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Article << Previous     |     Next >>   Contents Vol 25(4)

Barcoding type specimens helps to identify synonyms and an unnamed new species in Eumunida Smith, 1883 (Decapoda : Eumunididae)

Nicolas Puillandre A E , Enrique Macpherson B , Josie Lambourdière C , Corinne Cruaud D , Marie-Catherine Boisselier-Dubayle A C and Sarah Samadi A C

A ‘Systématique, Adaptation et Evolution’, UMR 7138 UPMC-IRD-MNHN-CNRS (UR IRD 148), Muséum national d’Histoire naturelle, Département Systématique et Evolution, CP 26, 57 Rue Cuvier, F-75231 Paris Cedex 05, France.
B Centro de Estudios Avanzados de Blanes (CEAB-CSIC), C. acc. Cala Sant Francesc 14, 17300 Blanes, Girona, Spain.
C Service de systématique moléculaire (CNRS-MNHN, UMS2700), Muséum national d’Histoire naturelle, Département Systématique et Evolution, CP 26, 57 Rue Cuvier, F-75231 Paris Cedex 05, France.
D GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP 5706, 91057 Evry Cedex France.
E Corresponding author. Email: puillandre@mnhn.fr

Invertebrate Systematics 25(4) 322-333 http://dx.doi.org/10.1071/IS11022
Submitted: 25 May 2011  Accepted: 9 November 2011   Published: 22 December 2011
 
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Abstract

The primary purpose of DNA-barcoding projects is to generate an efficient expertise and identification tool. This is an important challenge to the taxonomy of the 21st century, as the demand increases and the expert capacity does not. However, identifying specimens using DNA-barcodes requires a preliminary analysis to relate molecular clusters to available scientific names. Through a case study of the genus Eumunida (Decapoda : Eumunididae), we illustrate how naming molecule-based units, and thus providing an accurate DNA-based identification tool, is facilitated by sequencing type specimens. Using both morphological and unlinked molecular markers (COI and 28S genes), we analysed 230 specimens from 12 geographic areas, covering two-thirds of the known diversity of the genus, including type specimens of 13 species. Most hypotheses of species delimitation are validated, as they correspond to molecular units linked to only one taxonomic name (and vice versa). However, a putative cryptic species is also revealed and three entities previously named as distinct species may in fact belong to a single one, and thus need to be synonymised. Our analyses, which integrate the current naming rules, enhance the α-taxonomy of the genus and provide an effective identification tool based on DNA-barcodes. They illustrate the ability of DNA-barcodes, especially when type specimens are included, to pinpoint where a taxonomic revision is needed.



References

Ahyong, S. T., Chan, T.-Y., and Bouchet, P. (2010). Mighty claws: a new genus and species of lobster from the Philippine deep sea (Crustacea, Decapoda, Nephropidae). Zoosystema 32, 525–535.
| CrossRef |

Baba, K., Macpherson, E., Poore, G. C. B., Ahyong, S. T., Bermudez, A., Cabezas, P., Lin, C. W., Nizinski, M., Rodrigues, C., and Schnabel, K. E. (2008). Catalogue of squat lobsters of the world (Crustacea: Decapoda: Anomura – families Chirostylidae, Galatheidae and Kiwaidae). Zootaxa 1905, 1–220.

Bickford, D., Lohman, D. J., Sodhi, N. S., Ng, P. K. L., Meier, R., Winker, K., Ingram, K. K., and Das, I. (2007). Cryptic species as a window on diversity and conservation. Trends in Ecology & Evolution 22, 148–155.
| CrossRef |

Bouchet, P., Héros, V., Lozouet, P., and Maestrati, P. (2008). A quater-century of deep-sea malacological exploration in the South and West Pacific: Where do we stand? How far to go? Mémoires du Muséum national d’Histoire naturelle 196, 9–40.

Costa, F. O., deWaard, J. R., Boutillier, J., Ratsnasingham, S., Dooh, R. T., Hajibabaei, M., and Hebert, P. D. N. (2007). Biological identifications through DNA barcodes: the case of the Crustacea. Canadian Journal of Fisheries and Aquatic Sciences 64, 272–295.
| CrossRef | CAS |

Dayrat, B. (2006). A taxonomic revision of Paradoris sea slugs (Mollusca, Gastropoda, Nudibranchia, Doridina). Zoological Journal of the Linnean Society 147, 125–238.
| CrossRef |

Dayrat, B., Tillier, A., Lecointre, G., and Tillier, S. (2001). New clades of Euthyneuran gastropods (Mollusca) from 28S rRNA sequences. Molecular Phylogenetics and Evolution 19, 225–235.
| CrossRef | CAS |

