变，导致石首鱼类资源锐减，个别属种已经被列为易危或濒危种类，石首鱼类资源有效保护和合理利用前景令人担忧。此外、石首鱼科种类繁多且具分布有明显的地理区域性，是进化研究的好材料。本研究首先以控制区序列为分子标记解析东海鮸鱼群体遗传多样性；其次，测定10种石首鱼类线粒体基因组全序列，并解析基因组编码区和非编码区特征；最后，基于获得的石首鱼线粒体基因组序列构建11种石首鱼分子系统树，并结合分子定时技术估算物种分歧时间，以期为石首鱼类资源可持续利用和石首鱼类起源分化研究积累理论资料。
主要研究结果如下：
（1）东海鮸鱼群体存在轻微遗传结构，舟山群体与温岭、象山、乐清、瑞安、温州群体遗传分化显著。鮸鱼群体控制区序列偏离中性进化且群体曾经历过扩张历史，扩张事件发生于约17,4000年前，处于第四纪更新世末期。更新世海平面反复升降可能是导致鮸鱼群体扩张的原因。
（2）10种石首鱼线粒体基因组在基因编码及排列顺序、基因结构、碱基组成和密码子使用频率方面均高度保守，且符合脊椎动物线粒体基因组典型模式。非编码区则存在显著的结构变异现象。10种石首鱼类线粒体基因组轻链复制起始区环结构碱基分为三个类型：T碱基或偏T碱基密集，C碱基或偏C碱基密集，无明显碱基偏性组成。臂结构存在两种保守序列：5’-GCCGG-3’和5’-ACCGG-3’。控制区中央保守区在10种石首鱼线粒体基因组中存在不同程度缺失，其中的关键保守序列也存在变异。变异类型包括完全缺失，缺失CSB-F，以及CSB-E标志序列与典型序列不同。这些普遍的变异类型，提示石首鱼类线粒体基因组控制区可能存在不同类型的进化路径。
（3）构建的分子系统树强烈支持石首鱼科和黄鱼亚科单系性，但不支持白姑鱼亚科单系起源。黄鱼属与梅童鱼属属间关系极近，不支持两属的单系性。银彭纳石首鱼较勒氏枝鳔石首鱼、尖头黄鳍牙和黄姑鱼分化更早。分子定时技术估算出中国近海石首鱼类起源于约101万年前，处于更新世中期，时间上明显晚于美洲石首鱼类化石记录的年代，支持美洲所在的新大陆为石首鱼类起源中心，随后部分祖种迁移扩散至旧大陆并适应环境演化成为旧大陆现今属种原始祖先这一假说。
The sciaenid fishes (family Sciaenidae) are very important fisher resource andattractive species for aquaculture. China has the highest number of species in this family,with about30species in17genera. Due to a prolonged period of intensive fishing, theresources of sciaenid fishes have been remarkably declined, some species even was listedas endangered. In addition, sciaenid fishes commonly occur in temperate to tropical coastalwater and estuaries throughout the world, but are absent or poorly represented in oceanicislands group. Such pattern of distribution of sciaenid fishes provides a good model forstudying the fish evolution. In this study, the population genetic structure of miiuy croakerin East China Sea was investigated first. Secondly, ten mitochondrial genomes of croakerswere sequenced and characterized. Bioinformatic analyses were used to compare thecharacterization of coding regions and detect the variation in non-coding regions. Thirdly,phylogenetic relationships of eleven croakers were investigated and molecular datingtechnology was used to estimate the divergence time of those species with the aim to inferthe history of their origin and evolution.
This thesis mainly contains three parts as followings:
1. Weak genetic structure was detected among the six miiuy croaker populations, Fstanalysis revealed that ZS population showed significant genetic differentiations with theother five populations (RA, WL, WZ, YQ and XS). Neutrality test, mismatch distributionanalysis and minimum spanning network analysis indicated the miiuy croaker in the EastChina Sea might have experienced a rapid population expansion, and this event mayoccurred in late Pleistocene, about17,4000years ago. The climate change happened inPleistocene ice age and the resulting fluctuation of sea levels might explain the suddenexpansion of miiuy croaker population.
2. The mitochondrial genomes of ten croakers are much conserved in genomecomposition, gene order, gene structure, base composition and codon usage frequency, andare similar to the typical vertebrate mitochondrial genome. Significant structure variationswere detected in the non-coding region. The pattern of loop and stem are different amongten mitochondrial genomes. The loop of OLhas three types: T-rich or partial T-rich, C-rich or partial C-rich, and no base-bias. Two type of conserved motif were identified in stem ofOL:5’-GCCGG-3’ and5’-ACCGG-3’. The complete central conserved sequence domainwas absence in the mitochondrial genome of spinyhead croaker, bighead croaker, smallyellow croaker and large yellow croaker. The incomplete central conserved sequencesdomain was detected in the mitochondrial genome of silver croaker, with absence of CSB-F.Although the central conserved sequence domain in goatee croaker was complete, but theCSB-E was5’-GTGAGG-3’, rather than the typical5’-GTGGGG-3’, all these resultsindicated that the control region in mitochondrial genomes of sciaenid fishes may evolveunder different pattern.
3. The phylogenetic tree supported the monophyly of Sciaenidae and Pseudosciaeniae,but rejected the monophyly of Argyrosominae. Larimichthys and Collichthys have agenetically closet relationship, and the monophyly of both genera were rejected,introgressive hybridization may exits between Larimichthys and Collichthys fishes. Silvercroaker was found to be more evolutionarily older than goatee croaker, golden drum andyellow drum. Molecular dating analysis showed that the sciaenid fishes of coastal water ofChina may originate in the middle Pleistocene, about1.01million years ago (95%Posteriorprobability density0.7176mya to1.3132mya) and was obviously later than the ancestor ofAmerica sciaenid fishes documented by fossil record. This result could be another evidencefor the hypothesis that the common ancestor of family Sciaenidae may have a New Worldorigin, with subsequent dispersal of ancestor of the Old World group.
