双壳贝类DNA分类：贻贝科和牡蛎科DNA条形码及栉江珧隐存种研究
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摘要
如何准确地界定种和鉴定种对生物学家们来讲仍然是个难题。尽管已经提出许多界定种的方法，尤其是基于DNA的方法，但在实际应用中仍存在很大困难。近年来提出的DNA条形码技术由于能快速鉴别大量样品而迅速成为生物多样性研究的热点，但是其作为种界定工具的有效性却备受质疑。相反，基于多种不同来源标记的整合性种界定方法正逐渐成为种界定的有力工具。海洋双壳贝类虽然是海洋中一个多样性极丰富的门类，但由于多数种类研究不足以及研究手段的限制，其多样性很可能被低估。本论文中，我们验证了DNA条形码技术在两种双壳贝类（贻贝科和牡蛎科）种类鉴定中的应用，以及整合性分类方法在海洋隐存种（栉江珧）发现中的应用，为研究海洋物种分类、多样性保护和演化等问题提供借鉴。
1.基于线粒体COI的贻贝科DNA条形码的研究
本研究首次验证了DNA条形码技术在贻贝科中的应用性。通过线粒体COI（mtCOI）和16S rDNA片段对贻贝科11种52个样品进行DNA条形码分析。通过构建mtCOI和16S rDNA K2P邻接树，发现基本上所有种均可形成各自独立的单系。种内和种间K2P（Kimura’s2-parameter）遗传距离计算结果显示，除个别种和个体外，其种间距离一般高达20%以上，远远大于其种内遗传差异。同时在紫贻贝、凸壳肌蛤和曲线索贻贝中检测到线粒体异质性现象。结果说明，基于mtCOI的DNA条形码技术在贻贝科物种的鉴定中具有可行性；然而由于线粒体双单亲遗传模式和线粒体异质性现象的存在，应用DNA条形码进行贻贝科种类鉴定时要分外谨慎。
2.基于系统发生和距离法的牡蛎科DNA条形码研究
牡蛎科牡蛎是一类形态极多变而且分布较广泛的生物类群，其分类和发生关系长期以来一直困扰着分类学家和系统发生学家。本研究首次利用公共数据库的DNA序列（mtCOI和16S rDNA），通过基于距离法的DNA条形码技术和系统发生方法，对牡蛎科种类进行了鉴定分析。首先利用系统发生分析重构牡蛎科两种线粒体基因的系统发生关系，其次计算各种类种内和种间K2P遗传分化距离。通过系统发生关系的重建，发现所有种类（包括近缘种在内）在两种基因发生树上均可以形成分化明显的支系。16SrDNA种内变异与种间分化有所重叠。但是mtCOI基因的种内平均种内距离仅为0-1.4%（最大2.2%），平均种间距离则为2.6-32.2%（最小为2.2%），表明虽然距离差距较小，但是条形码间隙（barcoding gap）仍然是存在的。分析结果证实了DNA条形码和系统发生方法在牡蛎种类鉴定中的有效性。
3.基于多重标记分析的栉江珧隐存多样性和杂交研究
越来越多的研究通过结合多种数据类型（例如，mtDNA、核基因和形态）的分析方法在海洋中发现了隐存种的存在。对这些隐存种的阐释增加了我们对海洋物种多样性和演化历史的认识。栉江珧（Atrina Pectinata）具有多变的外部形态，因此被认为可能存在隐存种。本研究利用mtCOI、核ITS（nrITS）基因以及形态特征标记对采自中国沿海的16个及日本沿海的1个栉江珧群体进行分析，探讨隐存种的存在以及隐存种之间是否曾经发生过杂交。DNA条形码基因mtCOI系统发生分析结果发现了6个分化明显的线粒体支系，支系内变异仅为0.4-0.8%，而支系间分化则达4.3-22.0%，说明可能为6个隐存种。通过nrITS系统发生关系重建发现了5个分化显著的支系，支系间遗传距离为3.7-30.3%。这5个核基因演化支系分别与线粒体支系1-4和（5+6）基本相对应，证明了5个独特的演化支系的存在。同时发现单个个体中存在分化明显的多个nrITS序列，清楚地表明这些演化支系间在不远的过去曾经发生过杂交，这也是造成核基因和线粒体基因分析结果不完全一致的一个原因。形态上发现5种形态类型，虽然中间形态的存在模糊了形态类型间的清晰界限，但是这5个形态类型基本上与5个演化支系一一相对应。本研究结果证明了应用多种标记综合分析方法在隐存多样性及演化历史研究中的重要性。
Accurate species delimitation and identification is a challenging problem for biologists. Adozen operational methods, mostly based on DNA sequences, have been proposed, but it isstill problematic when delimiting species. DNA barcoding has become a well-funded, globalenterprise since its proposition as a rapid and practical molecular method to identify anddiscovery species, although the latter utility has been repeatedly criticized. On the contrary, anintegrative approach using multiple lines of evidence to delimit species is increasinglypopularized. As a big, diverse group in marine realm, bivalve biodiversity has probably beenunderestimated because of a lack of scrutiny of most taxa as well as the absence of powerfultools. In the present disertation, we assessed the utility of DNA barcoding techniques in theidentification of specimens from Mytilidae and Ostreidae, and we also explored the crypticdiversity in the pen shell Atrina pectinata in combination of different sources of data tomethodologically aid studies of taxonomy, biodiversity conservation and evolution of marinetaxa.
1. A test of the utility of DNA barcoding in the bivalve family Mytilidae
This study firstly tested whether the standard DNA barcoding method is suitable for speciesidentification of the bivalve family Mytilidae. Here,52samples belonging to eleven speciesof Mytilidae were analyzed using mitochondrial COI (mtCOI) gene as well as mitochondrial16S rDNA. Neighbor-joining trees of mtCOI and16S rDNA sequences using Kimura’s2-parameter (K2P) substitution model showed that most of the species were reciprocallymonophyletic with no exceptions. Pairwise K2P genetic distances among all species andwithin species were calculated in MEGA. And the results indicated that the genetic distancesbetween species showed up to>20%, much greater than distances within species when exceptional species and individuals were excluded. Mitochondrial DNA heteroplasmy wasdetected in Mytilus galloprovincialis, Musculus senhousia and Hormomya mutalilis. Ourresults suggested that DNA barcoding is a promising tool for species identification ofMytilidae, but the interpretation should be cautious in light of the doubly uniparentalinheritance of mtDNA (DUI) and mtDNA heteroplasmy.
2. Identifying the true oysters (Ostreidae) with mitochondrial phylogeny anddistance-based DNA barcoding
Oysters (family Ostreidae), with high levels of phenotypic plasticity and wide geographicdistribution, are a challenging group for taxonomists and phylogenetics. Based on theGenBank database, the present study used two mitochondrial fragments, mtCOI and16SrDNA, to assess whether oyster species could be identified by phylogeny and distance-basedDNA barcoding techniques. Relationships among species were estimated by the phylogeneticanalyses of both genes, and then pairwise K2P inter-and intraspecific genetic divergenceswere assessed. Species forming well differentiated clades in the molecular phylogenies wereidentical for both genes even when the closely related species were included. Intraspecificvariability of16S rDNA overlapped with interspecific divergence. However, average intra-and interspecific genetic divergences for mtCOI were0–1.4%(maximum2.2%) and2.6–32.2%(minimum2.2%), respectively, indicating the existence of a barcoding gap. Theseresults confirm the efficacy of species identification in oysters via DNA barcodes andphylogenetic analysis.
3. Cryptic diversity and hybridization revealed by multiple sources of data in Atrinapectinata
Cryptic species have been increasingly revealed in the marine realm through an analyticalapproach incorporating multiple lines of evidence (e.g., mtDNA, nuclear genes andmorphology). Illustrations of cryptic taxa improve our understanding of species diversity andevolutionary histories within marine animals. The pen shell Atrina pectinata is known toexhibit extensive morphological variations that may harbour cryptic diversity. In this study,we investigated16A. pectinata populations along the coast of China and one from Japan to explore possible cryptic diversity and hybridization using a combination of mitochondrial(mtCOI) and nuclear (ribosomal internal transcribed spacer, nrITS) genes as well asmorphology. Phylogenetic analyses of mtCOI ‘DNA barcoding gene’ sequences resolved sixdivergent lineages with intralineage divergences between0.4%and0.8%. Interlineagesequence differences ranged from4.3%to22.0%, suggesting that six candidate crypticspecies are present. The nrITS gene revealed five deep lineages with Kimura2-parameterdistances of3.7–30.3%. The five nuclear lineages generally corresponded to mtCOI lineages1–4and (5+6), suggestive of five distinct evolutionary lineages. Multiple nrITS sequences ofsignificant variance were found within an individual, clearly implying recent hybridizationevents between among the evolutionary lineages, which contributed to cytonucleardiscordance. Morphologically, five morphotypes matched the five genetic lineages, althoughthe intermediates may well blur the boundaries of different morphotypes. This studydemonstrates the importance of combining multiple lines of evidence to explore speciescryptic diversity and past evolutionary histories.
1.基于线粒体COI的贻贝科DNA条形码的研究
本研究首次验证了DNA条形码技术在贻贝科中的应用性。通过线粒体COI（mtCOI）和16S rDNA片段对贻贝科11种52个样品进行DNA条形码分析。通过构建mtCOI和16S rDNA K2P邻接树，发现基本上所有种均可形成各自独立的单系。种内和种间K2P（Kimura’s2-parameter）遗传距离计算结果显示，除个别种和个体外，其种间距离一般高达20%以上，远远大于其种内遗传差异。同时在紫贻贝、凸壳肌蛤和曲线索贻贝中检测到线粒体异质性现象。结果说明，基于mtCOI的DNA条形码技术在贻贝科物种的鉴定中具有可行性；然而由于线粒体双单亲遗传模式和线粒体异质性现象的存在，应用DNA条形码进行贻贝科种类鉴定时要分外谨慎。
2.基于系统发生和距离法的牡蛎科DNA条形码研究
牡蛎科牡蛎是一类形态极多变而且分布较广泛的生物类群，其分类和发生关系长期以来一直困扰着分类学家和系统发生学家。本研究首次利用公共数据库的DNA序列（mtCOI和16S rDNA），通过基于距离法的DNA条形码技术和系统发生方法，对牡蛎科种类进行了鉴定分析。首先利用系统发生分析重构牡蛎科两种线粒体基因的系统发生关系，其次计算各种类种内和种间K2P遗传分化距离。通过系统发生关系的重建，发现所有种类（包括近缘种在内）在两种基因发生树上均可以形成分化明显的支系。16SrDNA种内变异与种间分化有所重叠。但是mtCOI基因的种内平均种内距离仅为0-1.4%（最大2.2%），平均种间距离则为2.6-32.2%（最小为2.2%），表明虽然距离差距较小，但是条形码间隙（barcoding gap）仍然是存在的。分析结果证实了DNA条形码和系统发生方法在牡蛎种类鉴定中的有效性。
3.基于多重标记分析的栉江珧隐存多样性和杂交研究
越来越多的研究通过结合多种数据类型（例如，mtDNA、核基因和形态）的分析方法在海洋中发现了隐存种的存在。对这些隐存种的阐释增加了我们对海洋物种多样性和演化历史的认识。栉江珧（Atrina Pectinata）具有多变的外部形态，因此被认为可能存在隐存种。本研究利用mtCOI、核ITS（nrITS）基因以及形态特征标记对采自中国沿海的16个及日本沿海的1个栉江珧群体进行分析，探讨隐存种的存在以及隐存种之间是否曾经发生过杂交。DNA条形码基因mtCOI系统发生分析结果发现了6个分化明显的线粒体支系，支系内变异仅为0.4-0.8%，而支系间分化则达4.3-22.0%，说明可能为6个隐存种。通过nrITS系统发生关系重建发现了5个分化显著的支系，支系间遗传距离为3.7-30.3%。这5个核基因演化支系分别与线粒体支系1-4和（5+6）基本相对应，证明了5个独特的演化支系的存在。同时发现单个个体中存在分化明显的多个nrITS序列，清楚地表明这些演化支系间在不远的过去曾经发生过杂交，这也是造成核基因和线粒体基因分析结果不完全一致的一个原因。形态上发现5种形态类型，虽然中间形态的存在模糊了形态类型间的清晰界限，但是这5个形态类型基本上与5个演化支系一一相对应。本研究结果证明了应用多种标记综合分析方法在隐存多样性及演化历史研究中的重要性。
Accurate species delimitation and identification is a challenging problem for biologists. Adozen operational methods, mostly based on DNA sequences, have been proposed, but it isstill problematic when delimiting species. DNA barcoding has become a well-funded, globalenterprise since its proposition as a rapid and practical molecular method to identify anddiscovery species, although the latter utility has been repeatedly criticized. On the contrary, anintegrative approach using multiple lines of evidence to delimit species is increasinglypopularized. As a big, diverse group in marine realm, bivalve biodiversity has probably beenunderestimated because of a lack of scrutiny of most taxa as well as the absence of powerfultools. In the present disertation, we assessed the utility of DNA barcoding techniques in theidentification of specimens from Mytilidae and Ostreidae, and we also explored the crypticdiversity in the pen shell Atrina pectinata in combination of different sources of data tomethodologically aid studies of taxonomy, biodiversity conservation and evolution of marinetaxa.
