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

A first approach to the usefulness of cytochrome c oxidase I barcodes in the identification of closely related delphinid cetacean species

A. R. Amaral A C , M. Sequeira B and M. M. Coelho A

A Universidade de Lisboa, Faculdade de Ciências, Centro de Biologia Ambiental, Campo Grande, 1749-016 Lisboa, Portugal.

B Instituto de Conservação da Natureza, Rua de Santa Marta, 55, 1150-294 Lisboa, Portugal.

C Corresponding author. Email:

Marine and Freshwater Research 58(6) 505-510
Submitted: 9 March 2007  Accepted: 8 May 2007   Published: 25 June 2007


The DNA barcode initiative has gained particular popularity as a promising tool to assist in species identification by using a single mitochondrial gene, cytochrome c oxidase I (COI). In some animal groups, COI barcodes have proved efficient in separating closely related taxa. However, several issues remain for discussion, namely how efficient this tool will be in animal groups with an unresolved taxonomy. Here, we examined COI sequences in delphinid cetaceans, a group where taxonomic uncertainty still exists. We analysed species belonging to the genera Stenella, Tursiops and Delphinus in the North-east Atlantic using cytochrome b gene sequences for comparison. We obtained values of COI interspecific genetic divergence ranging from 1.47% to 2.45%, which suggests a recent separation of the analysed taxa. S. coeruleoalba and D. delphis were the most similar species, with COI phylogenetic trees failing to separate them. On the other hand, the phylogenetic tree obtained with cytochrome b sequences correctly clustered species with high bootstrap support values. We thus consider that the application of COI barcodes in delphinid cetaceans should be done with caution; not only has the cytochrome b gene been shown to be phylogenetically more informative, but relying only on mitochondrial DNA genes alone may be problematic.

Extra keywords: bottlenose dolphin, common dolphin, cytochrome c oxidase I, Delphinidae, phylogenetic inference, striped dolphin.


Amaral A. R.Sequeira M.Cedeira-Martínez J.Coelho M. M.2007New insights on population genetic structure of Delphinus delphis from the northeast Atlantic and phylogenetic relationships with the genus inferred from two mitochondrial markers.Marine Biologydoi:10.1007/S00227-007-0635-Y

Arnason U.Gullberg A.Janke A.2004Mitogenomic analyses provide new insights into cetacean origin and evolution.Gene3332734doi:10.1016/J.GENE.2004.02.010

Avise J. C.1995Mitochondrial DNA polymorphism and a connection between genetics and demography of relevance to conservation.Conservation Biology9686690doi:10.1046/J.1523-1739.1995.09030686.X

Baker C. S.Dalebout M. L.Lavery S.Ross H. A.2003www.DNA-surveillance: applied molecular taxonomy for species conservation and discovery.Trends in Ecology & Evolution18271272doi:10.1016/S0169-5347(03)00101-0

Ballard J. W. O.Whitlock M. C.2004The incomplete natural history of mitochondria.Molecular Ecology13729744doi:10.1046/J.1365-294X.2003.02063.X

Blaxter M.Mann J.Chapman T.Thomas F.Whitton C. Floyd R.Abebe E.2005Defining operational taxonomic units using DNA barcode data.Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences36019351943doi:10.1098/RSTB.2005.1725

Cavalli-Sforza L. L.1998The DNA revolution in population genetics.Trends in Genetics146065doi:10.1016/S0168-9525(97)01327-9

Cummings M. P.Otto S. P.Wakeley J.1995Sampling properties of DNA sequence data in phylogenetic analysis.Molecular Biology and Evolution12814822

DeSalle R.Egan M. G.Siddall M.2005The unholy trinity: taxonomy, species delimitation and DNA barcoding.Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences36019051916

Dizon A., Baker C. S., Cipriano F., Lento G., Palsboll P., and Reeves R., (2000). ‘Molecular Genetic Identification of Whales, Dolphins and Porpoises: Proceedings of a Workshop on the Forensic Use of Molecular Techniques to Identify Wildlife Products in the Market Place.’ NOAA Technical Memorandum NMFS NOAA-TM-NMFS-SWFSC-286. (National Oceanic and Atmospheric Administration: La Jolla, CA.)

Funk D. J.Omland K. E.2003Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA.Annual Review of Ecology, Evolution and Systematics34397423doi:10.1146/ANNUREV.ECOLSYS.34.011802.132421

Garcia-Martinez J.Barrio E.Raga J. A.Latorre A.1995Mitochondrial-DNA Variability of Striped Dolphins (Stenella-Coeruleoalba) in the Spanish Mediterranean Waters.Marine Mammal Science11183199doi:10.1111/J.1748-7692.1995.TB00517.X

Hajibabaei M.Singer G. A. C.Hebert P. D. N.Hickey D. A.2007DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics.Trends in Genetics.doi:10.1016/J.TIG.2007.02.001

Hebert P. D. N.Cywinska A.Ball S. L.deWaard J. R.2003aBiological identification through DNA barcodes.Proceedings of the Royal Society of London. Series B, Biological Sciences270313321

Hebert P. D. N.Ratnasingham S.deWaard J. R.2003bBarcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species.Proceedings of the Royal Society of London, Series B. Biological Sciences270S96S99

