三种海洋鱼类分子系统地理学研究
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摘要
本文以西北太平洋三种海洋鱼类白姑鱼、黄姑鱼和玉筋鱼为研究对象,采用线粒体DNA、AFLP和同工酶等标记技术开展了这三种海洋鱼类分子系统地理学研究,系统研究了三种鱼类的分子系统地理分布模式,分析了更新世冰期、洋流和温度等外界因素对海洋鱼类群体遗传结构和分子系统地理分布模式的影响。主要研究结果如下:
1、为了检测白姑鱼的分子系统地理分布模式和遗传结构,我们对白姑鱼分布区内12个群体共132个个体的线粒体DNA控制区序列和部分个体细胞色素b序列进行了测定和分析。在控制区序列和细胞色素b序列上,白姑鱼群体间有显著的遗传分化,明显分为中日两支,中日群体间无共享单倍型。中国群体的核苷酸多态度明显高于日本群体。中性检验和核苷酸不配对分布表明白姑鱼中日两支都经历了更新世的群体扩张。分子方差分析和FST显示白姑鱼日本群体间遗传差异显著,但中国群体间无明显遗传分化。白姑鱼这种地理分布模式显示这个种的扩散能力比较弱。中国白姑鱼群体间没有检测到显著的系统地理格局,这可能是因为末次冰期后白姑鱼群体在中国大陆架区发生大范围栖息地扩张所引起的,扩散后新建立的群体尚未在迁移与漂变之间取得平衡。
2、利用AFLP技术对白姑鱼中日四个群体共70个个体的群体遗传变异进行了研究,5对选择性引物在70个个体中共扩增出304个位点,其中多态位点200个。四个群体的多态位点比例在47.13%和57.63%之间。在四个群体中,有明海群体的Nei遗传多样性指数和Shannon多样性指数最高,而伊势弯群体遗传多样性最低。根据群体间和个体间的遗传距离,分别构建了群体和个体的UPGMA聚类树,显示中日群体分为明显的两支。分子方差分析和FST显示中日群体间有显著的遗传分化,并且中日两种群内都有显著的遗传分化。这表明白姑鱼不同群体间基因交流较弱。
3、采用水平淀粉凝胶电泳技术对5个白姑鱼群体的群体遗传结构和群体遗传分化进行了研究。结果表明,在11种同工酶共检测到15个位点,其中11个位点表现为多态。白姑鱼群体的平均多态位点比例在0.0667和0.5333之间;5个群体的平均观测杂合度和预期杂合度分别在0.0033到0.0133和0.0032到0.0191之间。同其他海水鱼类相比,白姑鱼群体的杂合度非常低。白姑鱼5个群体间的遗传距离在0.00005到0.00026之间; 5个群体的等位基因频率差异不显著,中日群体的遗传分化很弱。在5个群体中,中国3个群体遗传多样性高于日本两个群体。
4、采用线粒体DNA控制区部分序列对黄海和东海的黄姑鱼群体遗传结构和基因交流进行了研究。在3个群体65个个体共检测得到37个单倍型。三个群体的单倍型多样性指数和核苷酸多态性指数分别在0.9130±0.0308和0.9926±0.0230,0.0073±0.0043和0.0099±0.0057之间。分子方差分析显示群体间无显著的遗传分化。但是Exact检验不支持黄海和东海黄姑鱼是一个随机交配的群体。核苷酸不配对分析表明黄姑鱼群体在85,000–170,000年前经历了群体扩张。
5、对青岛和厦门黄姑鱼群体的遗传多样性进行了AFLP分析,5对选择性引物在两个群体47个个体中,共扩增出461个位点,多态位点265个。青岛和厦门群体的多态位点比例、Nei遗传多样性指数和Shannon遗传多样性指数分别为51.70%、51.99%,0.1022、0.0996,0.1643、0.1622;两个群体遗传多样性在同一水平上。基因分化系数GST、Shannon遗传多样性指数和AMOVA分析均显示黄姑鱼的遗传变异主要来源于群体内个体间,而群体间无明显的遗传分化。群体的显性基因型频率分布和位点差异数分布显示两个群体有基本相同的群体遗传结构。研究结果表明,黄姑鱼青岛和厦门群体间无明显的遗传差异,群体间有明显的基因交流。
6、为了检验更新世冰期和环境因子对海洋鱼类进化的影响,我们采用线粒体DNA对玉筋鱼的系统地理分布模式和遗传结构进行了研究。在玉筋鱼群体内我们检测到两个显著分化的单倍型类群,更新世冰期的隔离可能是这两个类型产生分化的原因。两个单倍型类群在地域上的分布频率具有显著差异,通过比较日本海和太平洋侧两个单倍型类型分布区域的不同,发现洋流和水温对玉筋鱼的分子系统地理模式具有显著影响。分子方差分析以及群体间分化指数FST值均显示玉筋鱼南北两个组群体内不存在明显的群体遗传结构。这可能是因为末次冰期后玉筋鱼群体在陆架区发生大范围栖息地扩张所引起的,扩散后新建立的群体尚未在迁移与漂变之间取得平衡;也可能是黑潮、亲潮和对马暖流洋流加强了组群内各群体间的联系。
7、为了进一步解决玉筋鱼南北两个组群的分类地位和研究环境因子对玉筋鱼核基因的影响,我们利用Ammodytes hexapterus作为外群,对玉筋鱼12个群体共211个个体进行了AFLP分析。结果表明玉筋鱼南北两个组群是互为单系的关系,并且两组群间有完全的基因隔离,玉筋鱼南北两个组群可能是不同的亚种或种。两个组群的分化可能是玉筋鱼从北太平洋向南扩散适应不同温度的结果。
In this study, the phylogeography and genetic structures of Pennahia argentata, Nibea albiflora and Ammodytes personatus were studied by mtDNA, AFLP and isozyme markers. We discussed the role of Pleistocene ice ages and present environmental factors in shaping the phylogeographic pattern and genetic structures of marine species.