1. A test of the utility of DNA barcoding in the bivalve family Mytilidae
This study firstly tested whether the standard DNA barcoding method is suitable for speciesidentification of the bivalve family Mytilidae. Here,52samples belonging to eleven speciesof Mytilidae were analyzed using mitochondrial COI (mtCOI) gene as well as mitochondrial16S rDNA. Neighbor-joining trees of mtCOI and16S rDNA sequences using Kimura’s2-parameter (K2P) substitution model showed that most of the species were reciprocallymonophyletic with no exceptions. Pairwise K2P genetic distances among all species andwithin species were calculated in MEGA. And the results indicated that the genetic distancesbetween species showed up to>20%, much greater than distances within species when exceptional species and individuals were excluded. Mitochondrial DNA heteroplasmy wasdetected in Mytilus galloprovincialis, Musculus senhousia and Hormomya mutalilis. Ourresults suggested that DNA barcoding is a promising tool for species identification ofMytilidae, but the interpretation should be cautious in light of the doubly uniparentalinheritance of mtDNA (DUI) and mtDNA heteroplasmy.
2. Identifying the true oysters (Ostreidae) with mitochondrial phylogeny anddistance-based DNA barcoding
Oysters (family Ostreidae), with high levels of phenotypic plasticity and wide geographicdistribution, are a challenging group for taxonomists and phylogenetics. Based on theGenBank database, the present study used two mitochondrial fragments, mtCOI and16SrDNA, to assess whether oyster species could be identified by phylogeny and distance-basedDNA barcoding techniques. Relationships among species were estimated by the phylogeneticanalyses of both genes, and then pairwise K2P inter-and intraspecific genetic divergenceswere assessed. Species forming well differentiated clades in the molecular phylogenies wereidentical for both genes even when the closely related species were included. Intraspecificvariability of16S rDNA overlapped with interspecific divergence. However, average intra-and interspecific genetic divergences for mtCOI were0–1.4%(maximum2.2%) and2.6–32.2%(minimum2.2%), respectively, indicating the existence of a barcoding gap. Theseresults confirm the efficacy of species identification in oysters via DNA barcodes andphylogenetic analysis.
3. Cryptic diversity and hybridization revealed by multiple sources of data in Atrinapectinata
Cryptic species have been increasingly revealed in the marine realm through an analyticalapproach incorporating multiple lines of evidence (e.g., mtDNA, nuclear genes andmorphology). Illustrations of cryptic taxa improve our understanding of species diversity andevolutionary histories within marine animals. The pen shell Atrina pectinata is known toexhibit extensive morphological variations that may harbour cryptic diversity. In this study,we investigated16A. pectinata populations along the coast of China and one from Japan to explore possible cryptic diversity and hybridization using a combination of mitochondrial(mtCOI) and nuclear (ribosomal internal transcribed spacer, nrITS) genes as well asmorphology. Phylogenetic analyses of mtCOI ‘DNA barcoding gene’ sequences resolved sixdivergent lineages with intralineage divergences between0.4%and0.8%. Interlineagesequence differences ranged from4.3%to22.0%, suggesting that six candidate crypticspecies are present. The nrITS gene revealed five deep lineages with Kimura2-parameterdistances of3.7–30.3%. The five nuclear lineages generally corresponded to mtCOI lineages1–4and (5+6), suggestive of five distinct evolutionary lineages. Multiple nrITS sequences ofsignificant variance were found within an individual, clearly implying recent hybridizationevents between among the evolutionary lineages, which contributed to cytonucleardiscordance. Morphologically, five morphotypes matched the five genetic lineages, althoughthe intermediates may well blur the boundaries of different morphotypes. This studydemonstrates the importance of combining multiple lines of evidence to explore speciescryptic diversity and past evolutionary histories.
引文
[1]‘Species are groups of actually or potentially interbreeding natural populations, which arereproductively isolated from other such groups.’(Mayr1942)
[2]‘…a lineage of an ancestor-descendent populations which maintains its identity from other suchlineages and which has its own evolutionary tendencies and historical fate.’(Wiley1981)
[3]‘A phylogenetic species is an irreducible (basal) cluster of organisms, diagnosably distinct from othersuch clusters, and with which there is a parental pattern of ancestry and descent.’(Cracraft1989)
[4]‘… a geographically constrained groups of individuals with some unique apomorphous character, is theunit of evolutionary significance.’(Rosen1978)
[5]‘…equates species with separately evolving metapopulation lineages…’(de Queiro2007)
李孝绪,齐钟彦(1994)中国牡蛎的比较解剖学及系统分类和演化的研究.海洋科学集刊,35,143–173.
齐钟彦(1989)黄渤海的软体动物.北京:农业出版社.
梁羡圆,林惠琼,吴萍茹,刘元(1986)福建沿海江珧科的形态比较研究.热带海洋,5,13–19.
彭居俐,王绪桢,何舜平（2008）DNA条形码技术的研究进展及其应用.水生生物学报,2008,32:916—919.
乔延龙,林昭进(2007)北部湾地形、底质特征与渔场分布的关系.海洋湖沼通报,增刊,232–238.
王梅芳，余祥勇，杨书婷，桂建芳（2000）无裂栉江珧种内同工酶表型差异的比较研究。热带海洋,19,45–50.
王祯瑞(1964)中国近海江珧科的初步报告.海洋科学集刊,5,31–41.
王祯瑞(1997)中国动物志，软体动物门，双壳纲，贻贝目.北京：科学出版社.
徐凤山,黄修明(1993)中国近海牡蛎超科的新记录.海洋科学集刊,34,175–179.
薛东秀,张涛,王海艳,郑小东,孟凡玉(2009)有棘无棘两种表型栉江珧28S和COI基因序列差异的比较.海洋科学，33,88–91.
余祥勇,王梅芳,李宏吾,蔡英亚(2000)无裂栉江珧形态差异的比较研究.热带海洋,19,39–44.
张玺,楼子康（1956）中国牡蛎的研究．动物学报，8,65–94.
朱伟林,吴国瑄,黎明碧（2004）南海北部陆架北部湾盆地古湖泊与烃源条件。海洋与湖沼，35，8–14.
Agapow PM, Binida-Emonds ORP, Crandall KA et al.(2004) The effect of species concept on biodiversity.The quarterly Review of Biology,79,161–179.
Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001) The problems with hybrids: setting conservationguidelines. Trends in Ecology and Evolution,16,613–622.
Amato A, Kooistra WHCF, Ghiron JHL et al.(2007) Reproductive Isolation among Sympatric CrypticSpecies in Marine Diatoms. Protist,158,193–207.
Arnot, D.E. et al.(1993) Digital codes from hypervariable tandemly repeated DNA sequences in thePlasmodium falciparum circumsporozoite gene can genetically barcode isolates. Molecular andBiochemical Parasitology,61,15–24.
Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press,Cambridge.
Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Molecular Ecology,13,729–744.
Banks MA, McGoldrick DJ, Borgeson W, Hedgecock D (1994) Gametic incompatibility and geneticdivergence of Pacific and Kumamoto oysters, Crassostrea gigas and C. sikamea. Marine Biology,121,127–135.
Barrett R D H, Hebert P D N (2005) Identifying spiders through DNA barcodes. Canadian Journal ofZoology,3,481–491.
Bensasson D, Zhang DX., Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: evolution’s misplacedwitnesses. Trends in Ecology and Evolution,16,314–321.
Bergmann T, Hadrys H, Breves G, Schierwater B (2009) Character-based DNA barcoding: a superior tool
for species classification. Berliner Und Münchener Tier rztliche Wochenschrift,122,446–450.
Bernard FR, Cai YY, Morton B (1993) Catalogue of Living Marine Bivalve Molluscs of China. HongKong University Press, Hong Kong.
Bickford D, Lohman DJ, Sodhi NS et al.(2006) Cryptic species as a window on diversity and conservation.Trends in Ecology and Evolution,22,148–155.
Bieler B, Mikkelsen PM, Lee T, óFoighil D (2004) Discovery of the Indo-Pacific oyster Hyotissa hyotis(Linnaeus,1758) in the Florida Keys (Biavalvia: Gryphaeidae). Molluscan Research,24,149-159.
Blaxter M L (2004) The promise of a DNA taxonomy. Philosophical Transactions of the Royal Society B,359,669–679.
Blaxter M, Elsworth B, Daub J (2004) DNA taxonomy of a neglected animal phylum: an unexpecteddiversity of tardigrades. Proceedings of the Royal Society of London Series B (Suppl.)271,S189–S192.
Boggs CL (2001) Species and Speciation. International Encyclopedia of the Social and BehavioralSciences. Oxford: Elsevier.
Bolnick DI, Fitzpatrick BM (2007) Sympatric speciation: models and empirical evidence. Annual Reviewof Ecology, Evolution and Systematics,38,459–487.
Borchsenius F (2009) FastGap1.2. Department of Biological Sciences, University of of Aarhus, Denmark.(Available at http://192.38.46.42/aubot/fb/FastGap_home.htm).
Boissin E, Féral JP, Chenuil A (2008) Defining reproductively isolated units in a cryptic and syntopicspecies complex using mitochondrial and nuclear markers: the brooding brittle star, Amphipholissquamata (Ophiuroidea). Molecular Ecology,17,1732–1744.
Breton S, Beaupré H D, Stewart D T, Hoeh W R, Blier P U (2007) The unusual system of doublyuniparental inheritance of mtDNA: isn’t one enough? Trends in Genetics,23,465–474.
Bryson RW, de Oca ANM, Jaeger JR, Riddle B （2010）Elucidation of cryptic diversity in a widespreadNearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamiclandscape. Evolution,64,2315–2330.
Burns J, Janzen D, Hajibabaei M, Hallwachs W, Hebert P.2008. DNA barcodes and cryptic species ofskipper butterflies in the genus Perichares in Area de Conservación Guannacaste, Costa Rica.Proceedings of the National Academy of Sciences of the United States of America,105,6350–6355.
Cameron S, Rubinoff D, Will K (2006) Who will actually use DNA barcoding and what will it cost?Systemtic Biology,55,844–847.
Cesari M, Bertolani R, Rebecchi L, Guidetti R (2008) DNA barcoding in Tardigrada: the first case study onMacrobiotus macrocalix Bertolani&Rebecchi1993(Eutardigrada, Macrobiotidae). MolecularEcology Resources,9,699–706.
Chan KMA, Levin SA (2005) Leaky prezygotic isolation and porous genomes: rapid introgression ofmaternally inherited DNA. Evolution,59,720–729.
Chen G, Hare MP (2008) Cryptic ecological diversification of a planktonic estuarine copepod, Acartiatonsa. Molecular Ecology,17,1451–1468.
Chen G, Hare M (2011) Cryptic diversity and comparative phylogeography of the estuarine copepodAcartia tonsa on the US Atlantic coast. Molecular Ecology,20,2425–2441.
Chen J, Li Q, Kong LF, Zheng XD, Yu RH (2010) COI-based DNA barcoding in Tapetinae species(Mollusca, Bivalvia, Veneridae) along the coast of China. Zoological Research,31,345–352.
Clavero, M. and García-Berthou, E.(2005) Invasive species are a leading cause of animal extinctions.Trends in Ecology and Evolution,20,110.
Cracraft J (1989) Speciation and its ontology: the empirical consequences of alternative species conceptsfor understanding patterns and processes of differentiation. In Speciation and its consequences (OtteD, Endler JA eds), pp.28–59. Sinauer Associates.
Cross Ismael, Rebordinos L (2006) Species identification of Crassostrea and Ostrea Oysters bypolymerase chain reaction amplification of the5S rDNA gene. Journal of AOAC International,89,144-148.
Damm S, Schierwater B, Hadrys H (2010)An integrative approach to species discovery in odonates: fromcharacter-based DNA barcoding to ecology. Molecular Ecology,19,3881–3893.
Darwin C (1859) On the origin of species by means of natural selection, or the preservation of favouredraces in the struggle for life. John Murray, London.
Dasmahapatra KK, Mallet J (2006) DNA barcodes: recent successes and future prospects. Heredity,97,254-255.
Davison A, Blackie R, Scothern G (2009) DNA barcoding of stylommatophoran land snails: a test ofexisting sequences. Molecular Ecology Resources,9,1092–1101.