主要研究结果如下：
（1）东海鮸鱼群体存在轻微遗传结构，舟山群体与温岭、象山、乐清、瑞安、温州群体遗传分化显著。鮸鱼群体控制区序列偏离中性进化且群体曾经历过扩张历史，扩张事件发生于约17,4000年前，处于第四纪更新世末期。更新世海平面反复升降可能是导致鮸鱼群体扩张的原因。
（2）10种石首鱼线粒体基因组在基因编码及排列顺序、基因结构、碱基组成和密码子使用频率方面均高度保守，且符合脊椎动物线粒体基因组典型模式。非编码区则存在显著的结构变异现象。10种石首鱼类线粒体基因组轻链复制起始区环结构碱基分为三个类型：T碱基或偏T碱基密集，C碱基或偏C碱基密集，无明显碱基偏性组成。臂结构存在两种保守序列：5’-GCCGG-3’和5’-ACCGG-3’。控制区中央保守区在10种石首鱼线粒体基因组中存在不同程度缺失，其中的关键保守序列也存在变异。变异类型包括完全缺失，缺失CSB-F，以及CSB-E标志序列与典型序列不同。这些普遍的变异类型，提示石首鱼类线粒体基因组控制区可能存在不同类型的进化路径。
（3）构建的分子系统树强烈支持石首鱼科和黄鱼亚科单系性，但不支持白姑鱼亚科单系起源。黄鱼属与梅童鱼属属间关系极近，不支持两属的单系性。银彭纳石首鱼较勒氏枝鳔石首鱼、尖头黄鳍牙和黄姑鱼分化更早。分子定时技术估算出中国近海石首鱼类起源于约101万年前，处于更新世中期，时间上明显晚于美洲石首鱼类化石记录的年代，支持美洲所在的新大陆为石首鱼类起源中心，随后部分祖种迁移扩散至旧大陆并适应环境演化成为旧大陆现今属种原始祖先这一假说。
The sciaenid fishes (family Sciaenidae) are very important fisher resource andattractive species for aquaculture. China has the highest number of species in this family,with about30species in17genera. Due to a prolonged period of intensive fishing, theresources of sciaenid fishes have been remarkably declined, some species even was listedas endangered. In addition, sciaenid fishes commonly occur in temperate to tropical coastalwater and estuaries throughout the world, but are absent or poorly represented in oceanicislands group. Such pattern of distribution of sciaenid fishes provides a good model forstudying the fish evolution. In this study, the population genetic structure of miiuy croakerin East China Sea was investigated first. Secondly, ten mitochondrial genomes of croakerswere sequenced and characterized. Bioinformatic analyses were used to compare thecharacterization of coding regions and detect the variation in non-coding regions. Thirdly,phylogenetic relationships of eleven croakers were investigated and molecular datingtechnology was used to estimate the divergence time of those species with the aim to inferthe history of their origin and evolution.
This thesis mainly contains three parts as followings:
1. Weak genetic structure was detected among the six miiuy croaker populations, Fstanalysis revealed that ZS population showed significant genetic differentiations with theother five populations (RA, WL, WZ, YQ and XS). Neutrality test, mismatch distributionanalysis and minimum spanning network analysis indicated the miiuy croaker in the EastChina Sea might have experienced a rapid population expansion, and this event mayoccurred in late Pleistocene, about17,4000years ago. The climate change happened inPleistocene ice age and the resulting fluctuation of sea levels might explain the suddenexpansion of miiuy croaker population.
2. The mitochondrial genomes of ten croakers are much conserved in genomecomposition, gene order, gene structure, base composition and codon usage frequency, andare similar to the typical vertebrate mitochondrial genome. Significant structure variationswere detected in the non-coding region. The pattern of loop and stem are different amongten mitochondrial genomes. The loop of OLhas three types: T-rich or partial T-rich, C-rich or partial C-rich, and no base-bias. Two type of conserved motif were identified in stem ofOL:5’-GCCGG-3’ and5’-ACCGG-3’. The complete central conserved sequence domainwas absence in the mitochondrial genome of spinyhead croaker, bighead croaker, smallyellow croaker and large yellow croaker. The incomplete central conserved sequencesdomain was detected in the mitochondrial genome of silver croaker, with absence of CSB-F.Although the central conserved sequence domain in goatee croaker was complete, but theCSB-E was5’-GTGAGG-3’, rather than the typical5’-GTGGGG-3’, all these resultsindicated that the control region in mitochondrial genomes of sciaenid fishes may evolveunder different pattern.
3. The phylogenetic tree supported the monophyly of Sciaenidae and Pseudosciaeniae,but rejected the monophyly of Argyrosominae. Larimichthys and Collichthys have agenetically closet relationship, and the monophyly of both genera were rejected,introgressive hybridization may exits between Larimichthys and Collichthys fishes. Silvercroaker was found to be more evolutionarily older than goatee croaker, golden drum andyellow drum. Molecular dating analysis showed that the sciaenid fishes of coastal water ofChina may originate in the middle Pleistocene, about1.01million years ago (95%Posteriorprobability density0.7176mya to1.3132mya) and was obviously later than the ancestor ofAmerica sciaenid fishes documented by fossil record. This result could be another evidencefor the hypothesis that the common ancestor of family Sciaenidae may have a New Worldorigin, with subsequent dispersal of ancestor of the Old World group.
引文
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