Invertebrate Systematics Invertebrate Systematics Society
Systematics, phylogeny and biogeography
RESEARCH ARTICLE

COI barcoding of Hydroides: a road from impossible to difficult

Y. Sun A , E. K. Kupriyanova B and J. W. Qiu A C
+ Author Affiliations
- Author Affiliations

A Hong Kong Baptist University, Department of Biology, 224 Waterloo Road, Kowloon, Hong Kong, China.

B The Australian Museum, Marine Invertebrates Section, 6 College Street, Sydney, Australia.

C Corresponding author. Email: qiujw@hkbu.edu.hk

Invertebrate Systematics 26(6) 539-547 https://doi.org/10.1071/IS12024
Submitted: 11 April 2012  Accepted: 13 September 2012   Published: 19 December 2012

Abstract

A fragment of the cytochrome c oxidase subunit I (COI) gene has been used increasingly for species identification and discovery in eukaryotes. However, amplifying COI has proven difficult, or even impossible, in some taxa due to non-homology between the universal primers and the target DNA region. Among the most problematic animal groups is Serpulidae (Annelida). These sedentary marine animals live in self-secreted calcareous tubes and many of them, especially of the genus Hydroides, are economically important reef-builders, foulers, and biological invaders. We developed novel taxon-specific primers for amplifying COI from Hydroides, and for the first time generated 460-bp COI sequences from 11 of 14 species attempted. Average Kimura-2-parameter interspecific sequence distance (26.2%) was >60 times greater than the average intraspecific distance (0.43%), indicating that the COI gene is effective for species delimitation in Hydroides. Although applicability of the new primers for a wide range of serpulids needs to be tested, barcoding of Hydroides is now on its way from impossible to difficult. We anticipate that COI barcoding will provide a modern species identification tool and, combined with other molecular markers, yield important insights in phylogeny and evolutionary ecology of this large and important genus.

Additional keywords: DNA, polychaeta, serpulidae.


References

Arakawa, K. Y. (1971). Notes on a serious damage to cultured oyster crops in Hiroshima caused by unique and unprecedented outbreak of a serpulid worm, Hydroides norvegica (Gunnerus) in 1969. Venus (Fukuyama-Shi, Japan) 30, 75–82.

Barroso, R., Klautau, M., Solé-Cava, A. M., and Paiva, P. C. (2010). Eurythoe complanata (Polychaeta: Amphinomidae), the ‘cosmopolitan’ fireworm, consists of at least three cryptic species. Marine Biology 157, 69–80.
Eurythoe complanata (Polychaeta: Amphinomidae), the ‘cosmopolitan’ fireworm, consists of at least three cryptic species.CrossRef |

Bastida-Zavala, J. R., and ten Hove, H. A. (2002). Revision of Hydroides Gunnerus, 1768 (Polychaeta: Serpulidae) from the western Atlantic region. Beaufortia 53, 103–178.

Bastida-Zavala, J. R., and ten Hove, H. A. (2003). Revision of Hydroides Gunnerus, 1768 (Polychaeta: Serpulidae) from the eastern Pacific Region and Hawaii. Beaufortia 53, 67–110.

Carr, C. M., Hardy, S. M., Brown, T. M., Macdonald, T. A., and Hebert, P. H. N. (2011). A tri-oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes. PLoS ONE 6, e22232.
A tri-oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes.CrossRef | 1:CAS:528:DC%2BC3MXhtVSlt7%2FI&md5=c744dbcb5d011aec7db057e5c7d13cc6CAS |

Dürr, S., and Watson, D. I. (2010). Biofouling and antifouling in Aquaculture. In ‘Biofouling’. (Eds S. Dürr and J. C. Thomason.) pp. 267–287. (Wiley-Blackwell: Oxford.)

Erpenbeck, D., Hooper, J. N. A., and Worheide, G. (2006). COI phylogenies in diploblasts and the ‘Barcoding of Life’ – are we sequencing a suboptimal partition? Molecular Ecology Notes 6, 550–553.
COI phylogenies in diploblasts and the ‘Barcoding of Life’ – are we sequencing a suboptimal partition?CrossRef | 1:CAS:528:DC%2BD28XmtlGqurw%3D&md5=022734f149f63791ff98358ffda3f920CAS |

Fiege, D., and Sun, R. (1999). Polychaeta of Hainan Island, South China Sea. Part I. Serpulidae (Annelida: Polychaeta: Serpulidae). Senckenbergiana Biologica 79, 109–141.