Dayrat B (2005) Towards integrative taxonomy. Biological Journal of the Linnean Society,85,407–415.
deMelo AGC, Varela ES, Beasley CR et al.(2010) Molecular identification, phylogeny and geographicdistribution of Brazilian mangrove oysters (Crassostrea). Genetics Molecular Biology,33,564-572.
de Queiroz K (1998) The general lineage concept of species, species criteria, and the process of speciation:A conceptual unification and terminological recommendations. In Endless forms: Species andspeciation (Howard DJ, Berlocher SH eds.), pp.57–75. Oxford University Press, New York.
de Queiroz K (1999) The general lineage concept of species and the defining properties of the speciescategory. In Species (Wilson RA eds.), pp.49–89. MIT Press.
de Queiroz K (2007) Species concepts and species delimitation. Systematic Biology,56,879–886.
DeSalle R (2006) What's in a character? Journal of Biomedical Informatics,39,6–17.
DeSalle R (2007) Phenetic and DNA taxonomy; a comment on Waugh. BioEssays,29,1289–1290.
DeSalle R, Egan MG, Siddall M (2005): The unholy trinity: taxonomy, species delimitation and DNAbarcoding. Philosophical Transactions of the Royal Society B,360,1905–1916.
Dincǎ V, Lukhtanov VA, Talavera1G, Vila1R (2011) Unecpected layers of cryptic diversity in wood whiteLeptidea butterflies. Nature Communications,2,324.
Dinc V, Zakharov EV, Hebert PDN, Vila R (2010) Complete DNA barcode reference library for acountry’s butterfly fauna reveals high performance for temperate Europe. Proceedings of the RoyalSociety of London Series B,2011,278,1704347–355.
Distel D (2000) Phylogenetic relationships among Mytilidae (Bivalvia):18S rRNA data suggestconvergence in Mytilid body plans. Molecular Phylogenetics and Evolution,15,25–33.
Dowling TE, Secor CL (1997) The role of hybridization and introgression in the diversification of animals.Annual Review Ecology and Systematics,28,593–619.
Duncan KM, Martin AP, Bowen BW, DeCouet HG (2006) Global phylogeography of the scallopedhammerhead shark (Sphyrna lewini). Molecular Ecology,15,2239-2251.
Ebach MC, Holdrege C (2005) DNA barcoding is no substitute for taxonomy. Nature,434,697.
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Research,32,1792–1797.
Elias M, Hill RI, Willmott KR et al (2007) Limited performance of DNA barcoding in a diversecommunity of tropical butterflies. Proceedings of the Royal Society of London Series B,274,2881–2889.
Erpenbeck D, Duran S, Rützler K et al.(2007) Towards a DNA taxonomy of Caribbean demosponges: agene tree reconstructed from partial mitochondrial CO1gene sequences supports previous rDNAphylogenies and provides a new perspective on the systematics of Demospongiae. Journal of theMarine Biological Association of the United Kingdom,87,1563–1570.
Esteban GF, Finaly BJ (2010) Conservation work is incomplete without cryptic biodiversity. Nature,463,293.
FAO (1998) FAO species identification guide for fishery purpose. The Living Marine Resources of theWestern Central Pacific. Volume1: Seaweeds, Corals, Bivalves and Gastropods.
Fernandez CC, Shevock JR, Glazer AN, Thompson JN (2006) Cryptic species within the cosmopolitandesiccation-tolerant moss Grimmia Laevigata. Proceedings of the National Academy of Sciences ofthe United States of America,103,637–642.
Ferri E, Barbuto M, Bain O et al.(2009) Integrated taxonomy: traditional approach and DNA barcoding forthe identification of filarioid worms and related parasites (Nematoda). Frontier in Zoology,6,1.
Fisher BL, Smith MA (2008) A revision of Malagasy Species of Anochetus Mayr and OdontomachusLatreille (Hymenoptera: Formicidae). Plos One,3, e1787.
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification ofmitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular MarineBiology and Biotechnology,3,294–299.
Foottit RGF, Maw HEL, Von Dohlen CD, Hebert (2008) Species identification of aphids (Insecta:Hemiptera: Aphididae) through DNA barcodes. Molecular Ecology Resources,8,1189–1201.
Frost DR, Kluge AG (1994) A consideration of epistemology in systematic biology, with special referenceto species. Cladistics,10,259–94.
Funk DJ, Omland KE (2003) Species–level paraphyly and polyphyly: frequency, causes, and consequences,with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution andSystematics,34,397–423.
Galtier N, Nabholz B, Glémin S, Hurst GDD (2009) Mitochondrial DNA as a marker of moleculardiversity: a reappraisal. Molecular Ecology,18,4541–4550.
Gaulkes CG, Bennett NC, Cotterill FPD et al (2011) Phylogeography and cryptic diversity of thesolitary-dwelling silvery mole-rat, genus Heliophobius (family: Bathyergidae). Journal of Zoology,285,324–338.
Geller JB (1999) Decline of a native mussel masked by sibling species invasion. Conservation Biology,13,661–664.
Geml J, Laursen AL, O’Neill K, Nusbaum C, Taylor L (2006) Beringian origins and cryptic speciationevents in the fly agaric (Amanita muscaria) Molecular Ecology,15,225–239.
Giribet G, Okusu A, Lindgren AR et al.(2006) Evidence for a clade composed of molluscs with seriallyrepeated structures: monoplacophorans are related to chitons. Proceeding of the National Academy ofSciences of the United States of America,103,7723-7728.
Griffiths AM, Sims DW, Cotterell SP et al.(2010) Molecular markers reveal spatially segregated crypticspecies in a critically endangered fish, the common skate (Dipturus batis). Proceedings of the RoyalSociety of London Series B,277,1497–1503.
Guindon S, Gascuel O (2003) A simple, fast and accurate method to estimate large phylogenies bymaximum-likelihood. Systematic Biology,52,696–704.
Gunter G (1950) The generic status of living oysters and the scientific name of the common Americanspecies. The American Midland Naturalist,43,438-449.
Hageskal G, Bralstad T, Knutsen AK, Skaar I (2008) Exploring the species diversity of Trichoderma inNorwegian drinking water systems by DNA barcoding. Molecular Ecology Resources,8,1178–1188.
Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish speciesof tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States ofAmerica,103,968–971.
Hall T A (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program forWindows95/98/NT. Nucleic Acids Symposium Series,41,95–98.
Hansen H, Bakke TA, Bachmann L (2007) DNA taxonomy and barcoding of monogenean parasites:lessons from Gyrodactylus. Trends in Parasitology,23,363–367.
Harper FM, Hart MW (2007) Morphological and phylogenetic evidence for hybridization and introgressionin a sea star secondary contact zone. Invertebrate Biology,126,373–384.
Harris DJ, Froufe E (2005) Taxonomic inflation: species concept or historical geogpolitical bias? Trends inEcology and Evolution,20,6–7.
Harry HW (1985) Synopsis of the supraspecific classification of living oysters (Bivalvia: Gryphaeidae andOstreidae). Veliger,28,121–158.
Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes.Proceedings of the Royal Society of London Series B,270,323–321.
Hebert PDN, Penton EH, Burns JM et al.(2004b) Ten species in one: DNA barcoding reveals crypticspecies in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the NationalAcademy of Sciences of the United States of America,101,14812–14817.
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004a) Identification of birds through DNA barcodes.PLoS Biology,2, e312.
Hausdorf B (2010) Progress toward a general concept. Evolution,65,923–931.
Hedgecock D, Li G, Banks MA, Kain Z (1999) Occurrence of the Kumamoto oyster Crassostrea sikameain the Ariake Sea, Japan. Marine biology,133,65–68.
Hellberg ME, Vacquier VD (1999) Rapid evolution of fertilization selectivity and
Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. QuarterlyReview of Biology,66,411–453.
Hsieh C, Chen CS, Chiu TS (2005) Composition and abundance of copepods and ichthyoplankton inTaiwan Strait (western North Pacific) are influenced by seasonal monsoons. Marine and FreshwaterResearch,56,153–161.
Hutchinson GE (1957) Concluding remarks. Cold Spring Harbor Symposium on Quantitative Biology,22,415–427.
Hwang JS, Wong CK (2005) The China Coastal Current as a driving force for transporting Calanus sinicus(Copepoda: Calanoida) from its population centers to waters off Taiwan and Hong Kong during thewinter northeast monsoon period. Journal of Plankton Research,27,205–210.
Imbrie J, Berger A, Boyle EA et al.(1993) On the structure and origin of major glaciation cycles2. The100,000-year cycle. Paleoceanography,8,699–735.
Johnson SB, Warén A, Vrijenhoek RC (2008) DNA barcoding of Lepetodrilus limpets reveals crypticspecies. Journal of Shellfish Research,27,43–51.
Jouventin P, Cuthbert J, Ottvall R (2006) Genetic isolation and divergence in sexual traits: evidence for thenorthern rockhopper penguin Eudyptes moseleyi being a sibling species. Molecular Ecology,15,3413–3423.
Jozefowicz CJ, ó Foighil D (1998) Phylogenetic Analysis of Southern Hemisphere Flat Oysters Based onPartial Mitochondrial16S rDNA Gene Sequences. Molecular Phylogenetics and Evolution,10,426-435.
Linares M, Soto-Calderon I, Lees D, Anthony N (2009) High mitochondrial diversity in geographicallywidespread butterflies of Madagasca: A test of the DNA barcoding approach. MolecularPhylogenetics and Evolution,50,485-495.
lysin cDNA sequences in teguline gastropods. Molecular Biology Evolution,16,839–848.
Kangethe EK, JonesSJ, Patterson RLS (1982) Identification of the species origin of fresh meat using anenzyme-linked immunosorbent assay procedure. Meat Science,7,229–240.
Kelly RP, Sarkar IN, Eernisse DJ, Desalle R (2007) DNA barcoding using chitons (genus Mopalia).Molecular Ecology Notes,7,177–183.
Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions throughcomparative studies of nucleotide sequences. Journal of Molecular Evolution,16,111–120.
Klinbunga S, Ampayup P, Tassanakajon A, Jarayabhand P, Yoosukh W (2001) Genetic diversity andmolecular markers of cupped oysters (genera Crassostrea, Saccostrea and Striostrea) in Thailandrevealed by randomly amplified polymorphic DNA analysis. Marine Biotechnology,3,133–144.
Klinbunga S, Khamnamtong N, Tassanakajon A, Puanglarp N, Jarayabhand P (2003) Molecular geneticidentification tools for three commercially cultured oysters (Crassostrea belcheri, Crassostreairedalei, and Saccostrea cucullata) in Thailand. Marine Biotechnology,5,27–36.
Klinbunga S, Khamnamtong B, Puanglarp N et al.(2005) Molecular taxonomy of cupped oysters(Crassostrea, Saccostrea, and Striostrea) in Thailand based on COI,16S, and18S rDNApolymorphism. Marine Biotechnology,7,306-317.
Kmiec B, Woloszynska M, Janska H (2006) Heteroplasmy as a common state of mitochondrial geneticinformation in the plants and animals. Current Genetics,50,149–159.
Knowles LL, Carstens BC (2007) Delimiting species without monophyletic gene trees. Systematic Biology,56,887–895.
Knowlton N (1993) Sibling species in the sea. Annual Review of Ecology and Systemaics,24,189–216.
Knowlton N (2000) Molecular genetic analyses of species boundaries in the sea. Hybrobiologia,420,73–90.
Koch H (2010) Combining morphology and DNA barcoding resolves the taxonomy of Western MalagasyLiotrigona Moure,1961(Hymenoptera: Apidae: Meliponini). African Invertebrates,51,413–421.
Kress WJ, Wrudack KJ, Zimmer EA, Weigh L, Janzen DH (2005) Use of DNA barcodes to identifyflowering plants. Proceedings of the National Academy of Sciences of the United States of America,102,8369–8374.
Laegdsgaard P, Johnson C (2001) Why do juvenile fish utilize mangrove habitats? Journal of ExperimentalMarine Biology and Ecology,257,229–253.
Lahaye R, van der Bank M, Bogarin D et al.(2008) DNA barcoding the floras of biodiversity hotspots.Proceedings of the National Academy of Sciences of the United States of America,105,2023–2928.
Lam K, Morton B (2003) Mitochondrial DNA and morphological identification of a new species ofCrassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China.Aquaculture,228,1–13.
Lam K, Morton B (2006) Morphological and mitochondrial-DNA analysis of the Indo-West Pacific rockoysters (Ostreidae: Saccostrea species). Journal of Molluscan Studies,72,235-245.
Lam K (2009) Oysters (Bivalvia: Ostreidae and Gryphaeidae) recorded from Malaysia and Singapore. TheRaffles Bulletin of Zoology,57,481-494.