Hebert P. D. N.Stoeckle M. Y.Zemlak T. S.Francis C. M.2004Identification of birds through DNA barcodes.PloS Biology216571663

Heyning J. E.Perrin W. F.1994Evidence for two species of common dolphins (Genus Delphinus) from the eastern north Pacific.Contributions in Science442135

Hillis D. M.Huelsenbeck J. P.1992Signal, noise, and reliability in molecular phylogenetic analyses.The Journal of Heredity83189195

Hoelzel A. R., Goldsworthy S. D., and Fleischer R. C. (2002). Population genetic structure. In ‘Marine Mammal Biology, An Evolutionary Approach’. (Ed. A. R. Hoelzel.) pp. 325–352. (Blackwell Science: Oxford.)

Hogg I. D.Hebert P. D. N.2004Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes.Canadian Journal of Zoology82749754

Huelsenbeck J. P.Ronquist F.2001MRBAYES: Bayesian inference of phylogenetic trees.Bioinformatics17754755

Kingston S. E.Rosel P. E.2004Genetic differentiation among recently diverged Delphinid taxa determined using AFLP markers.The Journal of Heredity95110doi:10.1093/JHERED/ESH010

LeDuc R. G.Perrin W. F.Dizon A. E.1999Phylogenetic relationships among the delphinid cetaceans based on full cytochrome b sequences.Marine Mammal Science15619648doi:10.1111/J.1748-7692.1999.TB00833.X

Meyer C. P.Paulay G.2005DNA barcoding: Error rates based on comprehensive sampling.PLoS Biology322292238

Milinkovitch M. C.Meyer A.Powell J. R.1994Phylogeny of all major groups of cetaceans based on DNA sequences from three mitochondrial genes.Molecular Biology and Evolution11939948

Natoli A.Peddemors V. M.Rus-Hoelzel A.2004Population structure and speciation in the genus Tursiops based on microsatellite and mitochondrial DNA analyses.Journal of Evolutionary Biology17363375

Perrin W. F., and Reeves R. R. (2004). Appendix 5: report of the working group on species- and subspecies-level taxonomy. In ‘Report of the Workshop on Shortcomings of Cetacean Taxonomy in Relation to Needs of Conservation and Management, April 30–May 2’. (Eds R. R. Reeves, W. F. Perrin, B. L. Taylor, C. S. Baker and S. L. Mesnick.) pp. 25–60. (National Oceanic and Atmospheric Administration: La Jolla, CA.)

Pichler F. B.Dawson S. M.Slooten E.Baker C. S.1998Geographic isolation of Hector's dolphin populations described by mitochondrial DNA sequences.Conservation Biology12676682doi:10.1046/J.1523-1739.1998.96390.X

Posada D.Crandall K. A.1998MODELTEST: testing the model of DNA substitution.Bioinformatics14817818doi:10.1093/BIOINFORMATICS/14.9.817

Rosel P. E.Block B. A.1996Mitochondrial control region variability and global population structure in the swordfish, Xiphias gladius.Marine Biology1251122doi:10.1007/BF00350756

Rosel P. E.Dizon A. E.Heyning J. E.1994Genetic analysis of sympatric morphotypes of common dolphins (genus Delphinus).Marine Biology119159168doi:10.1007/BF00349552

Rosel P. E.France S. C.Wang J. Y.Kocher T. D.1999Genetic structure of harbour porpoise Phocoena phocoena populations in the northwest Atlantic based on mitochondrial and nuclear markers.Molecular Ecology8S41S54doi:10.1046/J.1365-294X.1999.00758.X

Ross H. A.Lento G. M.Dalebout M. L.Goode M.Ewing G.McLaren P.Rodrigo A. G.Lavery S.Baker C. S.2003DNA surveillance: web-based molecular identification of whales, dolphins, and porpoises.Journal of Heredity94111114

Rozen S., and Skaletsky H. J. (2000). Primer3 on WWW for general users and for biologist programmars. In ‘Bioinformatics Methods and Protocols: Methods in Molecular Biology’. (Eds S. Krawetz and S. Misener.) pp. 365–386. (Humana Press: Totowa, NJ.)

Rubinoff D.2006Utility of mitochondrial DNA barcodes in species conservation.Conservation Biology2015481549

Rubinoff D.Cameron C.Will K.2006A genomic perspective on the shortcomings of mitochondrial DNA for barcoding identification.The Journal of Heredity97581594doi:10.1093/JHERED/ESL036

Savolainen V.Cowan R. S.Vogler A. P.Roderick G. K.Lane R.2005Towards writing the encyclopaedia of life: an introduction to DNA barcoding.Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences36018051811doi:10.1098/RSTB.2005.1730

Swofford D. L. (2003). ‘PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods).’ (Sinauer Associates: Sunderland, MA.)

Ward R. D.Zemlak T. S.Innes B. H.Last P. R.Hebert P. D. N.2005DNA barcoding Australia's fish species.Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences36018471857doi:10.1098/RSTB.2005.1716

Witt J. D. S.Threloff D. L.Hebert P. D. N.2006DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation.Molecular Ecology1530733082

Rent Article Export Citation Cited By (16)