Folmer, O., Black, M., Hoeh, W., Lutz, R., and Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3, 294–299.
| 1:CAS:528:DyaK2MXjt12gtLs%3D&md5=0a6e1d841a9ef8fafdf936427c59141bCAS |

Halanych, K. M., and Janosik, A. M. (2006). The state of annelid phylogenetics. Integrative and Comparative Biology 46, 533–543.
The state of annelid phylogenetics.CrossRef |

Halt, M. N., Kupriyanova, E. K., Cooper, S. B., and Rouse, G. W. (2009). Naming species with no morphological indicators: species status of Galeolaria caespitosa (Annelida: Serpulidae) inferred from nuclear and mitochondrial gene sequences and morphology. Invertebrate Systematics 23, 205–222.
Naming species with no morphological indicators: species status of Galeolaria caespitosa (Annelida: Serpulidae) inferred from nuclear and mitochondrial gene sequences and morphology.CrossRef | 1:CAS:528:DC%2BD1MXosleisLY%3D&md5=e9513b2a03b7cd8cb5bde44925a48bbdCAS |

Hardy, S. M., Carr, C. M., Hardman, M., Steinke, D., Corstorphine, E., and Mah, C. (2011). Biodiversity and phylogeography of Arctic marine fauna: insights from molecular tools. Marine Biodiversity 41, 195–210.
Biodiversity and phylogeography of Arctic marine fauna: insights from molecular tools.CrossRef |

Hebert, P. D. N., Cywinska, A., Ball, S. L., and deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings. Biological Sciences 270, 313–321.
Biological identifications through DNA barcodes.CrossRef | 1:CAS:528:DC%2BD3sXktVWiu7g%3D&md5=bacde07336013937477a1e8839a85156CAS |

Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., and Francis, C. M. (2004a). Identification of birds through DNA barcodes. PLoS Biology 2, e312.
Identification of birds through DNA barcodes.CrossRef |

Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H., and Hallwachs, W. (2004b). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America 101, 14 812–14 817.
Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator.CrossRef | 1:CAS:528:DC%2BD2cXovVyju7g%3D&md5=0ae4f5812affc4879a365a936524c001CAS |

Hutchings, P. (1998). Biodiversity and functioning of polychaetes in benthic sediments. Biodiversity and Conservation 7, 1133–1145.
Biodiversity and functioning of polychaetes in benthic sediments.CrossRef |

Imajima, M. (1976). Serpulinae (Annelida, Polychaeta) from Japan. I. The genus Hydroides. Bulletin of the National Science Museum (A, Zoology) 2, 229–248.

Jolly, M. T., Jollivet, D., Gentil, F., Thiebaut, E., and Viard, F. (2005). Sharp genetic break between Atlantic and English Channel populations of the polychaete Pectinaria koreni, along the north coast of France. Heredity 94, 23–32.
Sharp genetic break between Atlantic and English Channel populations of the polychaete Pectinaria koreni, along the north coast of France.CrossRef | 1:CAS:528:DC%2BD2cXhtVOnu7vO&md5=dbbff5dde95aa4be837f977c636b2c02CAS |

Kondo, T., Gullan, P. J., and Williams, D. J. (2008). Coccidology. The study of scale insects (Hemiptera: Sternorrhyncha: Coccoidea). Revista Corpoica – Ciencia y Technologia Agropecuaria 9, 55–61.

Kumar, S., and Gadagkar, S. R. (2000). Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. Journal of Molecular Evolution 51, 544–553.
| 1:CAS:528:DC%2BD3MXjs1Khtw%3D%3D&md5=6bdf9c0b6276cf262618d9fb712165eaCAS |

Kupriyanova, E. K., and Rouse, G. W. (2008). Yet another example of paraphyly in Annelida: molecular evidence that Sabellidae contains Serpulidae. Molecular Phylogenetics and Evolution 46, 1174–1181.
Yet another example of paraphyly in Annelida: molecular evidence that Sabellidae contains Serpulidae.CrossRef | 1:CAS:528:DC%2BD1cXjtlGrs7s%3D&md5=8f052b86b2a29a48fae4aea8607b3689CAS |

Kupriyanova, E. K., Macdonald, T. A., and Rouse, G. W. (2006). Phylogenetic relationships within Serpulidae (Annelida: Polychaeta) inferred from molecular and morphological data. Zoologica Scripta 35, 421–439.
Phylogenetic relationships within Serpulidae (Annelida: Polychaeta) inferred from molecular and morphological data.CrossRef |

Kupriyanova, E. K., Bastida-Zavala, R., Halt, M. N., Lee, M. S. Y., and Rouse, G. W. (2008). Phylogeny of the Serpula–Crucigera–Hydroides clade (Serpulidae: Annelida) using molecular and morphological data: implications for operculum evolution. Invertebrate Systematics 22, 425–437.
Phylogeny of the Serpula–Crucigera–Hydroides clade (Serpulidae: Annelida) using molecular and morphological data: implications for operculum evolution.CrossRef | 1:CAS:528:DC%2BD1cXht1eqtLzE&md5=dff9cac2f9024f3430d604843c457664CAS |

Lehrke, J., ten Hove, H. A., Macdonald, T. A., Bartolomaeus, T., and Bleidorn, C. (2007). Phylogenetic relationships of Serpulidae (Annelida: Polychaeta) based on 18S rDNA sequence data, and implications for opercular evolution. Organisms, Diversity & Evolution 7, 195–206.
Phylogenetic relationships of Serpulidae (Annelida: Polychaeta) based on 18S rDNA sequence data, and implications for opercular evolution.CrossRef |

Lewis, J. A. (2006). Establishment of the Caribbean serpulid tubeworm Hydroides sanctaecrucis Krøyer [in] Mörch, 1863, in northern Australia. Biological Invasions 8, 665–671.
Establishment of the Caribbean serpulid tubeworm Hydroides sanctaecrucis Krøyer [in] Mörch, 1863, in northern Australia.CrossRef |

Nei, M., and Kumar, S. (2000). ‘Molecular Evolution and Phylogenetics.’ (Oxford University Press: New York.)

Nishi, E., and Kato, T. (2004). Introduced and globally invaded polychaetous annelids. Japanese Journal of Benthology 59, 83–95.

Nygren, A., and Pleijel, F. (2011). From one to ten in a single stroke – resolving the European Eumida sanguinea (Phyllodocidae, Annelida) species complex. Molecular Phylogenetics and Evolution 58, 132–141.
From one to ten in a single stroke – resolving the European Eumida sanguinea (Phyllodocidae, Annelida) species complex.CrossRef |

Otani, M., and Yamanishi, R. (2010). Distribution of the alien species Hydroides dianthus (Verrill, 1873) (Polychaeta: Serpulidae) in Osaka Bay, Japan, with comments on the factors limiting its invasion. Plankton and Benthos Research 5, 62–68.
Distribution of the alien species Hydroides dianthus (Verrill, 1873) (Polychaeta: Serpulidae) in Osaka Bay, Japan, with comments on the factors limiting its invasion.CrossRef |

Park, D.-S., Suh, S.-J., Hebert, P. D. N., Oh, H.-W., and Hong, K.-J. (2011). DNA barcodes for two scale insect families, mealybugs (Hemiptera: Pseudococcidae) and armored scales (Hemiptera: Diaspididae). Bulletin of Entomological Research 101, 429–434.
DNA barcodes for two scale insect families, mealybugs (Hemiptera: Pseudococcidae) and armored scales (Hemiptera: Diaspididae).CrossRef | 1:CAS:528:DC%2BC3MXnvFertL0%3D&md5=b1ea1dca730abaa96a9832bfc8c16c5eCAS |

Pettengill, J. B., Wendt, D. E., Schug, M. D., and Hadfield, M. G. (2007). Biofouling likely serves as a major mode of dispersal for the polychaete tubeworm Hydroides elegans as inferred from microsatellite loci. Biofouling 23, 161–169.
Biofouling likely serves as a major mode of dispersal for the polychaete tubeworm Hydroides elegans as inferred from microsatellite loci.CrossRef | 1:CAS:528:DC%2BD2sXotFSjtbo%3D&md5=6fee79012e7e039faaee1b62762a077cCAS |

Pillai, T. G. (2009). Descriptions of new serpulid polychaetes from the Kimberleys of Australia and discussion of Australian and Indo-West Pacific species of Spirobranchus and superficially similar taxa. Records of the Australian Museum 61, 93–199.
Descriptions of new serpulid polychaetes from the Kimberleys of Australia and discussion of Australian and Indo-West Pacific species of Spirobranchus and superficially similar taxa.CrossRef |

Pleijel, F., Rouse, G., and Nygren, A. (2009). Five colour morphs and three new species of Gyptis (Hesionidae, Annelida) under a jetty in Edithburgh, South Australia. Zoologica Scripta 38, 89–99.
Five colour morphs and three new species of Gyptis (Hesionidae, Annelida) under a jetty in Edithburgh, South Australia.CrossRef |

Qiu, J. W., and Qian, P. Y. (1997). Combined effects of salinity, temperature and food on early development of the polychaete Hydroides elegans. Marine Ecology Progress Series 152, 79–88.
Combined effects of salinity, temperature and food on early development of the polychaete Hydroides elegans.CrossRef |

Schwindt, E., Bortolus, A., and Iribarne, O. O. (2001). Invasion of a reef-builder polychaete: direct and indirect impacts on the native benthic community structure. Biological Invasions 3, 137–149.
Invasion of a reef-builder polychaete: direct and indirect impacts on the native benthic community structure.CrossRef |