Lambeck K, Esat TM, Potter EK (2002) Links between climate and sea levels for the past three millionyears. Nature,419,199–206.
Lapègue S, Batista RM, Heurtebise S Yu ZN, Boudry P (2004) Evidence for the presence of the Portugueseoyster, Crassostrea angulata, in Northern China. Journal of Shellfish Research,23,759-763.
Lee MSY (2003) Species concepts and species reality: salvaging a Linnaean rank. Journal of EvolutionaryBiology,16,179–188.
Lee T, Foighil Dó (2004) Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal fourcryptic species within the scorched mussel, Brachidontes exusturs, species complex. MolecularEcology,13,3527–3542.
Lee T, Foighil Dó (2005) Placing the Floridian marine genetic disjunction into a regional evolutionarycontext using the scorched mussel, Brachidontes exusturs, species complex. Evolution,59,2139–2158.
Leliaer F, Verbruggen H, Wysor B, De Clerck O (2009) DNA taxonomy in morphologically plastic taxa:Algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales). MolecularPhylogenetics and Evolution,53,122–133.
Lessios HA, Pearse JS (1996) Hybridization and introgression between Indo-Pacific species of Diadema.Marine Biology,126,715–723.
Li Q, Yu H, Yu RH (2006) Genetic variability assessed by microsatellites in cultured populations of thePacific oyster (Crassostrea gigas) in China. Aquaculture,259,95–102.
Lipscomb D, Platnick N, Wheeler Q (2003) The intellectual content of taxonomy: a comment on DNAtaxonomy. Trends in Ecology and Evolution,18,65–66.
Littlewood DTJ (1994) Molecular Phylogenetics of Cupped Oysters Based on Partial28S rRNA GeneSequences. Molecular Phylogenetics and Evolution,3,221-229.
Liu JX, Gao TX, Wu SF, Zhang YP (2007) Pleistocene isolation in the Northowestern Pacific marginal seasand limited dispersal in a marine fish, Chelon haematocheilus (Temminck&Schlegel,1845).Molecular Ecology,16,275–288.
Locke SA, Mclaughlin JD, Marcogliese DJ (2010) DNA barcodes show cryptic diversity and a potentialphysiological basis for host specificity among Diplostomoidea (Platyhelminthes: Digenea)parasitizing freshwater fishes in the St. Lawrence River, Canada. Molecular Ecology,19,2813–2827.
López-Flores I, de la Herrán R, Garrido-Ramos MA et al.(2004) The molecular phylogeny of oystersbased on a satellite DNA related to transposons. Gene,339,181-188.
López-Flores I, Ruiz-Rejón, Cross I et al.(2010) Molecular characterizaition and evolution of aninterspersed repetitive DNA family of oysters. Genetica,138,1211-1219.
Lowenstein JH, Amato G, Kolokotronis SO (2009) The real maccoyii: identifying tuna sushi with DNAbarcodes–contrasting characteristic attributes and genetic distances. PLoS One,4, e7866.
Mallet J (2001) Species, concepts of. In Encyclopedia of Biodiversity (Levin S et al. eds), pp.427–440.Academic Press.
Mallet J (2006) Species concepts. In: Evolutionary genetics: concepts and case studies (Fox CW, Wolf JBeds), pp.367–373. Oxford: Oxford University Press.
Mallet J,Willmott K (2003) Taxonomy: Renaissance or Tower of Babel? Trends in Ecology and Evolution,18,57–59.
Makino W, Tanabe AS (2009) Extreme population genetic differentiation and secondary contact in thefreshwater copepod Acanthodiaptomus pacificus in the Japanese Archipelago. Marine Biology,18,2699–2713.
Manthey JD, Klicka J, Spellman GM (2011) Cryptic diversity in a widespread North American songbird:phylogeography of the Brown Creeper (Certhia americana). Molecular Phylogenetic Evolution,58,502–512.
Marko PB (2002) Fossil calibration of molecular clocks and the divergence times of geminate species pairsseparated by the Isthmus of Panama. Molecular Biology Evolution,19,2005–2021.
Martin DP, Lemey P, Lott M et al.(2010). RDP3: a flexible and fast computer program for analyzingrecombination. Bioinformatics,26,2462–2463.
Matsumoto M (2003) Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COIsequences. Molecular Phylogenetics and Evolution,27,429-440.
Mathews LM (2006) Cryptic biodiversity and phylogeographical patterns in a snapping shrimp speciescomplex. Molecular Ecology,15,4049–4063.
Mayden RL (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. InSpecies: the Units of Biodiversity (Claridge MF et al., eds), pp.381–424. Chapman&Hall.
Mayr E (1942) Systematics and the origin of species from the viewpoint of a zoologist. New York:Columbia University Press.
Mayr E (1963) Animal Species and Evolution. Harvard University Press, Cambridge, Massachusetts.
Meier R, Shiyang K, Baidya G, Ng PKL (2006) DNA Barcoding and taxonomy in Diptera: a tale of highintraspecific variability and low identification success. Systematic Biology,55,715–728.
Meier R, Zhang GY, Ali F (2008) The use of mean instead of smallest interspecific distances exaggeratesthe size of the “barcoding gap” and leads to misidentification. Systematic Biology,57,809-813.
Melo CMR, Silva FC, Gomes CHAM, Solé-Caca AM, Lazoski C (2010) Crassostrea gigas in naturaloyster banks in southern Brazil. Biological Invasions,12,441-449.
Mengual X, Thompson FC (2008) A taxonomic review of the Palpada ruficeps species group, with thedescription of a new flower fly from Colombia (Diptera, Syrphidae). Zootaxa1741:31–36.
Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. Plos Biology,3,e422.
Milbury CA, Gaffney PM (2005) Complete mitochondrial DNA sequence of the eastern oyster Crassostreavirginica. Marine Biotechnology,7,697-712.
Monaghan MT, Balke M, Pons J, Bogler AP (2006) Beyond barcodes: complex DNA taxonomy of a SouthPacific Island radiation. Proceedings of the Royal Society of London Series B,273,887–893.
Milankov V, Stahls G, Stamenkovic J, Vujic A (2008) Genetic diversity of Merodon aureus and M. cinereusspecies complexes (Diptera, Syrphidae): integrative taxonomy and implications for conservationpriorities on the Balkan Peninsula. Conservation. Genetics,9,1125–1137.
Morton B (2004) The oysters of Hong Kong (Bivalvia: Ostreidae and Gryphaeidae). The Raffles Bulletinof Zoology,52,11-28.
Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carloapproach. Genetics,158,885–896.
Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York.
O’Meara BC (2010) New heuristic methods for joint species delimitation and species tree inference.Systematic biology,59,59-73.
Padial JM, De La Riva I (2009) Integrative taxonomy reveals cryptic Amazonian species of Pristimantis(Anura: Strabomantidae). Zoological Journal of the Linnean Society,155,97–122.
Passamonti M (2007) An unusual case of gender-associated mitochondrial DNA heteroplasmy the mytilidMusculista senhousia (Mollusca Bivalvia). BMC Evolutionary Biology,7(suppl2), S7.
Palumbi SR (1994) Genetic divergence, reproductive isolation, and marine speciation. Annual Review ofEcology and Systematics,25,547–572.
Palumbi SR (1996) Nucleic acids II: the polymerase chain reaction. In: Molecular Systematics (Hillis DM,Moritz C, Mable BK eds), pp.205–247. Sinauer&Associates Inc., Sunderland, MA.
Pavlic D, Slippers B, Coutinho TA, Wingfield MJ (2009) Multiple gene genealogies and phenotypic datareveal cryptic species of the Botryosphaeriaceae: a case study on the Neofusicoccum parvum/N. ribiscomplex. Molecular Phylogenetics and Evolution,51,259–268.
Pennisi E (2003) Modernizing the tree of life. Science,300,1692–1697.
Petit RJ, Excoffier L (2009) Gene flow and species delimitation. Trends in Ecology and Evolution,24,386–393.
Pires AC, Marinon L (2010) DNA barcoding and traditional taxonomy unified through IntegrativeTaxonomy: a view that challenges the debate questioning both methodologies. Biota Neotropica,10,339–346.
Plazzi F, Passamonti M (2010) Towards a molecular phylogeny of Mollusks: Bivalves’ early evolution asrevealed by mitochondrial genes. Molecular Phylogenetics and Evolution,57,641-657.
Polson MP, Hewson WE, Eernisse DJ, Baker PK, Zacherl D (2009) You say Conchaphila, I say lurida:molecular evidence for restricting the Olympia oyster to temperate western north America. Journal ofShellfish Research,28,11-21.
Posada D (2008) jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution,25,1253–1256.
PuillandreN, Lambert A, Brouillet S,AchazG (2011) ABGD, Automatic Barcode Gap Discovery forprimary species delimitation. Molecular Ecology, doi:10.1111/j.1365–294X.2011.05239.x.
Rach J, DeSalle R, Sarkar IN, Schierwater B, Hadrys H (2008) Character-based DNA barcoding allowsdiscrimination of genera, species and populations in Odonata. Proceedings of the Royal Society ofLondon Series B,275,237–247.
Ratnasingham S, Hebert PDN (2007) BOLD: the Barcode of life data system (www.barcodinglife.org).Mollecular Ecology Notes,7,355–364.
Reece KS, Cordes JF, Stubbs JB, Hudson KL, Francis EA (2008) Moleculare phylogenies help resolvetaxonomic confusion with Asian Crassostrea oyster species. Marine Biology,153,709-721.
Reeves PA, Richards CM (2011) Species delimitation under the general lineage concept: an empiricalexample using wild American hops (Cannabaceae: Humulus lupulus). Systematic Biology,60:45–59.
Ren JF, Liu X, Zhang GF, Liu B, Guo XM (2009)“Tandem duplication-random loss” is not a real featureof oyster mitochondrial genomes. BMC genomics,10,84.
Renard E, Bachmann V, Cariou ML, Moreteau JC (2000) Morphological and molecular differentiation ofinvasive freshwater species of the genus Corbicula (Bivalvia, Corbiculidea) suggest the presence ofthree taxa in French rivers. Molecular Ecology,9,2009–2016.
Renoult JP, Geniez P, Bacquet P, Benoit L, Crochet PA (2009) Morphology and nuclear markers revealextensive mitochondrial introgressions in the Iberian Wall Lizard species complex. Molecular Ecology,18,4298–4315.
Roe AD, Sperling FAH (2007) Population structure and species boundary delimitation of crypticDioryctria moths: an integrative approach. Molecular Ecology,16,3617–3633.
Ronquist F, Huelsenbeck JP (2003) MRBAYES3: Bayesian phylogenetic inference under mixed models.Bioinformatics,19,1572–1574.
Roques S, Sévigy JM, Bernatchez L (2001) Evidence for broadscale introgressive hybridization betweentwo redfish (geneus Sebastes) in the North-west Atlantic: a rare marine example. Molecular Ecology,10,149–165.
Rosen DE (1978) Vicariant patterns and historical explanation in biogeography. Systematic Zoology,27,159–88.
Rosewater J (1961) The family Pinnidae in the Indo-Pacific. Indo-Pacific Mollusca,1,175–226.
Ross KG, Gotzek D, Ascunce MS, Shoemaker DD (2010) Species delimitation: a case study in aproblematic ant taxon. Systematic Biology,59,162–184.
Rubinoff D (2005) Utility of mitochondrial DNA barcodes in species conservation. Conservation Biology,20,1026–1033.
Ruesink JL, Lenihan HS, Trimble AC et al.(2005) Introduction of non-native oysters: ecosystem effectsand restoration implications. Annual Review of Ecology, Evolution, and Systematics,36,643-689.
Schindel DE, Miller SE (2005) DNA barcoding a useful tool for taxonomists. Nature,435,17.
Schlick-Steiner BC, Steiner FM, Seifert MK et al.(2006) A multidisciplinary approach reveals crypticdiversity in Western Paleartic Tetramorium ants (Hymenoptera: Formcidae). Molecular PhylogeneticEvolution,40,259–273.
Schlick-Steiner BC, Steiner FM, Seifert B et al.(2010) A multisource approach to exploring biodiversity.Annual Review of Entomology,55,421–38.
Scott E (1980) A clarification of the genus Perna (Mytilidae). Bulletin of marine science,30,858–870.
Seberg O, Petersen G, Humphries CJ et al.(2003) Shortcuts in systematics? a commentary on DNA-basedtaxonomy. Trends in Ecology and Evolution,18,63–65.
Seifert KA, Samson RA, deWaard JR et al.(2007) Prospects for fungus identification using co1DNAbarcodes, with Penicillium as a test case. Proceeding of the National Academy of Sciences of theUnited States of America,104,3901-3906.
Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses.Systematic Biology,49,369–381.
Sites JW, Marshall C (2004) Operational criteria for delimiting species. Annual Review of Ecology andSystemaics,35,199–227.
