16S rRNA is a better choice than COI for DNA barcoding hydrozoans in the coastal waters of China
doi: 10.1007/s13131-014-0415-8
16S rRNA is a better choice than COI for DNA barcoding hydrozoans in the coastal waters of China
-
摘要: Identification of hydrozoan species is challenging, even for taxonomic experts, due to the scarcity of distinct morphological characters and phenotypic plasticity. DNA barcoding provides an efficient method for species identification, however, the choice between mitochondrial cytochrome c oxidase subunit Ⅰ (COI) and large subunit ribosomal RNA gene (16S) as a standard barcode for hydrozoans is subject to debate. Herein, we directly compared the barcode potential of COI and 16S in hydrozoans using 339 sequences from 47 pelagic hydrozoan species. Analysis of Kimura 2-parameter genetic distances (K2P) documented the mean intraspecific/interspecific variation for COI and 16S to be 0.004/0.204 and 0.003/0.223, respectively. An obvious "barcoding gap" was detected for all species in both markers and all individuals of a species clustered together in both the COI and 16S trees. These results suggested that the species within the studied taxa can be efficiently and accurately identified by COI and 16S. Furthermore, our results confirmed that 16S was a better phylogenetic marker for hydrozoans at the genus level, and in some cases at the family level. Considering the resolution and effectiveness for barcoding and phylogenetic analyses of Hydrozoa, we strongly recommend 16S as the standard barcode for hydrozoans.
-
关键词:
- DNAbarcoding /
- hydrozoan /
- COI /
- 16SrRNA
Abstract: Identification of hydrozoan species is challenging, even for taxonomic experts, due to the scarcity of distinct morphological characters and phenotypic plasticity. DNA barcoding provides an efficient method for species identification, however, the choice between mitochondrial cytochrome c oxidase subunit Ⅰ (COI) and large subunit ribosomal RNA gene (16S) as a standard barcode for hydrozoans is subject to debate. Herein, we directly compared the barcode potential of COI and 16S in hydrozoans using 339 sequences from 47 pelagic hydrozoan species. Analysis of Kimura 2-parameter genetic distances (K2P) documented the mean intraspecific/interspecific variation for COI and 16S to be 0.004/0.204 and 0.003/0.223, respectively. An obvious "barcoding gap" was detected for all species in both markers and all individuals of a species clustered together in both the COI and 16S trees. These results suggested that the species within the studied taxa can be efficiently and accurately identified by COI and 16S. Furthermore, our results confirmed that 16S was a better phylogenetic marker for hydrozoans at the genus level, and in some cases at the family level. Considering the resolution and effectiveness for barcoding and phylogenetic analyses of Hydrozoa, we strongly recommend 16S as the standard barcode for hydrozoans.-
Key words:
- DNA barcoding /
- hydrozoan /
- COI /
- 16S rRNA
-
