四种广布性贝类系统地理学研究—探讨中国近海贝类遗传格局形成过程和演化机制
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摘要
海洋生物现今的遗传格局是各种历史和当前环境因素在不同空间尺度共同作用的结果。海洋系统地理学的开展已在全球热点海区例如东北太平洋、大西洋-地中海等地区详细揭示了生物的遗传结构和遗传多样性分布等现状。然而直到现在，我们对于西北太平洋边缘海海洋生物的系统地理学知识仍然所知甚少。本研究即是在以上背景下对主要分布在中国海沿岸的四种双壳纲贝类，利用分子系统地理学的方法和基于溯祖理论的分析手段进行了系统研究。我们结合线粒体和核DNA分子标记的数据揭示了各个物种的系统地理格局，比较了种间进化历程的一致性，并讨论了历史事件、当前环境、生态因素等对塑造它们现今遗传结构的作用。
1.青蛤分子系统地理学研究
为了验证历史冰期和长江冲淡水对青蛤遗传结构的影响，我们采集了来自东海、南海、日本海共21个群体的335个青蛤样品。MtCOI和nrITS-1两个分子标记的结果都表明每个边缘海由不同的谱系主导，三个边缘海群体间存在显著的遗传分化。基于mtCOI的分子钟估算结果显示三个谱系的分化时间发生在更新世。群体动态分析显示东海和南海谱系经历了明显的历史群体扩张。我们的结果表明青蛤在东亚地区的系统地理格局主要是受更新世冰期边缘海的隔离造成的，而非先前认为的长江冲淡水。更新世时，边缘海之间隆起的陆桥成为阻碍不同海盆间群体基因交流的地理屏障。各个避难所内的群体在漫长进化历程中不断累积突变，最终形成三个分化较深的谱系。当海平面上升屏障移除后，青蛤有限的扩散能力和中国近岸的海流环境可能是青蛤能长久维持这种历史格局的原因。
2.泥蚶分子系统地理学研究
海洋生物现今的系统地理格局不仅受到各种历史和当代生态因素的影响，而且越来越多的受到人类活动的影响。分析这些因素的相互作用可以为生物资源的利用和保护提供必要的遗传学背景。我们利用mtCOI和nrITS-1标记对中国东海和南海10个地点的泥蚶群体进行了遗传学研究。系统发生分析表明该种内存在2个进化显著性单元（ESUs），其形成可能和冰期海平面下降造成的两海区的隔离有关。其中一个ESU分布在所有群体中，而另一个仅分布在南海两个不相邻的两群体中。通过距离隔离模式分析和对比同海域的其它海洋生物遗传格局，泥蚶两个ESU的分布最可能是人为易位养殖而不是自然扩散造成的。从保护角度讲，仅分布在南海的ESU有灭绝的危险，需要合理的管理措施对其保护。
3.中国蛤蜊和四角蛤蜊的比较系统地理学研究
生物的进化历程和地理历史事件之间存在紧密的联系。在良好的地理模型系统下进行系统地理学研究有助于验证各种难解的生物假说。东海的地形独特且冰期避难所的信息非常明确，是研究冰后期生物进化的理想场所。我们采集了主要分布于东海的中国蛤蜊和四角蛤蜊各9个群体，结合mtCOI和微卫星（SSR）数据分析比较了它们的系统地理结构。MtCOI单倍型网络关系图显示两个物种系统发生关系均为“星状”，这和两个物种单一东海避难所起源的假说相符合。但是二者的群体遗传结构明显不同：四角蛤蜊的群体间不存在显著的遗传分化；而中国蛤蜊的连云港、平潭群体和其他群体间存在显著分化，来自SSR的数据也支持这一观点。栖息地分布、有效种群大小和“sweepstakes”式的繁殖模式可能是造成种间差异的原因。基于溯祖理论的IMa分析显示中国蛤蜊三组群体间几乎不存在基因交流。本研究表明具有相同起源的冰后期群体间可以产生显著的遗传分化，而且这种结果可能在近缘种间不平行。
Present genetic patterns of marine species result from the interaction of varioushistorical and contemporary factors on different spatial scales. Phylogeographicalstudies have been widely carried out in some marine hotspots such as the northeasternPacific and the Atlantic-Mediterranean. The vast region of the northwestern Pacific,however, has yet attracted little such attention. Our understanding of historicalphylogeographical processes for this area lags surprisingly far behind that hasachieved for other areas.