Sevilla, R. G., Diez, A., Noren, M., Mouchel, O., Jerome, M., Verrez-Bagnis, V., van Pelt, H., Favre-Krey, L., and Bautista, J. M. (2007). Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes. Molecular Ecology Notes 7, 730–734.
Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes.CrossRef | 1:CAS:528:DC%2BD2sXht1ertL3M&md5=5cb2aff94dfecfa6dfb8e8dcaac85c2eCAS |

Siddall, M. E., Fontanella, F. M., Watson, S. C., Kvist, S., and Erseus, C. (2009). Barcoding bamboozled by bacteria: convergence to metazoan mitochondrial primer targets by marine microbes. Systematic Biology 58, 445–451.
Barcoding bamboozled by bacteria: convergence to metazoan mitochondrial primer targets by marine microbes.CrossRef |

Smith, M. A., Woodley, N. E., Janzen, D. H., Hallwachs, W., and Hebert, P. D. N. (2006). DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). Proceedings of the National Academy of Sciences of the United States of America 103, 3657–3662.
DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae).CrossRef | 1:CAS:528:DC%2BD28XivFWju7k%3D&md5=6ca3011e2f91cd90c3a4d3ad6d746dc6CAS |

Smith, M. A., Wood, D. M., Janzen, D. H., Hallwachs, W., and Hebert, P. D. N. (2007). DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists. Proceedings of the National Academy of Sciences of the United States of America 104, 4967–4972.
DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists.CrossRef | 1:CAS:528:DC%2BD2sXjvFKiurw%3D&md5=eda54524b1ef5504ecdc195a37686135CAS |

Straughan, D. (1967). Some Serpulidae (Annelida: Polychaeta) from Heron Island, Queensland. University of Queensland Papers 1, 27–45.

Streftaris, N., and Zenetos, A. (2006). Alien marine species in the Mediterranean – the 100 ‘worst invasives’ and their impact. Mediterranean Marine Science 7, 87–118.

Tamura, K., Dudley, J., Nei, M., and Kumar, S. (2007). Mega4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24, 1596–1599.
Mega4: molecular evolutionary genetics analysis (MEGA) software version 4.0.CrossRef | 1:CAS:528:DC%2BD2sXpsVGrsL8%3D&md5=d2738b052fcd210827e9d4fc638cc7d5CAS |

ten Hove, H. A. (1974). Notes on Hydroides elegans (Haswell, 1883) and Mercierella enigmatica Fauvel, 1923, alien serpulid polychaetes introduced into the Netherlands. Bulletin Zoologisch Museum Universiteit van Amsterdam 4, 45–51.

ten Hove, H. A., and Jansen-Jacobs, M. J. (1984). A revision of the genus Crucigera (Polychaeta; Serpulidae); a proposed methodical approach to serpulids, with special reference to variation in Serpula and Hydroides. In ‘Proceedings of the First International Polychaete Conference’. (Ed. P. A. Hutchings.) pp. 143–180. (Linnean Society of New South Wales: Sydney.)

ten Hove, H. A., and Kupriyanova, E. K. (2009). Taxonomy of Serpulidae (Annelida, Polychaeta): the state of affairs. Zootaxa 2036, 1–126.

Thomas, M., Raharivololoniaina, L., Glaw, F., Vences, M., and Vieites, D. R. (2005). Montane tadpoles in Madagascar: molecular identification and description of the larval stages of Mantidactylus elegans, Mantidactylus madecassus, and Boophis laurenti from the Andringitra Massif. Copeia 2005, 174–183.
Montane tadpoles in Madagascar: molecular identification and description of the larval stages of Mantidactylus elegans, Mantidactylus madecassus, and Boophis laurenti from the Andringitra Massif.CrossRef |

Tovar-Hernández, M. A., Méndez, N., and Villalobos-Guerrero, T. F. (2009). Fouling polychaete worms from the Southern Gulf of California: Sabellidae and Serpulidae. Systematics and Biodiversity 7, 319–336.
Fouling polychaete worms from the Southern Gulf of California: Sabellidae and Serpulidae.CrossRef |

Willassen, E. (2005). New species of Diamesa (Diptera: Chironomidae) from Tibet: conspecific males and females associated with mitochondrial DNA. Zootaxa 1049, 19–32.

Witt, J. D. S., Threloff, D. L., and Hebert, P. D. N. (2006). DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Molecular Ecology 15, 3073–3082.
DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation.CrossRef | 1:CAS:528:DC%2BD28XhtVKntr7N&md5=fb04869149409ffb3e77f0e19ceced0bCAS |

Wu, B. L., and Chen, M. (1980). Two new species of the family Serpulidae from South China Sea. Acta Zootaxonomica Sinica 6, 247–249.



Rent Article (via Deepdyve) Supplementary MaterialSupplementary Material (1.8 MB) Export Citation Cited By (6)