Bouillon J, Boero F. 2000. The Hydrozoa: A new classification in thelight of old knowledge. Thalassia Salentina, 24: 1-45 Bridge D, Cunningham C W, DeSalle R, et al. 1995. Class-level relationshipsin the Phylum Cnidaria: molecular and morphological evidence.Molecular Biology and Evolution, 12: 679-689 Bucklin A, Ortman B D, Jennings R M, et al. 2010. A "Rosetta Stone" forzooplankton: DNA barcode analysis of holozooplankton diversityof the Sargasso Sea (NW Atlantic Ocean). Deep-Sea Research Ⅱ, 57: 2234-2247 Bucklin A, Steinke D, Blanco-Bercial L. 2011. DNA barcoding of marinemetazoa. Annual Review of Marine Science, 3: 471-508 Cantero A L P, Sentandreu V, Latorre A. 2010. Phylogenetic relationshipsof the endemic Antarctic benthic hydroids (Cnidaria, Hydrozoa):what does the mitochondrial 16S rRNA tell us about it? Polar Biology,33: 41-57 Cartwright P, Evans N M, Dunn C W, et al. 2008. Phylogenetics of Hydroidolina(Hydrozoa: Cnidaria). Journal of the Marine BiologicalAssociation of the United Kingdom, 88: 1663-1672 Collins A G. 2000. Towards understanding the phylogenetic history of Hydrozoa: hypothesis testing with 18S gene sequence data. ScientiaMarina, 64: 5-22 Collins A G. 2002. Phylogeny of Medusozoa and the evolution of cnidarianlife cycles. Journal of Evolutionary Biology, 15: 418-432 Collins A G, Bentlage B, Lindner A, et al. 2008. Phylogenetics of Trachylina(Cnidaria: Hydrozoa) with new insights on the evolution ofsome problematic taxa. Journal of the Marine Biological Associationof the United Kingdom, 88: 1673-1685 Collins A G, Schuchert P, Marques A C, et al. 2006. Medusozoan phylogenyand character evolution clarified by new large and smallsubunit rDNA data and an assessment of the utility of phylogeneticmixture models. Systematic Biology, 55: 97-115 Collins A G, Winkelmann S, Hadrys H, et al. 2005. Phylogeny of Capitataand Corynidae (Cnidaria, Hydrozoa) in light of mitochondrial16S rDNA data. Zoologica Scripta, 34: 91-99 del-Prado R, Cubas P, Lumbsch H T, et al. 2010. Genetic distances withinand among species in monophyletic lineages of Parmeliceae(Ascomycota) as a tool for taxon delimitation. Molecular Phylogeneticsand Evolution, 56: 125-133 Dawson M N. 2003. Macro-morphological variation mong cryptic specieof the moon jellyfish, Aurelia (Cnidaria: Scyphozoa). MarineBiology, 143: 369-379 Dawson M N. 2005. Cyanea capillata is not a cosmopolitan jellyfish:morphological and molecular evidence for C. annaskala and C.rosea (Scyphozoa: Semaeostomeae: Cyaneidae) in south-easternAustralia. Invertebrate Systematics, 19: 361-370 Dawson M N, Jacobs D K. 2001. Molecular evidence for cryptic speciesof Aurelia aurita (Cnidaria, Scyphozoa). Biological Bulletin, 200:92-96 Dawson M N, Martin L E. 2001. Geographic variation and ecologicaladaptation in Aurelia (Scyphozoa, Semaeostomeae): some implicationsfrom molecular phylogenetics. Hydrobiologia, 451:259-273 Dunn C W, Pugh P R, Haddock S H D. 2005. Molecular phylogenetics ofthe siphonophora (Cnidaria), with implications for the evolutionof functional specialization. Systematic Biology, 54: 916-935 Ender A, Schierwater B. 2003. Placozoa are not derived cnidarians: evidencefrom molecular morphology. Molecuar Biology Evolution,20: 130-134 Faith D P, Williams K J. 2005. How large-scale DNA barcoding programscan boost biodiversity conservation planning: linking phylogeneticdiversity (PD) analyses to the barcode of life database(BoLD). Abstract. In: Australian entomological society's 36thAGM and scientific conference/7th invertebrate biodiversityand conservation conference/Australian systematics society,Canberra, Australia, 4-9 December 2005 Folino-Rorem N C, Darling J A, D'Ausilio C A. 2008. Genetic analysisreveals multiple cryptic invasive