1、One hundred and thirty two individuals of Pennahia argentata were sampled from 12 localities throughout its distribution range, to estimate the demographic history and genetic structure based on mitochondrial DNA cytochrome b gene and control region sequences. Two distinct clades with net genetic divergence of 3% in the control region were detected, one in the Chinese coastal waters and the other in the Japanese coastal waters. These clades may have been isolated and diverged during Pleistocene low sea levels. Nucleotide diversity was much higher in the Chinese clade than that in the Japanese clade. The demographic history of the two clades was examined using neutrality tests and mismatch analyses, and the results indicated Pleistocene population expansion in both clades. Molecular variance analyses and pairwise FST revealed significant differentiation between two Japanese populations and lack of genetic structure in the Chinese populations. The significant geographic structure in white croaker suggests low level of dispersal in this species. The lack of phylogeographical structure in China coastal waters may reflect a recent range expansion after the last glacial maximum and insufficient time to attain migration-drift equilibrium.
2、The genetic structures of four populations of P. argentata were analyzed by AFLP technology. A total of 304 putative loci were detected by the five primer combinations, of which 200 were polymorphic. The proportion of polymorphic loci among four populations varied from 47.13% to 57.63%. The population with the highest Nei’s genetic diversity and Shannon diversity index was Ariake Sea population, the lowest Nei’s genetic diversity and Shannon diversity index was found in Ise Bay population. Two clades were detected, molecular variance analyses and pairwise FST also supported the separation of Chinese and Japanese populations of P. argentata.
3、To investigate the genetic structure and differentiation of different wild populations of P. argentata, horizontal starch gel electrophoresis was performed on 133 individuals collected from five different locations in China and Japan. The eleven enzyme systems revealed 15 putative loci, of which eleven were polymorphic. The proportions of polymorphic loci of P. argentata populations varied from 0.0667 to 0.5333; the mean observed and expected heterozygosity varied from 0.0033 to 0.0133 and 0.0032 to 0.0191, respectively. The heterozygosity revealed a low genetic variability for P. argentata in comparison with other marine fishes. The genetic distance among populations varied from 0.00005 to 0.00026. A weak differentiation observed within each clade; and no significant differences in gene frequencies among populations were observed in P. argentata. Among five populations, Chinese populations showed more genetic variability than that in Japanese populations.
