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Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatan Peninsula, Mexico: potential in fisheries management

Martha Valdez-Moreno A C , Lourdes Vásquez-Yeomans A , Manuel Elías-Gutiérrez A , Natalia V. Ivanova B and Paul D. N. Hebert B
+ Author Affiliations
- Author Affiliations

A El Colegio de la Frontera Sur, Avenida Centenario km 5.5, Chetumal 77014, Quintana Roo, México.

B Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.

C Corresponding author. Email:

Marine and Freshwater Research 61(6) 655-671
Submitted: 7 September 2009  Accepted: 11 December 2009   Published: 25 June 2010


Barcoding has proven a useful tool in the rapid identification of all life stages of fish species. Such information is of critical importance for fisheries management and conservation, especially in high-diversity regions, such as Mexico’s marine waters, where more than 2200 species occur. The present study reports the barcode analysis of 1392 specimens from the Yucatan Peninsula, corresponding to 610 adults and juveniles, 757 larvae and 25 eggs, representing 181 species (179 teleosts and 2 rays), 136 genera and 74 families. Barcoding results revealed major range extensions and overlooked taxa, including three sympatric species of Albula (one likely undescribed) and a new taxon of Floridichthys. In total, six species of eggs and 34 species of larvae were identified through their barcode match with adults. These cases enabled the first discrimination of the larvae of four species of Eucinostomus, and new information about spawning locality and time was obtained from egg records for the hogfish, Lachnolaimus maximus, which is one of the most commercially important species in the Mexican Caribbean. Also, barcodes revealed mistakes in species recognition during a sport-fish contest. In the future, barcodes will help avoid similar errors and protect rare or endangered species, and will aid regulation of fisheries quotas.

Additional keywords: COI, coxI, Cytochrome c oxidase, identification, mitochondrial DNA.


We thank Carolina Quintal Lizama and Dalia Cazarez for their dedicated work as collectors and parataxonomists. Roberto Herrera and José Angel Cohuo also assisted in field collections. Most specimen photographs were taken by Humberto Bahena Basave and José Angel Cohuo. Juan Jacobo Schmitter Soto assisted with the identification of adult fish, while Maria Eugenia Vega and Víctor García from CINVESTAV Mérida kindly donated specimens from the Yucatan coast and helped with their identification. Margarita Ornelas and Uriel Ordóñez from CINVESTAV aided with some larval identifications. Part of this work was carried out during a sabbatical leave of Martha Valdez-Moreno and Manuel Elías-Gutiérrez at the Department of Integrative Biology, University of Guelph. We thank all members of this Department, especially Tyler Zemlak, Dirk Steinke and Gregory Downs, for discussions about molecular techniques. NOAA/UM project 517/04 supported the larval collections, while María del Carmen García, director of the National Park ‘Arrecifes de Xcalak’, assisted with the permits required to work in this area. All of the larval collections comprise part of the Ph.D. Thesis of Lourdes Vásquez-Yeomans, supported by the Consejo Nacional de Ciencia y Tecnología (CONACYT Grant 38516). DNA sequencing was carried out at the Biodiversity Institute of Ontario, University of Guelph, supported by grants to PDNH from Genome Canada through the Ontario Genomics Institute, and from NSERC. Part of this work was supported through Grant HE009 from Comisión Nacional Para el Uso y Conservación de la Biodiversidad (CONABIO). This paper represents a contribution from the Mexican Barcode of Life (MEXBOL) network. Comments from two anonymous referees improved the initial draft of this manuscript.


Adams A. J. , Wolfe R. K. , Tringali M. D. , Wallace E. , and Kellison G. T. (2007). Rethinking the status of Albula spp. biology in the Caribbean and western Atlantic. In ‘The Biology and Management of the World Tarpon and Bonefish Fisheries’. (Ed. J. S. Ault.) pp. 203–214. (CRC Press: Boca Raton, FL.)

Ault J. S. , Humston R. , Larkin M. F. , Perusquia E. , Farmer N. A. , et al. (2007). Population dynamics and resource ecology of Atlantic tarpon and bonefish. In ‘The Biology and Management of the World Tarpon and Bonefish Fisheries’. (Ed. J. S. Ault.) pp. 215–256. (CRC Press: Boca Raton, FL.)

Baldwin, C. C. , Mounts, J. H. , Smith, D. G. , and Weigt, L. A. (2009). Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with comments on identification of adult Phaeoptyx.  Zootaxa 2008, 1–22.