Smith VS (2005) DNA barcoding: perspectives from a “Partnerships for Enhancing Expertise inTaxonomy”(PEET) debate. Systematic Biology,54,841–844.
Smith M, Nikolai A, Poyarkov JR, Hebert PDN (2008) CO1DNA barcoding amphibians: take the chance,meet the challenge. Molecular Ecology Resources,8,235–246.
Stoeckle M (2003) Taxonomy, DNA, and the Bar Code of Life. BioScience,53:796–797.
Stoeckle M, Waggoner P, Ausubel J (2004) Bar-coding life: Ten reasons. Consortium for the Barcode ofLife. www.barcoding.si.edu/.
Stuart BL, Inger RF, Voris HK (2006) High level of cryptic species diversity revealed by sympatriclineages of Southeast Asian forest frogs. Biology Letters,2,470–474.
Swofford DL (2003) PAUP*: phylogenetic analysis using parsimony (*and other methods), Version4.Sinauer Associates, Sunderland, Massachusetts.
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region ofmitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution,10,512–526.
Tamura K, Dudley J, Nei M, Kumar S (2007). MEGA4: Molecular Evolutionary Genetics Analysis(MEGA) software version4.0. Molecular Biology and Evolution,24,1596–1599.
Tang RWK, Yau C, Ng WC (2010) Identification of stomatopod larvae (Crusacea: Stomatopoda) fromHong Kong waters using DNA barcodes. Molecular Ecology Resources,10,439-448.
Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2002) DNA points the way ahead in taxonomy.Nature,418,379.
Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2003) A plea for ＤNA taxonomy. Trends inEcology and Evolution,18,70–74.
Taylor HR, Harris WE (2012) An emergent science on the brink of irrelevance: a review of the past8yearsof DNA barcoding. Molecular Ecology Resources, doi:10.1111/j.1755–0998.2012.03119.x.
Thompson JD, Higgins DG, Gibson TJ (1994) ClustalW: Improving the sensitivity of progressive multiplesequence alignment through sequence weighting, position-specific gap penalties and weight matrixchoices. Nucleic Acids Research,22,4673–4680.
Thompson JD, Gibson TJ, Plewniak F, Jaanmougin F, Higgins DG (1997) The Clustal_X Windowsinterface: flexible strategies for multiple sequence alignment aided by quality analysis tools. NucleicAcids Research,24,4876–4882.
Tsang LM, Chan BKK, Ma Y, Chu KH (2008) Genetic differentiation, bybridiation and adaptivedivergence in two subspecies of the acorn barnacle Tetraclita japonica in the northwestern Pacific.Molecular Ecology,17,4151–4163.
UNEP (2007) Mangrove Demonstration Sites in the South China Sea. UNEP/GEF/SCS TechnicalPublication No.7.(Available at http://www.unepscs.org/)
Vaglia I, Haxaire J, Kitching IJ, Meusnier I, Rougerie R (2008) Morphology and DNA barcoding revealthree cryptic species within the Xylophanes neoptolemus and loelia species-groups (Lepidoptera:Sphingidae). Zootaxa,1923,18–36.
Valentini A, Pompanon F, Taberlet (2005) DNA barcoding for ecologists. Trends in Ecology and Evolution,24,110–117.
Vuataz L, Sartori M, Wagner A, Monaghan MT (2011) Toward a DNA Taxonomy of Alpine Rhithrogena(Ephemeroptera: Heptageniidae) Using a Mixed Yule-Coalescent Analysis of Mitochondrial andNuclear DNA. Plos ONE,6, e19728.
Wang PX (1999) Response of Western Pacific marginal seas to glacial cycles: paleoceanographic andsedimentological features. Marine Geology,156,5–39.
Wang HY, Guo XM, Zhang GF, Zhang FS (2004) Classification of jingjiang oysters Crassostrea rivularis(Gould,1861) from China, based on morphology and phylogenetic analysis. Aquaculture,242,137-155.
Wang HY, Zhang GF, Liu X, Guo XM (2008a) Classification of common oysters from north China. Journalof Shellfish Research,27,495-503.
Wang HY, Guo XM (2008b) Identification of Crassostrea ariakensis and related oysters by multiplexspecies-specific PCR. Journal of Shellfish Research,27,481-487.
Ward BD, Holmes BH (2007) An analysis of nucleotide and amino acid variability in the barcode region ofcytochrome c oxidase I (cox1) in fishes. Molecular Ecology Notes,7,899-907.
Ward R D, Zemlak T S, Innes B H, Last P R, Hebert P D N (2005) DNA barcoding Australia’s fish species.Philosophical Transactions of the Royal Society B,360,1847–185.
Wheeler QD (2005) Losing the plot: DNA “barcodes” and taxonomy. Cladistics,21,405–407.
White DJ, Wolff JN, Pierson M, Gemmell NJ (2008) Revealing the hidden complexities of mtDNAinheritance. Molecular Ecology,17,4925–4942.
Wiemers M, Fiedler K (2007) Does the DNA barcoding gap exist?–a case study in blue butterflies(Lepidoptera: Lycaenidae). Frontiers in Zoology,4,8.
Wiens JJ (2007) Species delimitation: new approaches for discovering diversity. Systematic biology,56,875–878.
Wiley EO (1981) Phylogenetics: The Theory and Practice of Phylogenetic Systematics. John Wiley&Sons,New York.
Wilkins JS (2009) Species: a history of idea. University of California Press, Berkeley and Los Angeles,California.
Wilkins JS (2011) Philosophically speaking, how many species concepts are there? Zootaxa,2765,58–60.
Will KW, Mishler BD, Wheeler QD (2005) The perils of DNA barcoding and the need for integrativetaxonomy. Systematic biology,54,844–851.
Will KW, Rubinoff D (2004) Myth of the molecule: DNA barcodes for species cannot replace morphologyfor identification and classification. Cladistics,20,47–55.
Winckworth R (1929) Marine mollusca from south India and Ceylon. III: Pinna. With an index to therecent species of Pinna. Proceedings of the Malacological Society of London.18,276–297.
Winker K (2005) Sibling species were first recognized by William Derham (1718). The Auk,122,706–707.
Wolfe-Coote S (2005) The Handbook of Experimental Animals: The Laboratory Primate. ElsevierAcademic Press.
Wu XY, Xu XD,Yu ZN, Wei ZP,Xia JJ (2010) Comparison of seven Crassostrea mitogenomes andphylogenetic analyses. Molecular Phylogenetics and Evolution,57,448-454.
Yeates DK, Seago A, Nelson L et al.(2011) Integrative taxonomy, or iterative taxonomy? SystematicEntomology,36,209–217.
Yokogawa K (1996) Genetic divergence in two forms of pen shell Atrina pectinata. Venus,55,25–39.
Yu Z, Kong X, Zhang L, Guo X, Xiang J (2003) Taxonomic status of four Crassostrea oysters from Chinaas inferred from mitochondrial DNA sequences. Journal of Shellfish Research,22,31–38.
Yu H, Li Q (2011) Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalvemitochondrial genomes. Plos ONE,6, e16147.
Yu XY, Mao Y, Wang MF, Zhou L, Gui JF (2004) Genetic heterogeneity analysis and RAPD markersdetection among four forms of Atrina pectinata Linnaeus. Journal of Shellfish Research,23,165–171.
Yu ZN, Wei ZP, Kong XY, Shi W (2008) Complete mitochondrial DNA sequence of oyster Crassostreahongkongensis-a case of “Tandem duplication-random loss for” genome rearrangement in Crassostrea?BMC Genomics,9,477.
Xu JW, Chan TY, Tsang LM, Chu KH (2009) Phylogeography of the mitten crab Eriocheir sensu stricto inEast Asia: Pleistocence isolation, population expansion and secondary contact. MolecularPhylogenetics and Evolution,52,45–56.
Zak ek V, Sket B, Gottstein S, Franjevi D, Trontelj P (2009) The limits of cryptic diversity in groundwater:phylogeography of the cave shrimp Troglocaris anophthalmus (Crustacea: Decapoda: Atyidae).Molecular Ecology,18,931–46.
Zapata F, Jiménez I (2012) Species delimitaiton: inferring gaps in morphology across geography. SystmaticBiology,61,179-194.
Zhang DX, Hewitt GM (1996) Nuclear integrations: challenges for mitochondrial DNA markers. Trends inEcology and Evolution,11,247–251.
Zhao K, Duan ZY, Peng ZG et al.(2009) The youngest split in sympatric schizothoracine fish (Cyprinidae)is shaped by ecological adaptations in a Tibetan Plateau glacier lake. Molecular Ecology,18,3616–3628.
[2]‘…a lineage of an ancestor-descendent populations which maintains its identity from other suchlineages and which has its own evolutionary tendencies and historical fate.’(Wiley1981)
[3]‘A phylogenetic species is an irreducible (basal) cluster of organisms, diagnosably distinct from othersuch clusters, and with which there is a parental pattern of ancestry and descent.’(Cracraft1989)
[4]‘… a geographically constrained groups of individuals with some unique apomorphous character, is theunit of evolutionary significance.’(Rosen1978)
[5]‘…equates species with separately evolving metapopulation lineages…’(de Queiro2007)
李孝绪,齐钟彦(1994)中国牡蛎的比较解剖学及系统分类和演化的研究.海洋科学集刊,35,143–173.
齐钟彦(1989)黄渤海的软体动物.北京:农业出版社.
梁羡圆,林惠琼,吴萍茹,刘元(1986)福建沿海江珧科的形态比较研究.热带海洋,5,13–19.
彭居俐,王绪桢,何舜平（2008）DNA条形码技术的研究进展及其应用.水生生物学报,2008,32:916—919.
乔延龙,林昭进(2007)北部湾地形、底质特征与渔场分布的关系.海洋湖沼通报,增刊,232–238.
王梅芳，余祥勇，杨书婷，桂建芳（2000）无裂栉江珧种内同工酶表型差异的比较研究。热带海洋,19,45–50.
王祯瑞(1964)中国近海江珧科的初步报告.海洋科学集刊,5,31–41.
王祯瑞(1997)中国动物志，软体动物门，双壳纲，贻贝目.北京：科学出版社.
徐凤山,黄修明(1993)中国近海牡蛎超科的新记录.海洋科学集刊,34,175–179.
薛东秀,张涛,王海艳,郑小东,孟凡玉(2009)有棘无棘两种表型栉江珧28S和COI基因序列差异的比较.海洋科学，33,88–91.
余祥勇,王梅芳,李宏吾,蔡英亚(2000)无裂栉江珧形态差异的比较研究.热带海洋,19,39–44.
张玺,楼子康（1956）中国牡蛎的研究．动物学报，8,65–94.
朱伟林,吴国瑄,黎明碧（2004）南海北部陆架北部湾盆地古湖泊与烃源条件。海洋与湖沼，35，8–14.
Agapow PM, Binida-Emonds ORP, Crandall KA et al.(2004) The effect of species concept on biodiversity.The quarterly Review of Biology,79,161–179.
Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001) The problems with hybrids: setting conservationguidelines. Trends in Ecology and Evolution,16,613–622.
Amato A, Kooistra WHCF, Ghiron JHL et al.(2007) Reproductive Isolation among Sympatric CrypticSpecies in Marine Diatoms. Protist,158,193–207.
Arnot, D.E. et al.(1993) Digital codes from hypervariable tandemly repeated DNA sequences in thePlasmodium falciparum circumsporozoite gene can genetically barcode isolates. Molecular andBiochemical Parasitology,61,15–24.
Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press,Cambridge.
Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Molecular Ecology,13,729–744.
Banks MA, McGoldrick DJ, Borgeson W, Hedgecock D (1994) Gametic incompatibility and geneticdivergence of Pacific and Kumamoto oysters, Crassostrea gigas and C. sikamea. Marine Biology,121,127–135.
Barrett R D H, Hebert P D N (2005) Identifying spiders through DNA barcodes. Canadian Journal ofZoology,3,481–491.
Bensasson D, Zhang DX., Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: evolution’s misplacedwitnesses. Trends in Ecology and Evolution,16,314–321.
Bergmann T, Hadrys H, Breves G, Schierwater B (2009) Character-based DNA barcoding: a superior tool
for species classification. Berliner Und Münchener Tier rztliche Wochenschrift,122,446–450.
Bernard FR, Cai YY, Morton B (1993) Catalogue of Living Marine Bivalve Molluscs of China. HongKong University Press, Hong Kong.
Bickford D, Lohman DJ, Sodhi NS et al.(2006) Cryptic species as a window on diversity and conservation.Trends in Ecology and Evolution,22,148–155.
Bieler B, Mikkelsen PM, Lee T, óFoighil D (2004) Discovery of the Indo-Pacific oyster Hyotissa hyotis(Linnaeus,1758) in the Florida Keys (Biavalvia: Gryphaeidae). Molluscan Research,24,149-159.