4、The population genetic structure and level of gene flow of Nibea albiflora from the Yellow and the East China seas were examined with a 479bp segment of mtDNA control region. A total of 65 samples were collected from three locations and 37 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the three populations ranged from 0.9130±0.0308 (Zhoushan) to 0.9926±0.0230 (Xiamen), and from 0.0073±0.0043 (Qingdao) to 0.0099±0.0057 (Xiamen), respectively. AMOVA and pairwise FST revealed little genetic structure between the Yellow and the East China seas in N. albiflora. But based on the exact test of differentiation, the null hypothesis that N. albiflora within the Yellow and East China seas constitutes a panmictic mtDNA gene pool was rejected. This might be caused by the broad spawning areas but not by the Yangtze River outflow. Mismatch distribution revealed that N. albiflora has undergone population expansion, possibly before last 85,000–170,000 years. The existence of high gene flow between stocks in the studied area was supported by our results. Annual migrations, larval drift in the ocean currents, and recent range expansion could be the reasons for little genetic structure in the studied area.
5、AFLP was used to analyze the genetic diversity of two populations of N. albiflora from Qingdao and Xiamen sea area. A total of 47 individuals were studied using five primer combinations. A total of 461 loci were detected, of which 265 were polymorphic. The results showed that the genetic diversity of these two populations was at the same level. The proportion of polymorphic loci, the Nei’s genetic diversity and Shannon diversity index of Qingdao and Xiamen populations were 51.70% and 51.99%, 0.1022 and 0.0996, 0.1643 and 0.1622, respectively. Gst value, Shannon diversity index and AMOVA analysis indicated that the genetic variation mainly came from individuals within populations and there was no significant genetic differentiation between populations. Mismatch distribution analysis and dominant gene frequency revealed that these two populations have the same genetic population structure. The results of AFLP analysis indicated that there is no significant genetic differentiation between two populations due to high gene flow.
6、To assess the role of historical process and contemporary factors in shaping population structures in the northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species’range were sequenced. Two distinct lineages were detected, which might be divergent in the Sea of Japan and Pacific coastal waters of Japanese Island, during the low sea level. Significant genetic structure was revealed as expected between the Kuroshio and Oyashio Currents. However, significant genetic structure was also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao populations with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the north group and south group populations indicate that ocean currents within groups facilitate the dispersal of A. personatus.
7、AFLP markers were also used to analyze the genetic structures of A. personatus and status of north and south groups. Two hundred and eleven individuals of A. personatus and 37 individuals of Ammodytes hexapterus were amplified by four primer combinations. The results showed north group and south group were reciprocally monophyletic. Complete reproductive isolation may exist between the two groups. These results suggest that the two groups have already reached a stage of sufficient genetic differentiation to be considered as two distinct species.
