DNA Barcoding of Calanoid Copepods from the Gulf of California

  • Juan Ramon Beltrán-Castro
  • Sergio Hernández-TrujilloEmail author


The diversity of pelagic copepods was studied in different sites around the Gulf of California, to confirm their morphological identification with of CO1 gen analysis. This is the first study of its kind for the Gulf of California and we report the results of 101 barcode sequences for 27 species of copepods. The separation of species based on morphological characters was very clear for most species and consistent with the formation of genetic groups obtained with the CO1 gene and its corresponding barcode without overlap between the sequences, thus becoming the initial records a database of genetic sequences for the area.


Gulf of California Calanoid copepods Barcoding Cytochrome Oxidase 1 Marine zooplankton 



To the Instituto Politécnico Nacional and Centro Interdisciplinario de Ciencias Marinas by funding SIP20110224, 20120950 and 20130752 projects. Thank to Dr. Jaime Gómez by providing access to zooplankton samples from Islas Marias and Gulf of California. Thank the node Chetumal of Laboratorio Nacional de Código de Barras, especially Dr. Manuel Elias Gutierrez and MC Areli M. Arce for support in the processing of DNA extraction. To mexican Barcode iniciative by financially supporting the authors in obtaining results and their disclosure. Authors are thankful to BEIFI Programme, EDI and COFAA-IPN by grants received.


  1. Aceves-Medina G, Esqueda-Escárcega GM, Pacheco-Chávez R, Zárate-Villafranco A, Hernández-Alonso JR, Hernández-Trujillo S (2007) Cambios diarios en la composición y abundancia de copépodos planctónicos al sur de Bahía de La Paz (Octubre 2002). Hidrobiológica 17(2):185–188Google Scholar
  2. Beltrán-Castro R (2014) Diversidad de copépodos pontélidos (Copepoda: Calanoida: Pontellidae) en el Golfo de California y el valor taxonómico de un estudio con Citocromo c Oxidasa 1 (CO1). Master thesis, CICIMAR-IPN, La Paz, BCS, Mexico, p 80Google Scholar
  3. Blanco-Bercial L, Cornils A, Copley N, Bucklin A (2014) DNA barcoding of marine copepods: assessment of analytical approaches to species identification. PLOS Curr Tree Life. doi: 10.1371/currents.tol.cdf8b74881f87e3b01d56b43791626d2 Google Scholar
  4. Blanco-Bercial L, Álvarez-Marqués F, Bucklin A (2011) Comparative phylogeography and connectivity of sibling species of the marine copepod Clausocalanus (Calanoida). J Exp Mar Biol Ecol 404:108–115CrossRefGoogle Scholar
  5. Brinton E, Fleminger A, Siegel-Causey D (1986) The temperate and tropical planktonic biotas of the Gulf of California. CalCOFI Rep 27:228–266Google Scholar
  6. Briski E, Cristescu ME, Bailey SA, MacIsaac HJ (2011) Use of DNA barcoding to detect invertebrate invasive species from diapausing eggs. Biol Invasions 13:1325–1340CrossRefGoogle Scholar
  7. Brown B, Emberson RM, Paterson AM (1999) Mitochondrial COI and II provide useful markers for Wiseana (Lepidoptera: Hepialidae) species identification. Bull Entomol Res 89:287–293CrossRefGoogle Scholar
  8. Bucklin A, Bentley AM, Franzen SP (1998) Distribution and relative abundance of the copepods, Pseudocalanus moultoni and P. newmani, on Georges Bank based on molecular identification of sibling species. Mar Biol 132:97–106CrossRefGoogle Scholar
  9. Bucklin A, Frost BW, Bradford-Grieve J, Allen LD, Copley NJ (2003) Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae. Mar Biol 142:333–343Google Scholar
  10. Bucklin A, Hopcroft RR, Kosobokova KN, Nigro LM, Ortman BD, Jennings RM, Sweetman CJ (2010a) DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition. Deep-Sea Res II 57:40–48. doi: 10.1016/j.dsr2.2009.08.005 Google Scholar
  11. Bucklin A, Ortman BD, Jennings RM, Nigro LM, Sweetman CJ, Copley NJ, Sutton T, Wiebe PH (2010b) A ‘‘Rosetta Stone” for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean). Deep-Sea Res II 57:2234–2247. doi: 10.1016/j.dsr2.2010.09.025 Google Scholar
  12. