帘蛤科贝类分子系统学研究
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摘要
帘蛤科是异齿亚纲双壳贝类中种类最为丰富的一个科，该科包含14个亚科共800多种现生种类。因为帘蛤科贝类很多为大、中型种类且属于海洋底栖环境中的优势种，所以在生态及经济上都具有重要的价值。但是，由于多样性程度高却缺乏有效的研究，一直以来人们对帘蛤科贝类之间的进化关系不够了解，从而导致该科种上水平的分类学相对比较混乱。与此同时，因为受到种间平行进化与种内生态型繁杂等因素的影响，帘蛤科很多种类的种内与种间形态差异不甚明显甚至存在相互重叠的现象，所以这些贝类种的界限很难甚至不可能单靠形态特征进行有效地界定。
分子系统学是研究物种间相互关系的有效工具，而且已经有很多研究开始利用分子手段来解决帘蛤科贝类间的系统学问题。但是以往研究所包含的帘蛤科贝类种类与所使用的分子标记一般较少，所以该贝类类群间的相互关系至今还存在很多问题。这些问题从种的水平到整个科的水平普遍存在。本文拟利用多种分子系统学策略进一步研究帘蛤科贝类间特别是中国沿海类群内的系统学及分类学问题。
首先，选取135种双壳贝类（其中帘蛤科种类128种，帘蛤超科非帘蛤科种类5种，其它双壳贝类外类群2种），利用两个线粒体基因序列（COI、16S）和一个核编码蛋白基因序列（H3）进行了帘蛤科贝类种上水平的系统发生学研究：利用PAUP进行了最大俭约法分析，利用PhyML进行了最大似然法分析，并利用MrBayes进行了贝叶斯法分析。本研究的结果表明，传统意义上的帘蛤科并非单系发生的而且帘蛤科内大多数名义上的亚科和属也是并系甚至是复系发生的，这说明现行的帘蛤科分类体系并不能有效的反映这个贝类类群真实的进化关系。基于系统发生学分析结果，本研究对帘蛤科内中国沿海分布的某些类群进行了分类学修订。根据其系统发生学地位，本研究证明雪蛤属和密盖蛤属并非同物异名，并将后者置于帘蛤亚科之内，将雪蛤亚科内的杓拿蛤属和畸心蛤属分别置于帘蛤亚科和缀锦蛤亚科之内，同时，本研究将原帘蛤亚科皱纹蛤属的提加芒蛤亚属提升到了属的地位，但仍置于帘蛤亚科之内。
其次，利用中国沿海分布的60余种帘蛤科贝类的315个个体在种水平上进行了DNA条形码分析。由于种内和种间表型的多态性，很多帘蛤科贝类种的界限单靠形态特征很难界定。DNA条形码是加拿大人赫伯特于2003年提出的一种利用DNA序列来鉴定生物物种的分子技术。近年来，很多研究证实了DNA条形码在物种鉴定和隐存种发掘等方面具有强大的功能。所以，DNA条形码或许能够快速界定帘蛤科贝类的种的界限。本研究利用遗传距离和系统树两种分析手段进行了DNA条形码分析，并进一步利用TaxonDNA进行了MOTU分析。DNA条形码的研究结果表明，除了饼干镜蛤和铗镜蛤这两个种的条形码序列混杂在一起之外，其余种类都具有其独特的条形码簇；在利用形态不能确定种名的26个个体中，12个被鉴定到了已知种，其余的14个个体形成了5个单独的支系，这些支系可能代表着未描述的种，或者至少是在国内还未被记录的种类。另外，本研究在5个传统的形态种中发现可能有隐存种现象的存在。本研究证明了DNA条形码的确能够有效地进行帘蛤科贝类的种类鉴定，同时也能在种水平的分类学研究中为我们提供新的信息。本研究认为DNA条形码能通过指示鉴别性的形态特征、为分类学修订提供有用信息和标示隐存种等方式来辅助分类。
最后，以缀锦蛤亚科巴非蛤属原缀锦蛤亚属的贝类为例，探讨了如何通过增加基因位点数目与增加采样点和采样量来确定DNA条形码研究中揭示出的隐存种的种的地位。隐存种的研究对我们理解生物多样性及种的形成机制等都具有极其重要的意义。本研究共选取了两个线粒体基因（COI和16S）和四个核基因（H3、18S、28S和ITS1）进行了分析。利用DNASP对每个基因片段进行了遗传多样性分析，利用TaxonDNA将条形码（COI）归类到不同MOTUs，然后将这些MOTUs看做不同的种，利用6个基因片段对这些疑似的种进行了迭代性分析：首先，对每个基因片段进行了遗传距离的分析；其次，基于每个基因分别构建了邻接网络图；最后，将6个基因片段整合在一起利用PAUP和MrBayes分别构建了最大俭约树和贝叶斯树。多基因片段迭代性分析的结果表明锯齿巴非蛤在DNA条形码分析中揭示出的疑似隐存种为真正的生物学种，同时本研究发现屈巴非蛤中同样存在隐存的生物学种。另外，相对于锯齿巴非蛤复合种，屈巴非蛤复合种在系统树上占据着基础位置，说明这个支系较为原始。本研究的结果将西太平洋地区的原缀锦蛤亚属现生种类数由2个增加到4个，这意味着该亚属的生物多样性可能远比我们现有的认识要丰富。研究证实结合DNA条形码及后续的多证据迭代性分析的研究策略能够高效而准确地探索生物多样性。
The Veneridae (Rafinesque,1815), known as venus clams, is the most richly speciosefamily of heterodont bivalve mollusks. This family includes more than800extant speciesgrouped into about14subfamilies. Many species of Veneridae are economically importantand ecologically crucial due to their huge abundance in benthic environments. However,Because of great diversity and the lack of systematic studies, venus clams have a confusingtaxonomic history and their relationships remain poorly understood. Besides, due toparallelism of interspecific morphological variability and pronounced intraspecificecophenotypes, the intra-and interspecific phenotypic variability of many venerids areindistinct or even overlapping. Therefore, species boundaries of these clams are difficult oreven impossible to define accurately based solely on morphological features.
Molecular systematics is considered a robust test of evolutionary relationships recentlyand there have been a number of attempts to address venerid systematics using molecular data.Nevertheless, most of those efforts only included few venerid species and only used a singlemarker. Therefore, there are many pending problems about venerid systematics, from speciesto family level, to resolve. To further resolve the problems about evolutionary relationshipsand taxonomic system of the family Veneridae, especially within Chinese venerid fauna, anupdated molecular systematics of venus clams is presented herein.
First, DNA sequence information from fragments of two mitochondrial genes (COI and16S) and one nuclear protein-coding gene (H3) for135taxa (128venerids, five nonveneridveneroids and two other outgroups) were used to reconstruct the phylogenetic relationships ofvenus clams. The best-fit model of nucleotide substitution models were tested in jModeltestand MrModeltest. Phylogenetic analyses were inferred using maximum parsimony, maximumlikelihood and Bayesian approaches. According to the molecular results, Taxa of thetraditional family Veneridae divided into two major clades and is not recovered asmonophyletic. Besides, most of the nominal subfamilies and genera formed para-polyphyleticclades. The classification of taxa along the coast China are revised based on theirphylogenetic position. The synonymization of chionine genus Placamen with Clausinella isrejected. Chionine subgenera Anomalodiscus and Cryptonema are given full generic rankagain and incorporated into Venerinae and Tapetinae, respectively. The results also evidence that the synonymization of the genus Tigammona and Periglypta is inappropriate.
Second, a total of315specimens of around60venerid species sampled along the coastof China were used to explore species diversity under DNA barcoding approach. Geneticdistances were calculated using the Kimura2-parameter model in MEGA, and then COIsequences were grouped into provisional clusters as MOTUs in TaxonDNA. Aneighbor-joining tree was reconstructed for the complete dataset and to infer the systematicrelationships among species of certain groups more effectively, the maximum likelihoodapproach was applied using PhyML. Nearly all individuals identified to species level based onmorphological traits possessed distinct barcode clusters, except for the specimens of onespecies pair, Phacosoma biscoticum and P. fibulum. Among the26individuals that were notassigned binomial names a priori, twelve respectively nested within a species genealogy. Theremaining individuals formed five monophyletic clusters that potentially represent speciesnew to science or at least unreported in China. Five putative hidden species were alsouncovered. The present study shows that DNA barcoding is effective in species delimitationand can aid taxonomists by indicating useful diagnostic morphological traits, informingneedful revision, and flagging unseen species.
Finally, subgenus Protapes in seas of the south China were used as a case study toillustrate how multi-locus genes and increasing samples confirm the species status of crypticspecies uncovered in barcoding study and how these evidences provide us more insights. Sixgene sequences COI,16S, H3,18S,28S, and ITS1were used herein. Barcodes were groupedinto provisional clusters as MOTUs. These MOTUs were treated as potential species andthese species candidates were tested iteratively in both distance-based and phylogeny-basedapproaches. The results showed that the two species candidates within Paphia (Protapes)gallus uncovered in barcoding study are real biological species, and two hidden species existwithin P.(P.) sinuosa. In addition, the clade of P.(P.) sinuosa complex occupied the basalposition in the phylogenetic trees, indicating this lineage is more ancient than P.(P.) galluscomplex. The results double the number of Protapes living species in the western Pacific,suggesting we might have only scratched the surface of Protapes biodiversity in this region.The present study shows that the approach, combining DNA barcoding with subsequentmultiple-line analyses, is effective in biodiversity exploration.
分子系统学是研究物种间相互关系的有效工具，而且已经有很多研究开始利用分子手段来解决帘蛤科贝类间的系统学问题。但是以往研究所包含的帘蛤科贝类种类与所使用的分子标记一般较少，所以该贝类类群间的相互关系至今还存在很多问题。这些问题从种的水平到整个科的水平普遍存在。本文拟利用多种分子系统学策略进一步研究帘蛤科贝类间特别是中国沿海类群内的系统学及分类学问题。
首先，选取135种双壳贝类（其中帘蛤科种类128种，帘蛤超科非帘蛤科种类5种，其它双壳贝类外类群2种），利用两个线粒体基因序列（COI、16S）和一个核编码蛋白基因序列（H3）进行了帘蛤科贝类种上水平的系统发生学研究：利用PAUP进行了最大俭约法分析，利用PhyML进行了最大似然法分析，并利用MrBayes进行了贝叶斯法分析。本研究的结果表明，传统意义上的帘蛤科并非单系发生的而且帘蛤科内大多数名义上的亚科和属也是并系甚至是复系发生的，这说明现行的帘蛤科分类体系并不能有效的反映这个贝类类群真实的进化关系。基于系统发生学分析结果，本研究对帘蛤科内中国沿海分布的某些类群进行了分类学修订。根据其系统发生学地位，本研究证明雪蛤属和密盖蛤属并非同物异名，并将后者置于帘蛤亚科之内，将雪蛤亚科内的杓拿蛤属和畸心蛤属分别置于帘蛤亚科和缀锦蛤亚科之内，同时，本研究将原帘蛤亚科皱纹蛤属的提加芒蛤亚属提升到了属的地位，但仍置于帘蛤亚科之内。
其次，利用中国沿海分布的60余种帘蛤科贝类的315个个体在种水平上进行了DNA条形码分析。由于种内和种间表型的多态性，很多帘蛤科贝类种的界限单靠形态特征很难界定。DNA条形码是加拿大人赫伯特于2003年提出的一种利用DNA序列来鉴定生物物种的分子技术。近年来，很多研究证实了DNA条形码在物种鉴定和隐存种发掘等方面具有强大的功能。所以，DNA条形码或许能够快速界定帘蛤科贝类的种的界限。本研究利用遗传距离和系统树两种分析手段进行了DNA条形码分析，并进一步利用TaxonDNA进行了MOTU分析。DNA条形码的研究结果表明，除了饼干镜蛤和铗镜蛤这两个种的条形码序列混杂在一起之外，其余种类都具有其独特的条形码簇；在利用形态不能确定种名的26个个体中，12个被鉴定到了已知种，其余的14个个体形成了5个单独的支系，这些支系可能代表着未描述的种，或者至少是在国内还未被记录的种类。另外，本研究在5个传统的形态种中发现可能有隐存种现象的存在。本研究证明了DNA条形码的确能够有效地进行帘蛤科贝类的种类鉴定，同时也能在种水平的分类学研究中为我们提供新的信息。本研究认为DNA条形码能通过指示鉴别性的形态特征、为分类学修订提供有用信息和标示隐存种等方式来辅助分类。
最后，以缀锦蛤亚科巴非蛤属原缀锦蛤亚属的贝类为例，探讨了如何通过增加基因位点数目与增加采样点和采样量来确定DNA条形码研究中揭示出的隐存种的种的地位。隐存种的研究对我们理解生物多样性及种的形成机制等都具有极其重要的意义。本研究共选取了两个线粒体基因（COI和16S）和四个核基因（H3、18S、28S和ITS1）进行了分析。利用DNASP对每个基因片段进行了遗传多样性分析，利用TaxonDNA将条形码（COI）归类到不同MOTUs，然后将这些MOTUs看做不同的种，利用6个基因片段对这些疑似的种进行了迭代性分析：首先，对每个基因片段进行了遗传距离的分析；其次，基于每个基因分别构建了邻接网络图；最后，将6个基因片段整合在一起利用PAUP和MrBayes分别构建了最大俭约树和贝叶斯树。多基因片段迭代性分析的结果表明锯齿巴非蛤在DNA条形码分析中揭示出的疑似隐存种为真正的生物学种，同时本研究发现屈巴非蛤中同样存在隐存的生物学种。另外，相对于锯齿巴非蛤复合种，屈巴非蛤复合种在系统树上占据着基础位置，说明这个支系较为原始。本研究的结果将西太平洋地区的原缀锦蛤亚属现生种类数由2个增加到4个，这意味着该亚属的生物多样性可能远比我们现有的认识要丰富。研究证实结合DNA条形码及后续的多证据迭代性分析的研究策略能够高效而准确地探索生物多样性。
The Veneridae (Rafinesque,1815), known as venus clams, is the most richly speciosefamily of heterodont bivalve mollusks. This family includes more than800extant speciesgrouped into about14subfamilies. Many species of Veneridae are economically importantand ecologically crucial due to their huge abundance in benthic environments. However,Because of great diversity and the lack of systematic studies, venus clams have a confusingtaxonomic history and their relationships remain poorly understood. Besides, due toparallelism of interspecific morphological variability and pronounced intraspecificecophenotypes, the intra-and interspecific phenotypic variability of many venerids areindistinct or even overlapping. Therefore, species boundaries of these clams are difficult oreven impossible to define accurately based solely on morphological features.