Blaxter M L (2004) The promise of a DNA taxonomy. Philosophical Transactions of the Royal Society B,359,669–679.
Blaxter M, Elsworth B, Daub J (2004) DNA taxonomy of a neglected animal phylum: an unexpecteddiversity of tardigrades. Proceedings of the Royal Society of London Series B (Suppl.)271,S189–S192.
Boggs CL (2001) Species and Speciation. International Encyclopedia of the Social and BehavioralSciences. Oxford: Elsevier.
Bolnick DI, Fitzpatrick BM (2007) Sympatric speciation: models and empirical evidence. Annual Reviewof Ecology, Evolution and Systematics,38,459–487.
Borchsenius F (2009) FastGap1.2. Department of Biological Sciences, University of of Aarhus, Denmark.(Available at http://192.38.46.42/aubot/fb/FastGap_home.htm).
Boissin E, Féral JP, Chenuil A (2008) Defining reproductively isolated units in a cryptic and syntopicspecies complex using mitochondrial and nuclear markers: the brooding brittle star, Amphipholissquamata (Ophiuroidea). Molecular Ecology,17,1732–1744.
Breton S, Beaupré H D, Stewart D T, Hoeh W R, Blier P U (2007) The unusual system of doublyuniparental inheritance of mtDNA: isn’t one enough? Trends in Genetics,23,465–474.
Bryson RW, de Oca ANM, Jaeger JR, Riddle B （2010）Elucidation of cryptic diversity in a widespreadNearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamiclandscape. Evolution,64,2315–2330.
Burns J, Janzen D, Hajibabaei M, Hallwachs W, Hebert P.2008. DNA barcodes and cryptic species ofskipper butterflies in the genus Perichares in Area de Conservación Guannacaste, Costa Rica.Proceedings of the National Academy of Sciences of the United States of America,105,6350–6355.
Cameron S, Rubinoff D, Will K (2006) Who will actually use DNA barcoding and what will it cost?Systemtic Biology,55,844–847.
Cesari M, Bertolani R, Rebecchi L, Guidetti R (2008) DNA barcoding in Tardigrada: the first case study onMacrobiotus macrocalix Bertolani&Rebecchi1993(Eutardigrada, Macrobiotidae). MolecularEcology Resources,9,699–706.
Chan KMA, Levin SA (2005) Leaky prezygotic isolation and porous genomes: rapid introgression ofmaternally inherited DNA. Evolution,59,720–729.
Chen G, Hare MP (2008) Cryptic ecological diversification of a planktonic estuarine copepod, Acartiatonsa. Molecular Ecology,17,1451–1468.
Chen G, Hare M (2011) Cryptic diversity and comparative phylogeography of the estuarine copepodAcartia tonsa on the US Atlantic coast. Molecular Ecology,20,2425–2441.
Chen J, Li Q, Kong LF, Zheng XD, Yu RH (2010) COI-based DNA barcoding in Tapetinae species(Mollusca, Bivalvia, Veneridae) along the coast of China. Zoological Research,31,345–352.
Clavero, M. and García-Berthou, E.(2005) Invasive species are a leading cause of animal extinctions.Trends in Ecology and Evolution,20,110.
Cracraft J (1989) Speciation and its ontology: the empirical consequences of alternative species conceptsfor understanding patterns and processes of differentiation. In Speciation and its consequences (OtteD, Endler JA eds), pp.28–59. Sinauer Associates.
Cross Ismael, Rebordinos L (2006) Species identification of Crassostrea and Ostrea Oysters bypolymerase chain reaction amplification of the5S rDNA gene. Journal of AOAC International,89,144-148.
Damm S, Schierwater B, Hadrys H (2010)An integrative approach to species discovery in odonates: fromcharacter-based DNA barcoding to ecology. Molecular Ecology,19,3881–3893.
Darwin C (1859) On the origin of species by means of natural selection, or the preservation of favouredraces in the struggle for life. John Murray, London.
Dasmahapatra KK, Mallet J (2006) DNA barcodes: recent successes and future prospects. Heredity,97,254-255.
Davison A, Blackie R, Scothern G (2009) DNA barcoding of stylommatophoran land snails: a test ofexisting sequences. Molecular Ecology Resources,9,1092–1101.
Dayrat B (2005) Towards integrative taxonomy. Biological Journal of the Linnean Society,85,407–415.
deMelo AGC, Varela ES, Beasley CR et al.(2010) Molecular identification, phylogeny and geographicdistribution of Brazilian mangrove oysters (Crassostrea). Genetics Molecular Biology,33,564-572.
de Queiroz K (1998) The general lineage concept of species, species criteria, and the process of speciation:A conceptual unification and terminological recommendations. In Endless forms: Species andspeciation (Howard DJ, Berlocher SH eds.), pp.57–75. Oxford University Press, New York.
de Queiroz K (1999) The general lineage concept of species and the defining properties of the speciescategory. In Species (Wilson RA eds.), pp.49–89. MIT Press.
de Queiroz K (2007) Species concepts and species delimitation. Systematic Biology,56,879–886.
DeSalle R (2006) What's in a character? Journal of Biomedical Informatics,39,6–17.
DeSalle R (2007) Phenetic and DNA taxonomy; a comment on Waugh. BioEssays,29,1289–1290.
DeSalle R, Egan MG, Siddall M (2005): The unholy trinity: taxonomy, species delimitation and DNAbarcoding. Philosophical Transactions of the Royal Society B,360,1905–1916.
Dincǎ V, Lukhtanov VA, Talavera1G, Vila1R (2011) Unecpected layers of cryptic diversity in wood whiteLeptidea butterflies. Nature Communications,2,324.
Dinc V, Zakharov EV, Hebert PDN, Vila R (2010) Complete DNA barcode reference library for acountry’s butterfly fauna reveals high performance for temperate Europe. Proceedings of the RoyalSociety of London Series B,2011,278,1704347–355.
Distel D (2000) Phylogenetic relationships among Mytilidae (Bivalvia):18S rRNA data suggestconvergence in Mytilid body plans. Molecular Phylogenetics and Evolution,15,25–33.
Dowling TE, Secor CL (1997) The role of hybridization and introgression in the diversification of animals.Annual Review Ecology and Systematics,28,593–619.
Duncan KM, Martin AP, Bowen BW, DeCouet HG (2006) Global phylogeography of the scallopedhammerhead shark (Sphyrna lewini). Molecular Ecology,15,2239-2251.
Ebach MC, Holdrege C (2005) DNA barcoding is no substitute for taxonomy. Nature,434,697.
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Research,32,1792–1797.
Elias M, Hill RI, Willmott KR et al (2007) Limited performance of DNA barcoding in a diversecommunity of tropical butterflies. Proceedings of the Royal Society of London Series B,274,2881–2889.
Erpenbeck D, Duran S, Rützler K et al.(2007) Towards a DNA taxonomy of Caribbean demosponges: agene tree reconstructed from partial mitochondrial CO1gene sequences supports previous rDNAphylogenies and provides a new perspective on the systematics of Demospongiae. Journal of theMarine Biological Association of the United Kingdom,87,1563–1570.
Esteban GF, Finaly BJ (2010) Conservation work is incomplete without cryptic biodiversity. Nature,463,293.
FAO (1998) FAO species identification guide for fishery purpose. The Living Marine Resources of theWestern Central Pacific. Volume1: Seaweeds, Corals, Bivalves and Gastropods.
Fernandez CC, Shevock JR, Glazer AN, Thompson JN (2006) Cryptic species within the cosmopolitandesiccation-tolerant moss Grimmia Laevigata. Proceedings of the National Academy of Sciences ofthe United States of America,103,637–642.
Ferri E, Barbuto M, Bain O et al.(2009) Integrated taxonomy: traditional approach and DNA barcoding forthe identification of filarioid worms and related parasites (Nematoda). Frontier in Zoology,6,1.
Fisher BL, Smith MA (2008) A revision of Malagasy Species of Anochetus Mayr and OdontomachusLatreille (Hymenoptera: Formicidae). Plos One,3, e1787.
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification ofmitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular MarineBiology and Biotechnology,3,294–299.
Foottit RGF, Maw HEL, Von Dohlen CD, Hebert (2008) Species identification of aphids (Insecta:Hemiptera: Aphididae) through DNA barcodes. Molecular Ecology Resources,8,1189–1201.
Frost DR, Kluge AG (1994) A consideration of epistemology in systematic biology, with special referenceto species. Cladistics,10,259–94.
Funk DJ, Omland KE (2003) Species–level paraphyly and polyphyly: frequency, causes, and consequences,with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution andSystematics,34,397–423.
Galtier N, Nabholz B, Glémin S, Hurst GDD (2009) Mitochondrial DNA as a marker of moleculardiversity: a reappraisal. Molecular Ecology,18,4541–4550.
Gaulkes CG, Bennett NC, Cotterill FPD et al (2011) Phylogeography and cryptic diversity of thesolitary-dwelling silvery mole-rat, genus Heliophobius (family: Bathyergidae). Journal of Zoology,285,324–338.
Geller JB (1999) Decline of a native mussel masked by sibling species invasion. Conservation Biology,13,661–664.
Geml J, Laursen AL, O’Neill K, Nusbaum C, Taylor L (2006) Beringian origins and cryptic speciationevents in the fly agaric (Amanita muscaria) Molecular Ecology,15,225–239.
Giribet G, Okusu A, Lindgren AR et al.(2006) Evidence for a clade composed of molluscs with seriallyrepeated structures: monoplacophorans are related to chitons. Proceeding of the National Academy ofSciences of the United States of America,103,7723-7728.
Griffiths AM, Sims DW, Cotterell SP et al.(2010) Molecular markers reveal spatially segregated crypticspecies in a critically endangered fish, the common skate (Dipturus batis). Proceedings of the RoyalSociety of London Series B,277,1497–1503.
Guindon S, Gascuel O (2003) A simple, fast and accurate method to estimate large phylogenies bymaximum-likelihood. Systematic Biology,52,696–704.
Gunter G (1950) The generic status of living oysters and the scientific name of the common Americanspecies. The American Midland Naturalist,43,438-449.
Hageskal G, Bralstad T, Knutsen AK, Skaar I (2008) Exploring the species diversity of Trichoderma inNorwegian drinking water systems by DNA barcoding. Molecular Ecology Resources,8,1178–1188.
Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish speciesof tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States ofAmerica,103,968–971.
Hall T A (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program forWindows95/98/NT. Nucleic Acids Symposium Series,41,95–98.
Hansen H, Bakke TA, Bachmann L (2007) DNA taxonomy and barcoding of monogenean parasites:lessons from Gyrodactylus. Trends in Parasitology,23,363–367.
Harper FM, Hart MW (2007) Morphological and phylogenetic evidence for hybridization and introgressionin a sea star secondary contact zone. Invertebrate Biology,126,373–384.
Harris DJ, Froufe E (2005) Taxonomic inflation: species concept or historical geogpolitical bias? Trends inEcology and Evolution,20,6–7.
Harry HW (1985) Synopsis of the supraspecific classification of living oysters (Bivalvia: Gryphaeidae andOstreidae). Veliger,28,121–158.
Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes.Proceedings of the Royal Society of London Series B,270,323–321.
Hebert PDN, Penton EH, Burns JM et al.(2004b) Ten species in one: DNA barcoding reveals crypticspecies in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the NationalAcademy of Sciences of the United States of America,101,14812–14817.
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004a) Identification of birds through DNA barcodes.PLoS Biology,2, e312.
Hausdorf B (2010) Progress toward a general concept. Evolution,65,923–931.
Hedgecock D, Li G, Banks MA, Kain Z (1999) Occurrence of the Kumamoto oyster Crassostrea sikameain the Ariake Sea, Japan. Marine biology,133,65–68.
Hellberg ME, Vacquier VD (1999) Rapid evolution of fertilization selectivity and
Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. QuarterlyReview of Biology,66,411–453.
Hsieh C, Chen CS, Chiu TS (2005) Composition and abundance of copepods and ichthyoplankton inTaiwan Strait (western North Pacific) are influenced by seasonal monsoons. Marine and FreshwaterResearch,56,153–161.
Hutchinson GE (1957) Concluding remarks. Cold Spring Harbor Symposium on Quantitative Biology,22,415–427.
Hwang JS, Wong CK (2005) The China Coastal Current as a driving force for transporting Calanus sinicus(Copepoda: Calanoida) from its population centers to waters off Taiwan and Hong Kong during thewinter northeast monsoon period. Journal of Plankton Research,27,205–210.
Imbrie J, Berger A, Boyle EA et al.(1993) On the structure and origin of major glaciation cycles2. The100,000-year cycle. Paleoceanography,8,699–735.