De Ley, P., Tandingam De Ley, I. T., Morris, K., Abebe, E., Mundo-Ocampo, M., Yoder, M., Heras, J., Waumann, D., Rocha-Olivares, A., Jay Burr, A. H., Baldwin, J. G., and Thomas, W. K. (2005). An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding. Philosophical Transactions of the Royal Society B 360, 1945–1958.
| CrossRef | CAS |

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.
| CAS |

Hajibabaei, M., Singer, G. A. C., Hebert, P. D. N., and Hickey, D. A. (2007). DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics 23, 167–172.
| CrossRef | CAS |

Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41, 95–98.
| CAS |

Hebert, P. D. N., and Gregory, T. R. (2005). The promise of DNA Barcoding for taxonomy. Systematic Biology 54, 852–859.
| CrossRef |

Huelsenbeck, J. P., Ronquist, F., and Hall, B. (2001). MrBayes: Bayesian inference of phylogeny. Bioinformatics (Oxford, England) 17, 754–755.
| CrossRef | CAS |

Jovelin, R., and Justine, J.-L. (2001). Phylogenetic relationships within the Polyopisthocotylean monogeneans (Plathyhelminthes) inferred from partial 28S rDNA sequences. International Journal for Parasitology 31, 393–401.
| CrossRef | CAS |

Keane, T. M., Creevey, C. J., Pentony, M. M., Naughton, T. J., and McInerney, J. O. (2006). Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evolutionary Biology 6, 29.
| CrossRef |

Knowlton, N. (2000). Molecular genetic analyses of species boundaries in the sea. Hydrobiologia 420, 73–90.
| CrossRef | CAS |

Machordom, A., and Macpherson, E. (2004). Rapid radiation and cryptic speciation in galatheid crabs of the genus Munida and related genera in the South West Pacific: molecular and morphological evidence. Molecular Phylogenetics and Evolution 33, 259–279.
| CrossRef | CAS |

Meier, R., Zhang, G., and Ali, F. (2008). The use of mean instead of smallest interspecific distances exaggerates the size of the “Barcoding Gap” and leads to misidentification. Systematic Biology 57, 809–813.
| CrossRef |

Meyer, C. P., and Paulay, G. (2005). DNA Barcoding: error rates based on comprehensive sampling. PLoS Biology 3, e422.
| CrossRef |

Padial, J. M., and De La Riva, I. (2007). Integrative taxonomists should use and produce DNA barcodes. Zootaxa 1586, 67–68.

Rambaut, A., and Drummond, A. J. (2007). Tracer v1.4. Available from http://beast.bio.ed.ac.uk/Tracer

Saint Laurent, M. d., and Poupin, J. (1996). Crustacea, Anomura: Les espèces indo-ouest pacifiques du genre Eumunida Smith, 1880 (Chirostylidae). Description de six espèces nouvelles. In ‘Résultats des Campagnes MUSORSTOM, volume 15. Vol. 168’. (Ed. A Crosnier.) pp. 337–385. (Mémoires du Museum national d’Histoire naturelle: Paris.)

Samadi, S., Bottan, L., McPherson, E., Richer De Forges, B., and Boisselier, M. C. (2006). Seamount endemism questioned by the geographic distribution and population genetic structure of marine invertebrates. Marine Biology 149, 1463–1475.
| CrossRef |

Savolainen, V., Cowan, R. S., Vogler, A. P., Roderick, G. K., and Lane, R. (2005). Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B 360, 1805–1811.
| CrossRef | CAS |

Schindel, D. E., and Miller, S. E. (2005). DNA barcoding a useful tool for taxonomists. Nature 435, 17.
| CrossRef | CAS |

Schnabel, K. E., and Ahyong, S. T. (2010). A new classification of the Chirostyloidea (Crustacea: Decapoda: Anomura). Zootaxa 2687, 56–64.

Shih, H.-T., Naruse, T., and Ng, P. K. L. (2010). Uca jocelynae sp. nov. a new species of fiddler crab (Crustacea: Brachyura: Ocypodidae) from the Western Pacific. Zootaxa 2337, 47–62.

Smith, A. M., 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.
| CrossRef | CAS |

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony methods. Molecular Biology and Evolution 28, 2731–2739.
| CrossRef | CAS |

Vences, M., Thomas, M., Bonett, R. M., and Vieites, D. R. (2005). Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philosophical Transactions of the Royal Society B 360, 1859–1868.
| CrossRef | CAS |

Wiemers, M., and Fiedler, K. (2007). Does the DNA barcoding gap exist? – a case study in blue butterflies (Lepidoptera: Lycaenidae). Frontiers in Zoology 4, 8.
| CrossRef |


   
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