Molecular systematics is considered a robust test of evolutionary relationships recentlyand there have been a number of attempts to address venerid systematics using molecular data.Nevertheless, most of those efforts only included few venerid species and only used a singlemarker. Therefore, there are many pending problems about venerid systematics, from speciesto family level, to resolve. To further resolve the problems about evolutionary relationshipsand taxonomic system of the family Veneridae, especially within Chinese venerid fauna, anupdated molecular systematics of venus clams is presented herein.
First, DNA sequence information from fragments of two mitochondrial genes (COI and16S) and one nuclear protein-coding gene (H3) for135taxa (128venerids, five nonveneridveneroids and two other outgroups) were used to reconstruct the phylogenetic relationships ofvenus clams. The best-fit model of nucleotide substitution models were tested in jModeltestand MrModeltest. Phylogenetic analyses were inferred using maximum parsimony, maximumlikelihood and Bayesian approaches. According to the molecular results, Taxa of thetraditional family Veneridae divided into two major clades and is not recovered asmonophyletic. Besides, most of the nominal subfamilies and genera formed para-polyphyleticclades. The classification of taxa along the coast China are revised based on theirphylogenetic position. The synonymization of chionine genus Placamen with Clausinella isrejected. Chionine subgenera Anomalodiscus and Cryptonema are given full generic rankagain and incorporated into Venerinae and Tapetinae, respectively. The results also evidence that the synonymization of the genus Tigammona and Periglypta is inappropriate.
Second, a total of315specimens of around60venerid species sampled along the coastof China were used to explore species diversity under DNA barcoding approach. Geneticdistances were calculated using the Kimura2-parameter model in MEGA, and then COIsequences were grouped into provisional clusters as MOTUs in TaxonDNA. Aneighbor-joining tree was reconstructed for the complete dataset and to infer the systematicrelationships among species of certain groups more effectively, the maximum likelihoodapproach was applied using PhyML. Nearly all individuals identified to species level based onmorphological traits possessed distinct barcode clusters, except for the specimens of onespecies pair, Phacosoma biscoticum and P. fibulum. Among the26individuals that were notassigned binomial names a priori, twelve respectively nested within a species genealogy. Theremaining individuals formed five monophyletic clusters that potentially represent speciesnew to science or at least unreported in China. Five putative hidden species were alsouncovered. The present study shows that DNA barcoding is effective in species delimitationand can aid taxonomists by indicating useful diagnostic morphological traits, informingneedful revision, and flagging unseen species.
Finally, subgenus Protapes in seas of the south China were used as a case study toillustrate how multi-locus genes and increasing samples confirm the species status of crypticspecies uncovered in barcoding study and how these evidences provide us more insights. Sixgene sequences COI,16S, H3,18S,28S, and ITS1were used herein. Barcodes were groupedinto provisional clusters as MOTUs. These MOTUs were treated as potential species andthese species candidates were tested iteratively in both distance-based and phylogeny-basedapproaches. The results showed that the two species candidates within Paphia (Protapes)gallus uncovered in barcoding study are real biological species, and two hidden species existwithin P.(P.) sinuosa. In addition, the clade of P.(P.) sinuosa complex occupied the basalposition in the phylogenetic trees, indicating this lineage is more ancient than P.(P.) galluscomplex. The results double the number of Protapes living species in the western Pacific,suggesting we might have only scratched the surface of Protapes biodiversity in this region.The present study shows that the approach, combining DNA barcoding with subsequentmultiple-line analyses, is effective in biodiversity exploration.
引文
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