To fulfill the gap, we conducted phylogeographical studies on four marine bivalvesmainly distributed along China’s coastline. Mitochondrial and nuclear DNAsequences were amplified for the samples and each data set was analyzed to infer thepopulation structure and spatial distribution of genetic diversity based on coalescenttheory. The genetic patterns were discussed to assess the relative effects of historical,contemporary, and ecological factors on shaping present phylogeographical patternsof each species, with views into the interspecific concordance of evolutionaryprocesses.
1. Phylogeography of Cyclina sinensis
The phylogeography of bivalve Cyclina sinensis was investigated to test the relativeinfluence of historical glaciations and the Changjiang River outflow on populationstructure. Samples were collected from the three marginal seas. Fragments of twomarkers (mitochondrial COI and nuclear ITS-1) were sequenced for335individuals from21populations. The results suggested significant population structure among thethree seas, and each sea was dominated by a distinct lineage. The divergence timesamong COI lineages were estimated dating from the Pleistocene. Thephylogeographical break revealed is congruent with the historical isolation of seabasins rather than the putative Changjiang River outflow barrier. The large landbridges extending between seas during glaciation allowed accumulation of mutationsand subsequently gave rise to deep divergent lineages. The low-dispersal capacity ofthe clam and current coastal oceanography may facilitate the maintenance of thehistorical patterns for a long time as barriers shift.
2. Phylogeography of Tegillarca granosa
Present genetic patterns of marine organisms not only result from historical andcontemporary ecological factors, but also from anthropogenic activities.Disentangling the relative effects of these factors can provide valuable insights intomanagement and protection of exploitable species. The commercially importantmarine clam Tegillarca granosa is representative of species that are translocatedwithin East Asia for coastal aquaculture purposes. We conducted a nucleotidesequence analysis of mtCOI and nuclear ITS-1markers in T. granosa to investigate itsgenetic diversity and distribution in two marginal seas (the East and South China Seas)of the northwestern Pacific. Based on phylogenetic inferences, we identified twoevolutionarily significant units (ESUs) with high genetic distance between them forboth markers. The high genetic distance may be associated with the historicalisolation of the marginal seas during low sea level periods. One ESU was widelydistributed in both seas, whereas the other was restricted to two disjunct localities inthe South China Sea. Based on the isolation by distance analysis and comparison ofpatterns of co-occurring species, this pattern appears to be mostly attributable to thehuman-mediated translocations among coastal waters rather than natural rangeexpansion. Furthermore, from a conservation viewpoint, the southern ESU is nowfacing high extinction risk because of mitochondrial introgression and smaller, fragmented populations; consequently, immediate proper management is required toprotect the endangered populations representing this lineage.
3. Comparative phylogeography of Mactra chinensis and M. veneriformis
There is complex interaction between biological evolution and topographic features.Studies carried out in regions with a clear geographical context will benefit the test ofvarious biological hypotheses. The East China Sea, a marginal sea with explicitrefugial information in northwestern Pacific, provides an elegant setting for studyingpostglacial evolution of marine species. Here we examined and compared thephylogeographical structure of two congeneric bivalves (M. chinensis and M.veneriformis) in this region, using both mtCOI and SSR. A star-like genealogy ofmitochondrial haplotypes with shallow genetic divergence was constructed for bothspecies. However, the two clams carried signals of different postglacial evolutionaryhistories: no significant population differentiation was detected for M. veneriformis,whereas substantial population structure was revealed for M. chinensis by both COIand microsatellite data. The habitat distribution, effective population size and the‘sweepstakes’ mode of reproduction and survival are suspected to have driven thediscordance. Three groups were defined for M. chinensis and coalescent approachesrevealed effectively zero migration between most pairwise comparisons, suggestive ofrestricted gene flow despite a pelagic larval duration. The study highlights the role ofpostglacial evolution contributing to present-day marine biodiversity and thespecies-specific evolutionary processes for closely related organisms even undershared environmental factors.
1.青蛤分子系统地理学研究
为了验证历史冰期和长江冲淡水对青蛤遗传结构的影响，我们采集了来自东海、南海、日本海共21个群体的335个青蛤样品。MtCOI和nrITS-1两个分子标记的结果都表明每个边缘海由不同的谱系主导，三个边缘海群体间存在显著的遗传分化。基于mtCOI的分子钟估算结果显示三个谱系的分化时间发生在更新世。群体动态分析显示东海和南海谱系经历了明显的历史群体扩张。我们的结果表明青蛤在东亚地区的系统地理格局主要是受更新世冰期边缘海的隔离造成的，而非先前认为的长江冲淡水。更新世时，边缘海之间隆起的陆桥成为阻碍不同海盆间群体基因交流的地理屏障。各个避难所内的群体在漫长进化历程中不断累积突变，最终形成三个分化较深的谱系。当海平面上升屏障移除后，青蛤有限的扩散能力和中国近岸的海流环境可能是青蛤能长久维持这种历史格局的原因。
2.泥蚶分子系统地理学研究
海洋生物现今的系统地理格局不仅受到各种历史和当代生态因素的影响，而且越来越多的受到人类活动的影响。分析这些因素的相互作用可以为生物资源的利用和保护提供必要的遗传学背景。我们利用mtCOI和nrITS-1标记对中国东海和南海10个地点的泥蚶群体进行了遗传学研究。系统发生分析表明该种内存在2个进化显著性单元（ESUs），其形成可能和冰期海平面下降造成的两海区的隔离有关。其中一个ESU分布在所有群体中，而另一个仅分布在南海两个不相邻的两群体中。通过距离隔离模式分析和对比同海域的其它海洋生物遗传格局，泥蚶两个ESU的分布最可能是人为易位养殖而不是自然扩散造成的。从保护角度讲，仅分布在南海的ESU有灭绝的危险，需要合理的管理措施对其保护。
3.中国蛤蜊和四角蛤蜊的比较系统地理学研究
生物的进化历程和地理历史事件之间存在紧密的联系。在良好的地理模型系统下进行系统地理学研究有助于验证各种难解的生物假说。东海的地形独特且冰期避难所的信息非常明确，是研究冰后期生物进化的理想场所。我们采集了主要分布于东海的中国蛤蜊和四角蛤蜊各9个群体，结合mtCOI和微卫星（SSR）数据分析比较了它们的系统地理结构。MtCOI单倍型网络关系图显示两个物种系统发生关系均为“星状”，这和两个物种单一东海避难所起源的假说相符合。但是二者的群体遗传结构明显不同：四角蛤蜊的群体间不存在显著的遗传分化；而中国蛤蜊的连云港、平潭群体和其他群体间存在显著分化，来自SSR的数据也支持这一观点。栖息地分布、有效种群大小和“sweepstakes”式的繁殖模式可能是造成种间差异的原因。基于溯祖理论的IMa分析显示中国蛤蜊三组群体间几乎不存在基因交流。本研究表明具有相同起源的冰后期群体间可以产生显著的遗传分化，而且这种结果可能在近缘种间不平行。
Present genetic patterns of marine species result from the interaction of varioushistorical and contemporary factors on different spatial scales. Phylogeographicalstudies have been widely carried out in some marine hotspots such as the northeasternPacific and the Atlantic-Mediterranean. The vast region of the northwestern Pacific,however, has yet attracted little such attention. Our understanding of historicalphylogeographical processes for this area lags surprisingly far behind that hasachieved for other areas.