Bowen B. W. , Karl S. A. , and Pfeiler E. (2007). Resolving evolutionary lineages and taxonomy of bonefishes (Albula spp.). In ‘The Biology and Management of the World Tarpon and Bonefish Fisheries’. (Ed. J. S. Ault.) pp. 147–154. (CRC Press: Boca Raton, FL.)

Carrillo, L. , Vásquez-Yeomans, L. , and de Jesús Navarrete, A. (2008). La incierta vida de las larvas marinas. Ecofronteras 34, 18–20.

Castro-Aguirre J. L. , Espinosa-Pérez H. , and Schmitter-Soto J. J. (1999). ‘Ictiofauna Estuarina Lagunar y Vicaria de México.’ (Noriega–Limusa/IPN: México, D.F.)

Colborn, J. , Crabtree, R. E. , Shaklee, J. B. , Pfeiler, E. , and Bowen, B. W. (2001). The evolutionary enigma of bonefishes (Albula spp.): cryptic species and ancient separations in a globally distributed shorefish. Evolution 55, 807–820.
CrossRef | CAS | PubMed |

Danylchuk, S. , Danylchuk, A. J. , Cooke, S. J. , Goldberg, T. L. , Koppelman, J. , and Philipp, D. P. (2007). Effects of recreational angling on the post-release behavior and predation of bonefish (Albula vulpes): the role of equilibrium at the time of release. Journal of Experimental Marine Biology and Ecology 346, 127–133.
CrossRef |

Escobar-Fernández R. , and Siri M. (1997). ‘Nombres Vernáculos y Científicos de los Peces del Pacífico Mexicano.’ (Universidad Autónoma de Baja California, Instituto de Investigaciones Oceanológicas, Sociedad Ictiológica Mexicana, A.C.: México.)

Fahay M. P. (2007). ‘Early Stages of Fishes in the Western North Atlantic Ocean (Davis Strait, Southern Greenland and Flemish Cap to Cape Hatteras).’ (Northwest Atlantic Fisheries Organization: Nova Scotia, Canada.)

Floeter, S. R. , Rocha, L. A. , Robertson, D. R. , Joyeux, J. C. , and Smith-Vaniz, W. F. , et al. (2008). Atlantic reef fish biogeography and evolution. Journal of Biogeography 35, 22–47.

Fox, C. J. , Taylor, M. I. , Pereyra, R. , Villasana, M. I. , and Rico, C. (2005). TaqMan DNA technology confirms likely overestimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg-based methods. Molecular Ecology 14, 879–884.
CrossRef | CAS | PubMed |

Froese R. , and Pauly D. (2006). FishBase. Available at [accessed August 2009].

Gregory, T. R. (2005). DNA barcoding does not compete with taxonomy. Nature 434, 1067.
CrossRef | CAS |

Hajibabaei, M. , deWaard, J. R. , Ivanova, N. V. , Ratnasingham, S. , Dooh, R. T. , Kirk, S. L. , Mackie, P. M. , and Hebert, P. D. N. (2005). Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360, 1959–1967.
CrossRef | CAS | PubMed |

Hidaka, K. , Iwatsuki, Y. , and Randall, J. E. (2008). A review of the Indo-Pacific bonefishes of the Albula argentea complex, with a description of a new species. Ichthylogical Research 55, 53–64.
CrossRef |

Ivanova, N. V. , de Waard, J. R. , and Hebert, P. D. N. (2006). An inexpensive, automation-friendly protocol for recovering high-quality DNA. Molecular Ecology Notes 6, 998–1002.
CrossRef | CAS |

Ivanova, N. V. , Zemlak, T. S. , Hanner, R. H. , and Hebert, P. D. N. (2007). Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7, 544–548.
CrossRef | CAS |

Jiménez-Rosenberg, S. P. A. , González-Navarro, E. A. , and Saldierna-Martínez, R. J. (2006). Larval, prejuvenile and juvenile development of Eucinostomus currani.  Journal of Fish Biology 69, 28–37.
CrossRef |

Kendall, A. W. , and Matarese, A. C. (1994). Status of early life history descriptions of marine teleosts. Fishery Bulletin 92, 725–736.

Kimura, M. (1980). A simple method of estimating evolutionary rate of base substitutions through comparative studies. Journal of Molecular Evolution 16, 111–120.
CrossRef | CAS | PubMed |

Lavett, S. C. , Tyler, J. C. , Davis, P. W. , Jones, S. R. , Smith, G. D. , and Baldwin, C. A. (2003). Fishes of the Pelican Cays, Belize. Atoll Research Bulletin 497, 1–88.

