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Marine and Freshwater Research Marine and Freshwater Research Society
Advances in the aquatic sciences
RESEARCH ARTICLE

The use of DNA barcode evidence for inferring species of Chlorophthalmus (Aulopiformes, Chlorophthalmidae) in the Indo-West Pacific

Martin F. Gomon A C , Robert D. Ward B , Stephanie Chapple A and Joshua M. Hale A
+ Author Affiliations
- Author Affiliations

A Sciences Department, Museum Victoria, GPO Box 666, Melbourne, Vic. 3001, Australia.

B CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, Tas. 7001, Australia.

C Corresponding author. Email: mgomon@museum.vic.gov.au

Marine and Freshwater Research 65(11) 1027-1034 https://doi.org/10.1071/MF13245
Submitted: 16 September 2013  Accepted: 25 March 2014   Published: 10 October 2014

Abstract

Recent studies have revealed evidence that the identities and distributions of several Indo-West Pacific species of Chlorophthalmus, as redefined by Sato and Nakabo (2002a), are inaccurately understood and reported in the literature. The current confusion is mostly attributable to the meristic conservatism of the genus and the individually variable nature of the morphology in those species. An analysis of the DNA barcode region of cytochrome c oxidase subunit I sequences was employed to independently group specimens into natural species assemblages, providing evidence for verifying or correcting species concepts and identities. A re-examination of the morphology of vouchers in the resultant 12 groupings identified features corroborating the distinctiveness of 10 of the 12 groups at the species level. Each of the other two groups comprised two presumed species on the basis of morphological evidence that do not appear to be separable by cytochrome c oxidase subunit I gene (COI) sequences. Two undescribed species of Chloropthalmus are now known to inhabit slope waters of Australia, and a further two undescribed species were identified elsewhere.

Additional keywords: CO1, cytochrome c oxidase subunit 1, undescribed species.


References

Gomon, M. F. (2010). A new species of Paraulopus (Aulopiformes: Paraulopidae) from seamounts of the Tasman Sea. Memoirs of Museum Victoria 67, 15–18.

Gomon, M. F., and Sato, T. (2004). A new cucumberfish (Paraulopidae) of the Paraulopus nigripinnis complex from central eastern Australia. Records of the Australian Museum 56, 195–199.
A new cucumberfish (Paraulopidae) of the Paraulopus nigripinnis complex from central eastern Australia.Crossref | GoogleScholarGoogle Scholar |

Hoese, D. F., Bray, D. J., Paxton, J. R., and Allen, G. R. (2006). Fishes. In ‘Zoological Catalogue of Australia. Vol. 35. Australia’. (Eds P. L. Beesley and A. Wells.) Part 1, pp. xxiv, 1–670; Part 2, pp. xxi, 671–1472; Part 3, pp. xxi, 1473–2178. (ABRS & CSIRO Publishing: Melbourne.)

Ivanova, N. V., Dewaard, J. R., and Hebert, P. D. N. (2006). An inexpensive automation-friendly protocol for recovering high-quality DNA. Molecular Ecology Notes 6, 998–1002.
An inexpensive automation-friendly protocol for recovering high-quality DNA.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXmsl2ksw%3D%3D&md5=7ee1fca47f88ef6ae3e500ae6ce593d6CAS |

Ivanova, N. V., Zemlak, T. S., Hanner, R., and Hebert, P. D. N. (2007). Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7, 544–548.
Universal primer cocktails for fish DNA barcoding.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXpslOhtbo%3D&md5=e5702dc5ca9f08688862e1e2af6a7f2aCAS |

Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16, 111–120.
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaL3MXmtFSktg%3D%3D&md5=3bac076995f41cdb59e7979deedea5c9CAS | 7463489PubMed |

Kobyliansky, S. G. (2013). Two new species of green eyes of the genus Chlorophthalmus (Chlorophthalmidae, Aulopidae) from the continental slope and submarine rises of the western tropical part of the Indian Ocean. Voprosy Ikhtiologii 53, 381–388.
Two new species of green eyes of the genus Chlorophthalmus (Chlorophthalmidae, Aulopidae) from the continental slope and submarine rises of the western tropical part of the Indian Ocean.Crossref | GoogleScholarGoogle Scholar |

Kotlyar, A. N., and Parin, N. V. (1986). Two new species of Chlorophthalmus (Osteichthyes, Myctophiformes, Chlorophthalmidae) from submarine mountain ridges in the south-eastern part of the Pacific Ocean. Зоологический журнал 65, 369–377.

Last, P. R., Lyne, V. D., Yearsley, G. K., Gledhill, D. C., Gomon, M. F., Rees, A. J. J., and White, N. J. (2005). ‘Validation of National Demersal Fish Datasets for the Regionalisation of the Australian Continental Slope and Outer Shelf (>40 m depth).’ (National Oceans Office: Hobart.)