species of the hydrozoan genusCordylophora. Biological Invasions, 11: 1869-1882 Folmer O, Black M, Hoeh W, et al. 1994. DNA primers for amplificationof mitochondrial cytochrome c oxidase subunit I from diversemetazoan invertebrates. Molecular Marine Biology and Biotechnology,3: 294-299 Govindarajan A F, Boero F, Halanych K M. 2006. Phylogenetic analysiswith multiple markers indicates repeated loss of the adult medusastage in Campanulariidae (Hydrozoa, Cnidaria). MolecularPhylogenetics and Evolution, 38: 820-834 Govindarajan A F, Halanych K M, Cunningham C W. 2005a. Mitochondrialevolution and phylogeography in the hydrozoan Obelia geniculata(Cnidaria). Marine Biology, 146: 213-222 Govindarajan A F, Piraino S, Gravili C, et al. 2005b. Species identificationof bivalve-inhabiting marine hydrozoans of the genus Eugymnanthea.Invertebrate Biology, 124: 1-10 Hajibabaei M, Janzen D H, Burns J M, et al. 2006. DNA barcodes distinguishspecies of tropical Lepidoptera. Proceedings of the NationalAcademy of Sciences of the United States of America, 103:968-971 Hajibabaei M, Singer G A C, Hebert P D N, et al. 2007. DNA barcoding:how it complements taxonomy, molecular phylogenetics andpopulation genetics. Trends in Genetics, 23: 167-172 Hebert P D N, Gregory T R. 2005. The promise of DNA barcoding fortaxonomy. Systematic Biology, 54: 852-859 Hebert P D N, Penton E H, Burns J M, et al. 2004a. Ten species in one:DNA barcoding reveals cryptic species in the neotropical skipperbutterfly Astraptes fulgerator. Proceedings of the National Academyof Science of the United States of America, 101: 14812-14817 Hebert P D N, Ratnasingham S, deWaard J R. 2003. Barcoding animallife: cytochrome c oxidase subunit I divergences among closelyrelated species. Proceedings of the Royal Society B-BiologicalSciences, 270: S96-S99 Hebert P D N, Stoeckle M Y, Zemlak T S, et al. 2004b. Identification ofbirds through DNA barcodes. PloS Biology, 2: 1657-1663 Hellberg M E. 2006. No variation and low synonymous substitutionrates in coral mtDNA despite high nuclear variation. BMC EvolutionaryBiology, 6: 1-8 Holland B S, Dawson M N, Crow G L, et al. 2004. Global phylogeographyof Cassiopea (Scyphozoa: Rhizostomeae): molecular evidencefor cryptic species and multiple invasions of the HawaiianIslands. Marine Biology, 145: 1119-1128 Huang D, Meier R, Todd P A, et al. 2008. Slow mitochondrial COI sequenceevolution at the base of the metazoan tree and its implicationsfor DNA barcoding. Journal of Molecular Evolution, 66:167-174 Kimura M. 1980. A simple method for estimating evolutionary rates ofbase substitutions through comparative studies of nucleotidesequences. Journal of Molecular Evolution, 16: 111-120 Köhler F. 2007. From DNA taxonomy to barcoding: how a vague ideaevolved into a biosystematic tool. Mitteilungen aus dem Museumfür Naturkunde Berlin Zoologische Reihe, 83: 44-51 Krishnamurthy P K, Francis R A. 2012. A critical review on the utilityof DNA barcoding in biodiversity conservation. Biodiversity andConservation, 21: 1901-1919 Kubota S. 1983. Studies on life history and systematics of the Japanesecommensal hydroids living in bivalves, with some reference totheir evolution. Journal of the Faculty of Science Hokkaido UniversitySeries VI Zoology, 23: 296-402 Kubota S. 2000. Parallel, paedomorphic evolutionary processes of thebivalve-inhabiting hydrozoans (Leptomedusae, Eirenidae) deducedfrom morphology, life cycle and biogeography, with specialreference to taxonomic treatment of Eugymnanthea. ScientiaMarina, 64: 241-247 Larkin M A, Blackshields G, Brown N P, et al. 2007. Clustal W and clustalX version 2.0. Bioinformatics, 23: 2947-2948 Leclère L, Schuchert P, Cruaud C, et al. 2009. Molecular phylogeneticsof Thecata (Hydrozoa, Cnidaria) reveals long-term maintenanceof life history traits despite high frequency of recent characterchanges. Systematic Biology, 58: 509-526 Leclère L, Schuchert P, Manuel M. 2007. Phylogeny of the Plumularioidea(Hydrozoa, Leptothecata): evolution of colonial organizationand life cycle. Zoologica Scripta, 36: 371-394 Le Goff-Vitry M C, Rogers A D, Baglo牷椠湄攮?椲漰氰漴朮椠捁愠汤??獰猠潳捥楡愠瑳楬潡湮?漠景?琠桴敨?啭湯楬瑥散摵??楲渠杰摨潹浬???????て???????leractinia. Molecular Phylogeneticsand Evolution, 30: 167-177 Martinez D E, Iniguez A R, Percell K M, et al. 2010. Phylogeny and biogeographyof Hydra (Cnidaria: Hydridae) using mitochondrialand nuclear DNA sequences. Molecular Phylogenetics and Evolution,57: 403-410 McFadden C S, Benayahu Y, Pante E, et al. 2011. Limitations of mitochondrialgene barcoding in Octocorallia. Molecular EcologyResources, 11: 19-31 McFadden C S, Tullis I, Hutchinson M B, et al. 2000. Rates of evolutionof cnidarian mitochondrial genes. American Zoologist, 40:1124-1124 Meyer C P, Paulay G. 2005. DNA barcoding: error rates based on comprehensivesampling. PLoS Biolog, 3: 2229-2238 Miglietta M P, Piraino S, Kubota S, et al. 2007. Species in the genus Turritopsis(Cnidaria, Hydrozoa): a molecular evaluation. Journal ofZoological Systematics and Evolutionary Research, 45: 11-19 Miglietta M P, Schuchert P, Cunningham C W. 2009. Reconciling genealogicaland morphological species in a worldwide study of theFamily Hydractiniidae (Cnidaria, Hydrozoa). Zoologica Scripta,38: 403-430 Mills C E. 1995. Medusae, siphonophores, and ctenophores as planktivorouspredators in changing global ecosystems. ICES Journalof Marine Science, 52: 575-581 Miranda L S, Collins A G, Marques A C. 2010. Molecules clarify a Cnidarianlife cycle—the “Hydrozoan” Microhydrula limopsicola isan early life stage of the Staurozoan Haliclystus antarcticus. PLoSOne, 5: e10182 Moritz C, Cicero C. 2004. DNA barcoding: promise and pitfalls. Plos Biology,2: 1529-1531 Moura C J, Cunha M R, Porteiro F M, et al. 2011a. Polyphyly and crypticdiversity in the hydrozoan families Lafoeidae and Hebellidae(Cnidaria:Hydrozoa). Invertebrate Systematics, 25: 454-470 Moura C J, Cunha M R, Porteiro F M, et al. 2011b. The use of the DNAbarcode gene 16S mRNA for the clarification of taxonomicproblems within the family Sertulariidae (Cnidaria, Hydrozoa).Zoologica Scripta, 40: 520-537 Moura C J, Cunha M R, Porteiro F M, et al. 2012. A molecular phylogeneticappraisal of the systematics of the Aglaopheniidae (Cnidaria:Hydrozoa, Leptothecata) from the north-east Atlantic andwest Mediterranean. Zoological Journal of the Linnean Society,164: 717-727 Moura C J, Harris D J, Cunha M R, et al. 2008. DNA barcoding revealscryptic diversity in marine hydroids (Cnidaria, Hydrozoa) fromcoastal and deep-sea environments. Zoologica Scripta, 37: 93-108 Nawrocki A M, Schuchert P, Cartwright P. 2010. Phylogenetics and evolutionof Capitata (Cnidaria: Hydrozoa), and the status of thefamily Corynidae. Zoological Scripta, 39: 290-304 Ortman B D, Bucklin A, Pagès