Leis J. M. , and Carson-Ewart B. M. (2000). ‘The Larvae of Indo-Pacific Coastal Fishes: An Identification Guide to Marine Fish Larvae.’ (Brill: Leiden, The Netherlands.)

McBride, R. H. , and Horodysky, A. J. (2004). Mechanisms maintaining sympatric distributions of two ladyfish (Elopidae: Elops) morphs in the Gulf of Mexico and western North Atlantic Ocean. Limnology and Oceanography 49, 1173–1181.

Mojica, R. , Shenker, J. M. , Harnden, C. W. , and Wagner, D. E. (1995). Recruitment of bonefish, Albula vulpes around Lee Stocking Island, Bahamas. Fishery Bulletin 93, 666–674.

Moser H. G. (1996). ‘The Early Stages of Fishes in the California Current.’ (CALCOFI Atlas: La Jolla, CA.)

Moura, T. , Silva, M. C. , Figueiredo, I. , Neves, A. , Muñoz, P. D. , Coelho, M. M. , and Gordo, L. S. (2008). Molecular barcoding of north-east Atlantic deep-water sharks: species identification and application to fisheries management and conservation. Marine and Freshwater Research 59, 214–223.
CrossRef | CAS |

Nelson J. S. (2006). ‘Fishes of the World.’ 3rd edn. (J. Wiley and Sons: New York.)

Pegg, G. G. , Sinclair, B. , Briskey, L. , and Aspden, W. J. (2006). MtDNA barcode identification of fish larvae in the southern Great Barrier Reef, Australia. Scientia Marina 70, 7–12.
CrossRef | CAS |

Pfeiler, E. (2008). Resurrection of the name Albula pacifica (Beebe, 1942) for the shafted bonefish (Albuliformes: Albulidae) from the eastern Pacific. Revista de Biologia Tropical 56, 839–844.
PubMed |

Pfeiler, E. , Bitler, B. G. , Ulloa, R. , van der Heiden, A. M. , and Hastings, P. A. (2008). Molecular identification of the bonefish Albula esuncula (Albuliformes: Albulidae) from the tropical eastern Pacific, with comments on distribution and morphology. Copeia 2008, 763–770.
CrossRef |

Powell A. B. , and Greene M. D. (2006). Gerreidae: Mojarras. In ‘Early Stages of Atlantic Fishes: An Identification Guide for Western Central North Atlantic’. (Ed. W. J. Richards.) pp. 1591–1596. (CRC Press: Boca Raton, FL.)

Quiroz-Vázquez, P. , and Elías-Gutiérrez, M. (2009). A new species of the freshwater cladoceran genus Scapholeberis Schoedler, 1858 (Cladocera: Anomopoda) from the semidesert northern Mexico, highlighted by DNA barcoding. Zootaxa 2236, 50–64.

Ratnasingham, S. , and Hebert, P. D. N. (2007). BOLD: the barcode of life data system ( Molecular Ecology Notes 7, 355–364.
CrossRef | CAS | PubMed |

Richards, W. J. (1985). Status of the identification of the early life stages of fishes. Bulletin of Marine Science 37, 756–760.

Richards W. J. (2006). ‘Early Stages of Atlantic Fishes: An Identification Guide for Western Central North Atlantic.’ (Taylor and Francis: Boca Raton, FL.)

Rivas, L. R. , and Warlen, M. (1967). Systematics and biology of the bonefish, Albula nemoptera (Fowler). US Fishery Bulletin 66, 251–258.

Rock, J. , Costa, F. O. , Walker, D. I. , North, A. W. , Hutchinson, W. F. , and Carvalho, G. R. (2008). DNA barcodes of fish of the Scotia Sea, Antarctica, indicate priority groups for taxonomic and systematics focus. Antarctic Science 20, 253–262.
CrossRef |

Saitou, N. , and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406–425.
CAS | PubMed |

Schlei, O. L. , Crete-Lafreniere, A. , Whiteley, A. R. , Brown, R. J. , Olsen, J. B. , Bernatchez, L. , and Wenburg, J. K. (2008). DNA barcoding of eight North American coregonine species. Molecular Ecology Resources 8, 1212–1218.
CrossRef | CAS |

Schmitter-Soto J. J. (1998). ‘Catálogo de los Peces Continentales de Quintana Roo.’ (El Colegio de la Frontera Sur: San Cristóbal de las Casas, México.)

Schmitter-Soto, J. J. , Vásquez-Yeomans, L. , Aguilar-Pereira, A. , Curiel-Mondragón, C. , and Caballero Vázquez, J. A. (2000). Lista de peces marinos del Caribe mexicano. Anales del Instituto de Biología Serie Zoología 71, 143–177.