1、为了检测白姑鱼的分子系统地理分布模式和遗传结构,我们对白姑鱼分布区内12个群体共132个个体的线粒体DNA控制区序列和部分个体细胞色素b序列进行了测定和分析。在控制区序列和细胞色素b序列上,白姑鱼群体间有显著的遗传分化,明显分为中日两支,中日群体间无共享单倍型。中国群体的核苷酸多态度明显高于日本群体。中性检验和核苷酸不配对分布表明白姑鱼中日两支都经历了更新世的群体扩张。分子方差分析和FST显示白姑鱼日本群体间遗传差异显著,但中国群体间无明显遗传分化。白姑鱼这种地理分布模式显示这个种的扩散能力比较弱。中国白姑鱼群体间没有检测到显著的系统地理格局,这可能是因为末次冰期后白姑鱼群体在中国大陆架区发生大范围栖息地扩张所引起的,扩散后新建立的群体尚未在迁移与漂变之间取得平衡。
2、利用AFLP技术对白姑鱼中日四个群体共70个个体的群体遗传变异进行了研究,5对选择性引物在70个个体中共扩增出304个位点,其中多态位点200个。四个群体的多态位点比例在47.13%和57.63%之间。在四个群体中,有明海群体的Nei遗传多样性指数和Shannon多样性指数最高,而伊势弯群体遗传多样性最低。根据群体间和个体间的遗传距离,分别构建了群体和个体的UPGMA聚类树,显示中日群体分为明显的两支。分子方差分析和FST显示中日群体间有显著的遗传分化,并且中日两种群内都有显著的遗传分化。这表明白姑鱼不同群体间基因交流较弱。
3、采用水平淀粉凝胶电泳技术对5个白姑鱼群体的群体遗传结构和群体遗传分化进行了研究。结果表明,在11种同工酶共检测到15个位点,其中11个位点表现为多态。白姑鱼群体的平均多态位点比例在0.0667和0.5333之间;5个群体的平均观测杂合度和预期杂合度分别在0.0033到0.0133和0.0032到0.0191之间。同其他海水鱼类相比,白姑鱼群体的杂合度非常低。白姑鱼5个群体间的遗传距离在0.00005到0.00026之间; 5个群体的等位基因频率差异不显著,中日群体的遗传分化很弱。在5个群体中,中国3个群体遗传多样性高于日本两个群体。
4、采用线粒体DNA控制区部分序列对黄海和东海的黄姑鱼群体遗传结构和基因交流进行了研究。在3个群体65个个体共检测得到37个单倍型。三个群体的单倍型多样性指数和核苷酸多态性指数分别在0.9130±0.0308和0.9926±0.0230,0.0073±0.0043和0.0099±0.0057之间。分子方差分析显示群体间无显著的遗传分化。但是Exact检验不支持黄海和东海黄姑鱼是一个随机交配的群体。核苷酸不配对分析表明黄姑鱼群体在85,000–170,000年前经历了群体扩张。
5、对青岛和厦门黄姑鱼群体的遗传多样性进行了AFLP分析,5对选择性引物在两个群体47个个体中,共扩增出461个位点,多态位点265个。青岛和厦门群体的多态位点比例、Nei遗传多样性指数和Shannon遗传多样性指数分别为51.70%、51.99%,0.1022、0.0996,0.1643、0.1622;两个群体遗传多样性在同一水平上。基因分化系数GST、Shannon遗传多样性指数和AMOVA分析均显示黄姑鱼的遗传变异主要来源于群体内个体间,而群体间无明显的遗传分化。群体的显性基因型频率分布和位点差异数分布显示两个群体有基本相同的群体遗传结构。研究结果表明,黄姑鱼青岛和厦门群体间无明显的遗传差异,群体间有明显的基因交流。
6、为了检验更新世冰期和环境因子对海洋鱼类进化的影响,我们采用线粒体DNA对玉筋鱼的系统地理分布模式和遗传结构进行了研究。在玉筋鱼群体内我们检测到两个显著分化的单倍型类群,更新世冰期的隔离可能是这两个类型产生分化的原因。两个单倍型类群在地域上的分布频率具有显著差异,通过比较日本海和太平洋侧两个单倍型类型分布区域的不同,发现洋流和水温对玉筋鱼的分子系统地理模式具有显著影响。分子方差分析以及群体间分化指数FST值均显示玉筋鱼南北两个组群体内不存在明显的群体遗传结构。这可能是因为末次冰期后玉筋鱼群体在陆架区发生大范围栖息地扩张所引起的,扩散后新建立的群体尚未在迁移与漂变之间取得平衡;也可能是黑潮、亲潮和对马暖流洋流加强了组群内各群体间的联系。
7、为了进一步解决玉筋鱼南北两个组群的分类地位和研究环境因子对玉筋鱼核基因的影响,我们利用Ammodytes hexapterus作为外群,对玉筋鱼12个群体共211个个体进行了AFLP分析。结果表明玉筋鱼南北两个组群是互为单系的关系,并且两组群间有完全的基因隔离,玉筋鱼南北两个组群可能是不同的亚种或种。两个组群的分化可能是玉筋鱼从北太平洋向南扩散适应不同温度的结果。
In this study, the phylogeography and genetic structures of Pennahia argentata, Nibea albiflora and Ammodytes personatus were studied by mtDNA, AFLP and isozyme markers. We discussed the role of Pleistocene ice ages and present environmental factors in shaping the phylogeographic pattern and genetic structures of marine species.
1、One hundred and thirty two individuals of Pennahia argentata were sampled from 12 localities throughout its distribution range, to estimate the demographic history and genetic structure based on mitochondrial DNA cytochrome b gene and control region sequences. Two distinct clades with net genetic divergence of 3% in the control region were detected, one in the Chinese coastal waters and the other in the Japanese coastal waters. These clades may have been isolated and diverged during Pleistocene low sea levels. Nucleotide diversity was much higher in the Chinese clade than that in the Japanese clade. The demographic history of the two clades was examined using neutrality tests and mismatch analyses, and the results indicated Pleistocene population expansion in both clades. Molecular variance analyses and pairwise FST revealed significant differentiation between two Japanese populations and lack of genetic structure in the Chinese populations. The significant geographic structure in white croaker suggests low level of dispersal in this species. The lack of phylogeographical structure in China coastal waters may reflect a recent range expansion after the last glacial maximum and insufficient time to attain migration-drift equilibrium.