F, et al. 2010. DNA barcoding the Medusozoausing mtCOI. Deep-Sea Research II: Topical Studies inOceanography, 57: 2148-2156 Pontin D R, Cruickshank R H. 2012. Molecular phylogenetics of the genusPhysalia (Cnidaria: Siphonophora) in New Zealand coastalwaters reveals cryptic diversity. Hydrobiologia, 686: 91-105 Ratnasingham S, Hebert P D N. 2007. BOLD: the barcode of life datasystem (http://www.barcodinglife.org). Molecular EcologyNotes, 7: 355-364 Schuchert P. 2005a. Species boundaries in the hydrozoan genus Coryne.Molecular Phylogenetics and Evolution, 36: 194-199 Schuchert P. 2005b. Rediscovery of Coryne fucicola (de Filippi, 1866)(Cnidaria: Hydrozoa). Cahiers de Biologie Marine, 46: 305-310 Schuchert P. 2006. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Capitata Part 1. Revue Suisse de Zoologie,113: 325-410 Schuchert P. 2007. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Filifera Part 2. Revue Suisse de Zoologie,114: 195-396 Schuchert P. 2008a. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Filifera Part 3. Revue Suisse de Zoologie,115: 221-302 Schuchert P. 2008b. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Filifera Part 4. Revue Suisse de Zoologie,115: 677-757 Schuchert P. 2009. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Filifera Part 5. Revue Suisse de Zoologie,116: 441-507 Schuchert P, Reiswig H M. 2006. Brinckmannia hexactinellidophila,n.genera, n. sp. a hydroid living in tissues of glass sponges of thereefs, fjords, and seamounts of Pacific Canada and Alaska. CanadianJournal of Zoology, 84: 564-572 Shearer T L, van Oppen M J H, Romano S L, et al. 2002. Slow mitochondrialDNA sequence evolution in the Anthozoa (Cnidaria). MolecularEcology, 11: 2475-2487 Sinniger F, Reimer J D, Pawlowski J. 2008. Potential of DNA sequencesto identify zoanthids (Cnidaria: Zoantharia). Zoological Science,25: 1253-1260 Stampar S N, Maronna M M, Vermeij M J A, et al. 2012. Evolutionarydiversification of banded tube-dwelling anemones (Cnidaria;Ceriantharia; Isarachnanthus) in the Atlantic Ocean. PLoS One,7: e41091 Sun Yan, Li Qi, Kong Lingfeng, et al. 2012. DNA barcoding of Caenogastropodaalong coast of China based on the COI gene. MolecularEcology Resources, 12: 209-218 Tamura K, Peterson D, Peterson N, et al. 2011. MEGA5: Molecular evolutionarygenetics analysis using maximum likelihood, evolutionarydistance, and maximum parsimony methods. MolecularBiology and Evolution, 28: 2731-2739 Ward R D, Zemlak T S, Innes B H, et al. 2005. DNA barcoding Australia'sfish species. Philosophical Transactions of the Royal Society B—Biological Sciences, 360: 1847-1857 Xia Yun, Gu Haifeng, Peng Rui, et al. 2012. COI is better than 16S rRNAfor DNA barcoding Asiatic salamanders (Amphibia: Caudata:Hynobiidae). Molecular Ecology Resources, 12: 48-56 Zemlak T S, Ward R D, Connell A D, et al. 2009. DNA barcoding revealsoverlooked marine fishes. Molecular Ecology Resources, 9: 237-242 Zheng Lianming, Lin Yuanshao, Li Shaojing, et al. 2009. Aequorea taiwanensisn. sp (Hydrozoa, Leptomedusae) and mtCOI sequenceanalysis for the genus Aequorea. Acta Oceanologica Sinica, 28:109-115 Zhou Konglin, Zheng Lianming, He Jinru, et al. 2013. Detection of anew Clytia species (Cnidaria: Hydrozoa: Campanulariidae) withDNA barcoding and life cycle analyses. Journal of the Ma
点击查看大图
计量
- 文章访问数: 2152
- HTML全文浏览量: 151
- PDF下载量: 3661
- 被引次数: 0