Schmitter-Soto J. J. , Vásquez-Yeomans L. , Pimentel-Cadena E. , Herrera-Pavón R. , Paz G. , and García-Téllez N. (2009). In ‘El sistema ecológico de la bahía de Chetumal/Corozal: Costa occidental del Mar Caribe (2009)’. (Eds J. Espinoza, G. Islebe and H. Hernández.) pp. 102–114. (ECOSUR: Chetumal, Mexico.)

Shaklee, J. B. , and Tamaru, C. S. (1981). Biochemical and morphological evolution of Hawaiian bonefishes (Albula). Systematic Zoology 30, 125–146.
CrossRef |

Smith D. G. (1989). Order Elopiformes; Families Elopidae, Megalopidae, and Albulidae: Leptocephali. In ‘Fishes of the Western North Atlantic’. (Ed. E. B. Böhlke.) pp. 961–972. (Allen Press: Lawrence, KS.)

Smith, D. G. (1995). Preservation of color in larval fishes. American Society Ichthyology and Herpetetology Curation Newsletter 11, 5–6.

Smith, P. J. , Steinke, D. , Stewart, A. L. , Mcveagh, S. M. , Stewart, A. L. , Struthers, C. D. , and Roberts, C. D. (2008). Molecular analysis of Southern Ocean skates (Bathyraja) reveals a new species of Antarctic skate. Journal of Fish Biology 73, 1170–1182.
CrossRef | CAS |

Sponaugle, S. , Cowen, R. K. , Shanks, A. , Morgan, S. G. , and Leis, J. M. , et al. (2002). Predicting self-recruitment in marine populations: biophysical correlates and mechanisms. Bulletin of Marine Science 70, 341–375.

Steinke, D. , Zemlak, T. S. , and Hebert, P. D. N. (2009). Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS ONE 4, e6300.
CrossRef | PubMed |

Teletchea, F. (2009). Molecular identification methods of fish species: reassessment and possible applications. Reviews in Fish Biology and Fisheries 19, 265–293.
CrossRef |

Valdez-Moreno, M. , Ivanova, N. V. , Elías-Gutiérrez, M. , Contreras-Balderas, S. , and Hebert, P. D. N. (2009). Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes. Journal of Fish Biology 74, 377–402.
CrossRef | CAS |

Vásquez-Yeomans, L. , Sosa-Cordero, E. , Lara, M. , Adams, A. , and Cohuo, J. A. (2009). Patterns of distribution and abundance of bonefish larvae Albula spp. (Albulidae) in the western Caribbean and adjacent areas. Ichthylogical Research 56, 266–275.
CrossRef |

Victor, B. C. (2007). Coryphopterus kuna, a new goby (Perciformes: Gobiidae: Gobiinae) from the western Caribbean, with the identification of the late larval stage and an estimate of the pelagic larval duration. Zootaxa 1526, 51–61.

Victor, B. C. (2008). Redescription of Coryphopterus tortugae (Jordan) and a new allied species Coryphopterus bol (Perciformes: Gobiidae: Gobiinae) from the tropical western Atlantic Ocean. Journal of the Ocean Science Foundation 1, 1–19.

Victor, B. C. , Hanner, R. , Shivji, M. , Hyde, J. , and Caldow, C. (2009). Identification of the larval and juvenile stages of the cubera snapper, Lutjanus cyanopterus, using DNA barcoding. Zootaxa 2215, 24–36.

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.
CrossRef | CAS | PubMed |

Ward, R. D. , Costa, F. O. , Holmes, B. H. , and Steinke, D. (2008a). DNA barcoding of shared fish species from the North Atlantic and Australasia: minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species. Aquatic Biology 3, 71–78.
CrossRef |

Ward, R. D. , Holmes, B. H. , White, W. T. , and Last, P. R. (2008b). DNA barcoding Australasian chondrichthyans: results and potential uses in conservation. Marine and Freshwater Research 59, 57–71.
CrossRef | CAS |

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.
CrossRef | CAS |

Webb, K. E. , Barnes, D. K. A. , Clark, M. S. , and Bowden, D. A. (2006). DNA barcoding: a molecular tool to identify Antarctic marine larvae. Deep-Sea Research. Part II, Topical Studies in Oceanography 53, 1053–1060.
CrossRef | CAS |

Wong, E. H. K. , and Hanner, R. H. (2008). DNA barcoding detects market substitution in North American seafood. Food Research International 41, 828–837.
CrossRef | CAS |

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.
CrossRef | CAS |

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