2、The genetic structures of four populations of P. argentata were analyzed by AFLP technology. A total of 304 putative loci were detected by the five primer combinations, of which 200 were polymorphic. The proportion of polymorphic loci among four populations varied from 47.13% to 57.63%. The population with the highest Nei’s genetic diversity and Shannon diversity index was Ariake Sea population, the lowest Nei’s genetic diversity and Shannon diversity index was found in Ise Bay population. Two clades were detected, molecular variance analyses and pairwise FST also supported the separation of Chinese and Japanese populations of P. argentata.
3、To investigate the genetic structure and differentiation of different wild populations of P. argentata, horizontal starch gel electrophoresis was performed on 133 individuals collected from five different locations in China and Japan. The eleven enzyme systems revealed 15 putative loci, of which eleven were polymorphic. The proportions of polymorphic loci of P. argentata populations varied from 0.0667 to 0.5333; the mean observed and expected heterozygosity varied from 0.0033 to 0.0133 and 0.0032 to 0.0191, respectively. The heterozygosity revealed a low genetic variability for P. argentata in comparison with other marine fishes. The genetic distance among populations varied from 0.00005 to 0.00026. A weak differentiation observed within each clade; and no significant differences in gene frequencies among populations were observed in P. argentata. Among five populations, Chinese populations showed more genetic variability than that in Japanese populations.
4、The population genetic structure and level of gene flow of Nibea albiflora from the Yellow and the East China seas were examined with a 479bp segment of mtDNA control region. A total of 65 samples were collected from three locations and 37 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the three populations ranged from 0.9130±0.0308 (Zhoushan) to 0.9926±0.0230 (Xiamen), and from 0.0073±0.0043 (Qingdao) to 0.0099±0.0057 (Xiamen), respectively. AMOVA and pairwise FST revealed little genetic structure between the Yellow and the East China seas in N. albiflora. But based on the exact test of differentiation, the null hypothesis that N. albiflora within the Yellow and East China seas constitutes a panmictic mtDNA gene pool was rejected. This might be caused by the broad spawning areas but not by the Yangtze River outflow. Mismatch distribution revealed that N. albiflora has undergone population expansion, possibly before last 85,000–170,000 years. The existence of high gene flow between stocks in the studied area was supported by our results. Annual migrations, larval drift in the ocean currents, and recent range expansion could be the reasons for little genetic structure in the studied area.
5、AFLP was used to analyze the genetic diversity of two populations of N. albiflora from Qingdao and Xiamen sea area. A total of 47 individuals were studied using five primer combinations. A total of 461 loci were detected, of which 265 were polymorphic. The results showed that the genetic diversity of these two populations was at the same level. The proportion of polymorphic loci, the Nei’s genetic diversity and Shannon diversity index of Qingdao and Xiamen populations were 51.70% and 51.99%, 0.1022 and 0.0996, 0.1643 and 0.1622, respectively. Gst value, Shannon diversity index and AMOVA analysis indicated that the genetic variation mainly came from individuals within populations and there was no significant genetic differentiation between populations. Mismatch distribution analysis and dominant gene frequency revealed that these two populations have the same genetic population structure. The results of AFLP analysis indicated that there is no significant genetic differentiation between two populations due to high gene flow.
6、To assess the role of historical process and contemporary factors in shaping population structures in the northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species’range were sequenced. Two distinct lineages were detected, which might be divergent in the Sea of Japan and Pacific coastal waters of Japanese Island, during the low sea level. Significant genetic structure was revealed as expected between the Kuroshio and Oyashio Currents. However, significant genetic structure was also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao populations with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the north group and south group populations indicate that ocean currents within groups facilitate the dispersal of A. personatus.
7、AFLP markers were also used to analyze the genetic structures of A. personatus and status of north and south groups. Two hundred and eleven individuals of A. personatus and 37 individuals of Ammodytes hexapterus were amplified by four primer combinations. The results showed north group and south group were reciprocally monophyletic. Complete reproductive isolation may exist between the two groups. These results suggest that the two groups have already reached a stage of sufficient genetic differentiation to be considered as two distinct species.
引文
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