To fulfill the gap, we conducted phylogeographical studies on four marine bivalvesmainly distributed along China’s coastline. Mitochondrial and nuclear DNAsequences were amplified for the samples and each data set was analyzed to infer thepopulation structure and spatial distribution of genetic diversity based on coalescenttheory. The genetic patterns were discussed to assess the relative effects of historical,contemporary, and ecological factors on shaping present phylogeographical patternsof each species, with views into the interspecific concordance of evolutionaryprocesses.
1. Phylogeography of Cyclina sinensis
The phylogeography of bivalve Cyclina sinensis was investigated to test the relativeinfluence of historical glaciations and the Changjiang River outflow on populationstructure. Samples were collected from the three marginal seas. Fragments of twomarkers (mitochondrial COI and nuclear ITS-1) were sequenced for335individuals from21populations. The results suggested significant population structure among thethree seas, and each sea was dominated by a distinct lineage. The divergence timesamong COI lineages were estimated dating from the Pleistocene. Thephylogeographical break revealed is congruent with the historical isolation of seabasins rather than the putative Changjiang River outflow barrier. The large landbridges extending between seas during glaciation allowed accumulation of mutationsand subsequently gave rise to deep divergent lineages. The low-dispersal capacity ofthe clam and current coastal oceanography may facilitate the maintenance of thehistorical patterns for a long time as barriers shift.
2. Phylogeography of Tegillarca granosa
Present genetic patterns of marine organisms not only result from historical andcontemporary ecological factors, but also from anthropogenic activities.Disentangling the relative effects of these factors can provide valuable insights intomanagement and protection of exploitable species. The commercially importantmarine clam Tegillarca granosa is representative of species that are translocatedwithin East Asia for coastal aquaculture purposes. We conducted a nucleotidesequence analysis of mtCOI and nuclear ITS-1markers in T. granosa to investigate itsgenetic diversity and distribution in two marginal seas (the East and South China Seas)of the northwestern Pacific. Based on phylogenetic inferences, we identified twoevolutionarily significant units (ESUs) with high genetic distance between them forboth markers. The high genetic distance may be associated with the historicalisolation of the marginal seas during low sea level periods. One ESU was widelydistributed in both seas, whereas the other was restricted to two disjunct localities inthe South China Sea. Based on the isolation by distance analysis and comparison ofpatterns of co-occurring species, this pattern appears to be mostly attributable to thehuman-mediated translocations among coastal waters rather than natural rangeexpansion. Furthermore, from a conservation viewpoint, the southern ESU is nowfacing high extinction risk because of mitochondrial introgression and smaller, fragmented populations; consequently, immediate proper management is required toprotect the endangered populations representing this lineage.
3. Comparative phylogeography of Mactra chinensis and M. veneriformis
There is complex interaction between biological evolution and topographic features.Studies carried out in regions with a clear geographical context will benefit the test ofvarious biological hypotheses. The East China Sea, a marginal sea with explicitrefugial information in northwestern Pacific, provides an elegant setting for studyingpostglacial evolution of marine species. Here we examined and compared thephylogeographical structure of two congeneric bivalves (M. chinensis and M.veneriformis) in this region, using both mtCOI and SSR. A star-like genealogy ofmitochondrial haplotypes with shallow genetic divergence was constructed for bothspecies. However, the two clams carried signals of different postglacial evolutionaryhistories: no significant population differentiation was detected for M. veneriformis,whereas substantial population structure was revealed for M. chinensis by both COIand microsatellite data. The habitat distribution, effective population size and the‘sweepstakes’ mode of reproduction and survival are suspected to have driven thediscordance. Three groups were defined for M. chinensis and coalescent approachesrevealed effectively zero migration between most pairwise comparisons, suggestive ofrestricted gene flow despite a pelagic larval duration. The study highlights the role ofpostglacial evolution contributing to present-day marine biodiversity and thespecies-specific evolutionary processes for closely related organisms even undershared environmental factors.
引文
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