Leviton, A. E., Gibbs, R. H., Heal, E., and Dawson, C. E. (1985). Standards in herpetology and ichthyology, part 1. Standard symbolic codes for institutional resource collections in herpetology and ichthyology. Copeia 1985, 802–832.

Masuda, H., Amaoka, K., Araga, C., Uyeno, T., and Yoshino, T. (1984). ‘The Fishes of the Japanese Archipelago.’ (Tokai University Press: Tokyo.)

Nakabo, T. (Ed.) (2002). ‘Fishes of Japan with Pictorial Keys to the Species.’ English edn. (Tokai University Press: Tokyo.)

Nakabo, T. (Ed.) (2013). ‘Fishes of Japan with Pictorial Keys to the Species.’ 3rd edn. (Tokai University Press: Tokyo.)

Okamura, O., and Amaoka, K. (1997). ‘Sea Fishes of Japan.’ (Yama Kei Publishers: Tokyo.)

Okamura, O., and Kitajima, T. (Eds) (1984). ‘Fishes of the Okinawa Trough and the Adjacent Waters. Vol. 1. The Intensive Research of Unexploited Fishery Resources on Continental Slopes.’ (Japan Fisheries Resource Conservation Association: Tokyo.)

Paxton, J. R., and Niem, V. H. (1999). Chlorophthalmidae. In ‘Species Identification Guide for Fisheries Purposes. The Living Marine Resources of the Western Central Pacific. Batoid Fishes, Chimaeras and Bony Fishes, Part 1 (Elopidae to Linophrynidae). Vol. 3'. (Eds K. E. Carpenter and V. H. Niem.) pp. 1921–1924. iii–vi + 1398–2068, I–IV. (FAO: Rome.)

Sato, T., and Nakabo, T. (2002a). Paraulopidae and Paraulopus, a new family and genus of aulopiform fishes with revised relationships within the order. Ichthyological Research 49, 25–46.
Paraulopidae and Paraulopus, a new family and genus of aulopiform fishes with revised relationships within the order.Crossref | GoogleScholarGoogle Scholar |

Sato, T., and Nakabo, T. (2002b). Two new species of Paraulopus (Osteichthyes: Aulopiformes) from New Zealand and eastern Australia, and comparisons with P. nigripinnis. Species Diversity 7, 393–404.

Sato, T., and Nakabo, T. (2003). A revision of the Paraulopus oblongus group (Aulopiformes: Paraulopidae) with description of a new species. Ichthyological Research 50, 164–177.
A revision of the Paraulopus oblongus group (Aulopiformes: Paraulopidae) with description of a new species.Crossref | GoogleScholarGoogle Scholar |

Sato, T., Gomon, M. F., and Nakabo, T. (2010). Two new Australian species of the Paraulopus nigripinnis complex (Aulopiformes: Paraulopidae). Ichthyological Research 57, 254–262.
Two new Australian species of the Paraulopus nigripinnis complex (Aulopiformes: Paraulopidae).Crossref | GoogleScholarGoogle Scholar |

Tamura, K., and Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10, 512–526.
| 1:CAS:528:DyaK3sXks1CksL4%3D&md5=5e0c968139f454acbeea7f8663ef39a2CAS | 8336541PubMed |

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.
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXht1eiu73K&md5=afbe368a3bf41a18152be0ac69bac6eeCAS | 21546353PubMed |

Ward, R. D. (2009). DNA barcode divergence among species and genera of birds and fishes. Molecular Ecology Resources 9, 1077–1085.
DNA barcode divergence among species and genera of birds and fishes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXpt1Omur4%3D&md5=73a8d7ab79e4711dc2e2841fcd175952CAS | 21564845PubMed |

Ward, R. D., and Holmes, B. H. (2007). An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes. Molecular Ecology Notes 7, 899–907.
An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXls12lsg%3D%3D&md5=c4d8f6e4fdb578e99cb70339a01a8fc4CAS |

Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., and Hebert, P. D. N. (2005). DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360, 1847–1857.
DNA barcoding Australia's fish species.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXhtlSjsrjK&md5=c083fda074291777e5c693f2fa2aa79aCAS | 16214743PubMed |

Ward, R. D., Hanner, R., and Hebert, P. D. N. (2009). The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology 74, 329–356.
The campaign to DNA barcode all fishes, FISH-BOL.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXjvVWrsbw%3D&md5=babb877d216849925838ffbed455621dCAS | 20735564PubMed |

Zemlak, T. S., Ward, R. D., Connell, A. D., Holmes, B. H., and Hebert, P. D. N. (2009). DNA barcoding reveals overlooked marine fishes. Molecular Ecology Resources 9, 237–242.
DNA barcoding reveals overlooked marine fishes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXlslOjt78%3D&md5=e91861252a16a6a7b41120d721b9dbbfCAS | 21564983PubMed |