Johnson SB, Warén A, Vrijenhoek RC (2008) DNA barcoding of Lepetodrilus limpets reveals crypticspecies. Journal of Shellfish Research,27,43–51.
Jouventin P, Cuthbert J, Ottvall R (2006) Genetic isolation and divergence in sexual traits: evidence for thenorthern rockhopper penguin Eudyptes moseleyi being a sibling species. Molecular Ecology,15,3413–3423.
Jozefowicz CJ, ó Foighil D (1998) Phylogenetic Analysis of Southern Hemisphere Flat Oysters Based onPartial Mitochondrial16S rDNA Gene Sequences. Molecular Phylogenetics and Evolution,10,426-435.
Linares M, Soto-Calderon I, Lees D, Anthony N (2009) High mitochondrial diversity in geographicallywidespread butterflies of Madagasca: A test of the DNA barcoding approach. MolecularPhylogenetics and Evolution,50,485-495.
lysin cDNA sequences in teguline gastropods. Molecular Biology Evolution,16,839–848.
Kangethe EK, JonesSJ, Patterson RLS (1982) Identification of the species origin of fresh meat using anenzyme-linked immunosorbent assay procedure. Meat Science,7,229–240.
Kelly RP, Sarkar IN, Eernisse DJ, Desalle R (2007) DNA barcoding using chitons (genus Mopalia).Molecular Ecology Notes,7,177–183.
Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions throughcomparative studies of nucleotide sequences. Journal of Molecular Evolution,16,111–120.
Klinbunga S, Ampayup P, Tassanakajon A, Jarayabhand P, Yoosukh W (2001) Genetic diversity andmolecular markers of cupped oysters (genera Crassostrea, Saccostrea and Striostrea) in Thailandrevealed by randomly amplified polymorphic DNA analysis. Marine Biotechnology,3,133–144.
Klinbunga S, Khamnamtong N, Tassanakajon A, Puanglarp N, Jarayabhand P (2003) Molecular geneticidentification tools for three commercially cultured oysters (Crassostrea belcheri, Crassostreairedalei, and Saccostrea cucullata) in Thailand. Marine Biotechnology,5,27–36.
Klinbunga S, Khamnamtong B, Puanglarp N et al.(2005) Molecular taxonomy of cupped oysters(Crassostrea, Saccostrea, and Striostrea) in Thailand based on COI,16S, and18S rDNApolymorphism. Marine Biotechnology,7,306-317.
Kmiec B, Woloszynska M, Janska H (2006) Heteroplasmy as a common state of mitochondrial geneticinformation in the plants and animals. Current Genetics,50,149–159.
Knowles LL, Carstens BC (2007) Delimiting species without monophyletic gene trees. Systematic Biology,56,887–895.
Knowlton N (1993) Sibling species in the sea. Annual Review of Ecology and Systemaics,24,189–216.
Knowlton N (2000) Molecular genetic analyses of species boundaries in the sea. Hybrobiologia,420,73–90.
Koch H (2010) Combining morphology and DNA barcoding resolves the taxonomy of Western MalagasyLiotrigona Moure,1961(Hymenoptera: Apidae: Meliponini). African Invertebrates,51,413–421.
Kress WJ, Wrudack KJ, Zimmer EA, Weigh L, Janzen DH (2005) Use of DNA barcodes to identifyflowering plants. Proceedings of the National Academy of Sciences of the United States of America,102,8369–8374.
Laegdsgaard P, Johnson C (2001) Why do juvenile fish utilize mangrove habitats? Journal of ExperimentalMarine Biology and Ecology,257,229–253.
Lahaye R, van der Bank M, Bogarin D et al.(2008) DNA barcoding the floras of biodiversity hotspots.Proceedings of the National Academy of Sciences of the United States of America,105,2023–2928.
Lam K, Morton B (2003) Mitochondrial DNA and morphological identification of a new species ofCrassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China.Aquaculture,228,1–13.
Lam K, Morton B (2006) Morphological and mitochondrial-DNA analysis of the Indo-West Pacific rockoysters (Ostreidae: Saccostrea species). Journal of Molluscan Studies,72,235-245.
Lam K (2009) Oysters (Bivalvia: Ostreidae and Gryphaeidae) recorded from Malaysia and Singapore. TheRaffles Bulletin of Zoology,57,481-494.
Lambeck K, Esat TM, Potter EK (2002) Links between climate and sea levels for the past three millionyears. Nature,419,199–206.
Lapègue S, Batista RM, Heurtebise S Yu ZN, Boudry P (2004) Evidence for the presence of the Portugueseoyster, Crassostrea angulata, in Northern China. Journal of Shellfish Research,23,759-763.
Lee MSY (2003) Species concepts and species reality: salvaging a Linnaean rank. Journal of EvolutionaryBiology,16,179–188.
Lee T, Foighil Dó (2004) Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal fourcryptic species within the scorched mussel, Brachidontes exusturs, species complex. MolecularEcology,13,3527–3542.
Lee T, Foighil Dó (2005) Placing the Floridian marine genetic disjunction into a regional evolutionarycontext using the scorched mussel, Brachidontes exusturs, species complex. Evolution,59,2139–2158.
Leliaer F, Verbruggen H, Wysor B, De Clerck O (2009) DNA taxonomy in morphologically plastic taxa:Algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales). MolecularPhylogenetics and Evolution,53,122–133.
Lessios HA, Pearse JS (1996) Hybridization and introgression between Indo-Pacific species of Diadema.Marine Biology,126,715–723.
Li Q, Yu H, Yu RH (2006) Genetic variability assessed by microsatellites in cultured populations of thePacific oyster (Crassostrea gigas) in China. Aquaculture,259,95–102.
Lipscomb D, Platnick N, Wheeler Q (2003) The intellectual content of taxonomy: a comment on DNAtaxonomy. Trends in Ecology and Evolution,18,65–66.
Littlewood DTJ (1994) Molecular Phylogenetics of Cupped Oysters Based on Partial28S rRNA GeneSequences. Molecular Phylogenetics and Evolution,3,221-229.
Liu JX, Gao TX, Wu SF, Zhang YP (2007) Pleistocene isolation in the Northowestern Pacific marginal seasand limited dispersal in a marine fish, Chelon haematocheilus (Temminck&Schlegel,1845).Molecular Ecology,16,275–288.
Locke SA, Mclaughlin JD, Marcogliese DJ (2010) DNA barcodes show cryptic diversity and a potentialphysiological basis for host specificity among Diplostomoidea (Platyhelminthes: Digenea)parasitizing freshwater fishes in the St. Lawrence River, Canada. Molecular Ecology,19,2813–2827.
López-Flores I, de la Herrán R, Garrido-Ramos MA et al.(2004) The molecular phylogeny of oystersbased on a satellite DNA related to transposons. Gene,339,181-188.
López-Flores I, Ruiz-Rejón, Cross I et al.(2010) Molecular characterizaition and evolution of aninterspersed repetitive DNA family of oysters. Genetica,138,1211-1219.
Lowenstein JH, Amato G, Kolokotronis SO (2009) The real maccoyii: identifying tuna sushi with DNAbarcodes–contrasting characteristic attributes and genetic distances. PLoS One,4, e7866.
Mallet J (2001) Species, concepts of. In Encyclopedia of Biodiversity (Levin S et al. eds), pp.427–440.Academic Press.
Mallet J (2006) Species concepts. In: Evolutionary genetics: concepts and case studies (Fox CW, Wolf JBeds), pp.367–373. Oxford: Oxford University Press.
Mallet J,Willmott K (2003) Taxonomy: Renaissance or Tower of Babel? Trends in Ecology and Evolution,18,57–59.
Makino W, Tanabe AS (2009) Extreme population genetic differentiation and secondary contact in thefreshwater copepod Acanthodiaptomus pacificus in the Japanese Archipelago. Marine Biology,18,2699–2713.
Manthey JD, Klicka J, Spellman GM (2011) Cryptic diversity in a widespread North American songbird:phylogeography of the Brown Creeper (Certhia americana). Molecular Phylogenetic Evolution,58,502–512.
Marko PB (2002) Fossil calibration of molecular clocks and the divergence times of geminate species pairsseparated by the Isthmus of Panama. Molecular Biology Evolution,19,2005–2021.
Martin DP, Lemey P, Lott M et al.(2010). RDP3: a flexible and fast computer program for analyzingrecombination. Bioinformatics,26,2462–2463.
Matsumoto M (2003) Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COIsequences. Molecular Phylogenetics and Evolution,27,429-440.
Mathews LM (2006) Cryptic biodiversity and phylogeographical patterns in a snapping shrimp speciescomplex. Molecular Ecology,15,4049–4063.
Mayden RL (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. InSpecies: the Units of Biodiversity (Claridge MF et al., eds), pp.381–424. Chapman&Hall.
Mayr E (1942) Systematics and the origin of species from the viewpoint of a zoologist. New York:Columbia University Press.
Mayr E (1963) Animal Species and Evolution. Harvard University Press, Cambridge, Massachusetts.
Meier R, Shiyang K, Baidya G, Ng PKL (2006) DNA Barcoding and taxonomy in Diptera: a tale of highintraspecific variability and low identification success. Systematic Biology,55,715–728.
Meier R, Zhang GY, Ali F (2008) The use of mean instead of smallest interspecific distances exaggeratesthe size of the “barcoding gap” and leads to misidentification. Systematic Biology,57,809-813.
Melo CMR, Silva FC, Gomes CHAM, Solé-Caca AM, Lazoski C (2010) Crassostrea gigas in naturaloyster banks in southern Brazil. Biological Invasions,12,441-449.
Mengual X, Thompson FC (2008) A taxonomic review of the Palpada ruficeps species group, with thedescription of a new flower fly from Colombia (Diptera, Syrphidae). Zootaxa1741:31–36.
Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. Plos Biology,3,e422.
Milbury CA, Gaffney PM (2005) Complete mitochondrial DNA sequence of the eastern oyster Crassostreavirginica. Marine Biotechnology,7,697-712.
Monaghan MT, Balke M, Pons J, Bogler AP (2006) Beyond barcodes: complex DNA taxonomy of a SouthPacific Island radiation. Proceedings of the Royal Society of London Series B,273,887–893.
Milankov V, Stahls G, Stamenkovic J, Vujic A (2008) Genetic diversity of Merodon aureus and M. cinereusspecies complexes (Diptera, Syrphidae): integrative taxonomy and implications for conservationpriorities on the Balkan Peninsula. Conservation. Genetics,9,1125–1137.
Morton B (2004) The oysters of Hong Kong (Bivalvia: Ostreidae and Gryphaeidae). The Raffles Bulletinof Zoology,52,11-28.
Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carloapproach. Genetics,158,885–896.
Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York.
O’Meara BC (2010) New heuristic methods for joint species delimitation and species tree inference.Systematic biology,59,59-73.
Padial JM, De La Riva I (2009) Integrative taxonomy reveals cryptic Amazonian species of Pristimantis(Anura: Strabomantidae). Zoological Journal of the Linnean Society,155,97–122.
Passamonti M (2007) An unusual case of gender-associated mitochondrial DNA heteroplasmy the mytilidMusculista senhousia (Mollusca Bivalvia). BMC Evolutionary Biology,7(suppl2), S7.
Palumbi SR (1994) Genetic divergence, reproductive isolation, and marine speciation. Annual Review ofEcology and Systematics,25,547–572.
Palumbi SR (1996) Nucleic acids II: the polymerase chain reaction. In: Molecular Systematics (Hillis DM,Moritz C, Mable BK eds), pp.205–247. Sinauer&Associates Inc., Sunderland, MA.
Pavlic D, Slippers B, Coutinho TA, Wingfield MJ (2009) Multiple gene genealogies and phenotypic datareveal cryptic species of the Botryosphaeriaceae: a case study on the Neofusicoccum parvum/N. ribiscomplex. Molecular Phylogenetics and Evolution,51,259–268.
Pennisi E (2003) Modernizing the tree of life. Science,300,1692–1697.
Petit RJ, Excoffier L (2009) Gene flow and species delimitation. Trends in Ecology and Evolution,24,386–393.
Pires AC, Marinon L (2010) DNA barcoding and traditional taxonomy unified through IntegrativeTaxonomy: a view that challenges the debate questioning both methodologies. Biota Neotropica,10,339–346.
Plazzi F, Passamonti M (2010) Towards a molecular phylogeny of Mollusks: Bivalves’ early evolution asrevealed by mitochondrial genes. Molecular Phylogenetics and Evolution,57,641-657.
Polson MP, Hewson WE, Eernisse DJ, Baker PK, Zacherl D (2009) You say Conchaphila, I say lurida:molecular evidence for restricting the Olympia oyster to temperate western north America. Journal ofShellfish Research,28,11-21.
Posada D (2008) jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution,25,1253–1256.
PuillandreN, Lambert A, Brouillet S,AchazG (2011) ABGD, Automatic Barcode Gap Discovery forprimary species delimitation. Molecular Ecology, doi:10.1111/j.1365–294X.2011.05239.x.
Rach J, DeSalle R, Sarkar IN, Schierwater B, Hadrys H (2008) Character-based DNA barcoding allowsdiscrimination of genera, species and populations in Odonata. Proceedings of the Royal Society ofLondon Series B,275,237–247.
Ratnasingham S, Hebert PDN (2007) BOLD: the Barcode of life data system (www.barcodinglife.org).Mollecular Ecology Notes,7,355–364.
Reece KS, Cordes JF, Stubbs JB, Hudson KL, Francis EA (2008) Moleculare phylogenies help resolvetaxonomic confusion with Asian Crassostrea oyster species. Marine Biology,153,709-721.
Reeves PA, Richards CM (2011) Species delimitation under the general lineage concept: an empiricalexample using wild American hops (Cannabaceae: Humulus lupulus). Systematic Biology,60:45–59.
Ren JF, Liu X, Zhang GF, Liu B, Guo XM (2009)“Tandem duplication-random loss” is not a real featureof oyster mitochondrial genomes. BMC genomics,10,84.
Renard E, Bachmann V, Cariou ML, Moreteau JC (2000) Morphological and molecular differentiation ofinvasive freshwater species of the genus Corbicula (Bivalvia, Corbiculidea) suggest the presence ofthree taxa in French rivers. Molecular Ecology,9,2009–2016.
Renoult JP, Geniez P, Bacquet P, Benoit L, Crochet PA (2009) Morphology and nuclear markers revealextensive mitochondrial introgressions in the Iberian Wall Lizard species complex. Molecular Ecology,18,4298–4315.
Roe AD, Sperling FAH (2007) Population structure and species boundary delimitation of crypticDioryctria moths: an integrative approach. Molecular Ecology,16,3617–3633.
Ronquist F, Huelsenbeck JP (2003) MRBAYES3: Bayesian phylogenetic inference under mixed models.Bioinformatics,19,1572–1574.
Roques S, Sévigy JM, Bernatchez L (2001) Evidence for broadscale introgressive hybridization betweentwo redfish (geneus Sebastes) in the North-west Atlantic: a rare marine example. Molecular Ecology,10,149–165.
Rosen DE (1978) Vicariant patterns and historical explanation in biogeography. Systematic Zoology,27,159–88.
Rosewater J (1961) The family Pinnidae in the Indo-Pacific. Indo-Pacific Mollusca,1,175–226.
Ross KG, Gotzek D, Ascunce MS, Shoemaker DD (2010) Species delimitation: a case study in aproblematic ant taxon. Systematic Biology,59,162–184.
Rubinoff D (2005) Utility of mitochondrial DNA barcodes in species conservation. Conservation Biology,20,1026–1033.
Ruesink JL, Lenihan HS, Trimble AC et al.(2005) Introduction of non-native oysters: ecosystem effectsand restoration implications. Annual Review of Ecology, Evolution, and Systematics,36,643-689.
Schindel DE, Miller SE (2005) DNA barcoding a useful tool for taxonomists. Nature,435,17.
Schlick-Steiner BC, Steiner FM, Seifert MK et al.(2006) A multidisciplinary approach reveals crypticdiversity in Western Paleartic Tetramorium ants (Hymenoptera: Formcidae). Molecular PhylogeneticEvolution,40,259–273.
Schlick-Steiner BC, Steiner FM, Seifert B et al.(2010) A multisource approach to exploring biodiversity.Annual Review of Entomology,55,421–38.
Scott E (1980) A clarification of the genus Perna (Mytilidae). Bulletin of marine science,30,858–870.
Seberg O, Petersen G, Humphries CJ et al.(2003) Shortcuts in systematics? a commentary on DNA-basedtaxonomy. Trends in Ecology and Evolution,18,63–65.
Seifert KA, Samson RA, deWaard JR et al.(2007) Prospects for fungus identification using co1DNAbarcodes, with Penicillium as a test case. Proceeding of the National Academy of Sciences of theUnited States of America,104,3901-3906.
Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses.Systematic Biology,49,369–381.
Sites JW, Marshall C (2004) Operational criteria for delimiting species. Annual Review of Ecology andSystemaics,35,199–227.
Smith VS (2005) DNA barcoding: perspectives from a “Partnerships for Enhancing Expertise inTaxonomy”(PEET) debate. Systematic Biology,54,841–844.
Smith M, Nikolai A, Poyarkov JR, Hebert PDN (2008) CO1DNA barcoding amphibians: take the chance,meet the challenge. Molecular Ecology Resources,8,235–246.
Stoeckle M (2003) Taxonomy, DNA, and the Bar Code of Life. BioScience,53:796–797.
Stoeckle M, Waggoner P, Ausubel J (2004) Bar-coding life: Ten reasons. Consortium for the Barcode ofLife. www.barcoding.si.edu/.
Stuart BL, Inger RF, Voris HK (2006) High level of cryptic species diversity revealed by sympatriclineages of Southeast Asian forest frogs. Biology Letters,2,470–474.
Swofford DL (2003) PAUP*: phylogenetic analysis using parsimony (*and other methods), Version4.Sinauer Associates, Sunderland, Massachusetts.
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region ofmitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution,10,512–526.
Tamura K, Dudley J, Nei M, Kumar S (2007). MEGA4: Molecular Evolutionary Genetics Analysis(MEGA) software version4.0. Molecular Biology and Evolution,24,1596–1599.
Tang RWK, Yau C, Ng WC (2010) Identification of stomatopod larvae (Crusacea: Stomatopoda) fromHong Kong waters using DNA barcodes. Molecular Ecology Resources,10,439-448.
Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2002) DNA points the way ahead in taxonomy.Nature,418,379.
Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2003) A plea for ＤNA taxonomy. Trends inEcology and Evolution,18,70–74.
Taylor HR, Harris WE (2012) An emergent science on the brink of irrelevance: a review of the past8yearsof DNA barcoding. Molecular Ecology Resources, doi:10.1111/j.1755–0998.2012.03119.x.
Thompson JD, Higgins DG, Gibson TJ (1994) ClustalW: Improving the sensitivity of progressive multiplesequence alignment through sequence weighting, position-specific gap penalties and weight matrixchoices. Nucleic Acids Research,22,4673–4680.
Thompson JD, Gibson TJ, Plewniak F, Jaanmougin F, Higgins DG (1997) The Clustal_X Windowsinterface: flexible strategies for multiple sequence alignment aided by quality analysis tools. NucleicAcids Research,24,4876–4882.
Tsang LM, Chan BKK, Ma Y, Chu KH (2008) Genetic differentiation, bybridiation and adaptivedivergence in two subspecies of the acorn barnacle Tetraclita japonica in the northwestern Pacific.Molecular Ecology,17,4151–4163.
UNEP (2007) Mangrove Demonstration Sites in the South China Sea. UNEP/GEF/SCS TechnicalPublication No.7.(Available at http://www.unepscs.org/)
Vaglia I, Haxaire J, Kitching IJ, Meusnier I, Rougerie R (2008) Morphology and DNA barcoding revealthree cryptic species within the Xylophanes neoptolemus and loelia species-groups (Lepidoptera:Sphingidae). Zootaxa,1923,18–36.
Valentini A, Pompanon F, Taberlet (2005) DNA barcoding for ecologists. Trends in Ecology and Evolution,24,110–117.
Vuataz L, Sartori M, Wagner A, Monaghan MT (2011) Toward a DNA Taxonomy of Alpine Rhithrogena(Ephemeroptera: Heptageniidae) Using a Mixed Yule-Coalescent Analysis of Mitochondrial andNuclear DNA. Plos ONE,6, e19728.
Wang PX (1999) Response of Western Pacific marginal seas to glacial cycles: paleoceanographic andsedimentological features. Marine Geology,156,5–39.
Wang HY, Guo XM, Zhang GF, Zhang FS (2004) Classification of jingjiang oysters Crassostrea rivularis(Gould,1861) from China, based on morphology and phylogenetic analysis. Aquaculture,242,137-155.
Wang HY, Zhang GF, Liu X, Guo XM (2008a) Classification of common oysters from north China. Journalof Shellfish Research,27,495-503.
Wang HY, Guo XM (2008b) Identification of Crassostrea ariakensis and related oysters by multiplexspecies-specific PCR. Journal of Shellfish Research,27,481-487.
Ward BD, Holmes BH (2007) An analysis of nucleotide and amino acid variability in the barcode region ofcytochrome c oxidase I (cox1) in fishes. Molecular Ecology Notes,7,899-907.
Ward R D, Zemlak T S, Innes B H, Last P R, Hebert P D N (2005) DNA barcoding Australia’s fish species.Philosophical Transactions of the Royal Society B,360,1847–185.
Wheeler QD (2005) Losing the plot: DNA “barcodes” and taxonomy. Cladistics,21,405–407.
White DJ, Wolff JN, Pierson M, Gemmell NJ (2008) Revealing the hidden complexities of mtDNAinheritance. Molecular Ecology,17,4925–4942.
Wiemers M, Fiedler K (2007) Does the DNA barcoding gap exist?–a case study in blue butterflies(Lepidoptera: Lycaenidae). Frontiers in Zoology,4,8.
Wiens JJ (2007) Species delimitation: new approaches for discovering diversity. Systematic biology,56,875–878.
Wiley EO (1981) Phylogenetics: The Theory and Practice of Phylogenetic Systematics. John Wiley&Sons,New York.
Wilkins JS (2009) Species: a history of idea. University of California Press, Berkeley and Los Angeles,California.
Wilkins JS (2011) Philosophically speaking, how many species concepts are there? Zootaxa,2765,58–60.
Will KW, Mishler BD, Wheeler QD (2005) The perils of DNA barcoding and the need for integrativetaxonomy. Systematic biology,54,844–851.
Will KW, Rubinoff D (2004) Myth of the molecule: DNA barcodes for species cannot replace morphologyfor identification and classification. Cladistics,20,47–55.
Winckworth R (1929) Marine mollusca from south India and Ceylon. III: Pinna. With an index to therecent species of Pinna. Proceedings of the Malacological Society of London.18,276–297.
Winker K (2005) Sibling species were first recognized by William Derham (1718). The Auk,122,706–707.
Wolfe-Coote S (2005) The Handbook of Experimental Animals: The Laboratory Primate. ElsevierAcademic Press.
Wu XY, Xu XD,Yu ZN, Wei ZP,Xia JJ (2010) Comparison of seven Crassostrea mitogenomes andphylogenetic analyses. Molecular Phylogenetics and Evolution,57,448-454.
Yeates DK, Seago A, Nelson L et al.(2011) Integrative taxonomy, or iterative taxonomy? SystematicEntomology,36,209–217.
Yokogawa K (1996) Genetic divergence in two forms of pen shell Atrina pectinata. Venus,55,25–39.
Yu Z, Kong X, Zhang L, Guo X, Xiang J (2003) Taxonomic status of four Crassostrea oysters from Chinaas inferred from mitochondrial DNA sequences. Journal of Shellfish Research,22,31–38.
Yu H, Li Q (2011) Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalvemitochondrial genomes. Plos ONE,6, e16147.
Yu XY, Mao Y, Wang MF, Zhou L, Gui JF (2004) Genetic heterogeneity analysis and RAPD markersdetection among four forms of Atrina pectinata Linnaeus. Journal of Shellfish Research,23,165–171.
Yu ZN, Wei ZP, Kong XY, Shi W (2008) Complete mitochondrial DNA sequence of oyster Crassostreahongkongensis-a case of “Tandem duplication-random loss for” genome rearrangement in Crassostrea?BMC Genomics,9,477.
Xu JW, Chan TY, Tsang LM, Chu KH (2009) Phylogeography of the mitten crab Eriocheir sensu stricto inEast Asia: Pleistocence isolation, population expansion and secondary contact. MolecularPhylogenetics and Evolution,52,45–56.
Zak ek V, Sket B, Gottstein S, Franjevi D, Trontelj P (2009) The limits of cryptic diversity in groundwater:phylogeography of the cave shrimp Troglocaris anophthalmus (Crustacea: Decapoda: Atyidae).Molecular Ecology,18,931–46.
Zapata F, Jiménez I (2012) Species delimitaiton: inferring gaps in morphology across geography. SystmaticBiology,61,179-194.
Zhang DX, Hewitt GM (1996) Nuclear integrations: challenges for mitochondrial DNA markers. Trends inEcology and Evolution,11,247–251.
Zhao K, Duan ZY, Peng ZG et al.(2009) The youngest split in sympatric schizothoracine fish (Cyprinidae)is shaped by ecological adaptations in a Tibetan Plateau glacier lake. Molecular Ecology,18,3616–3628.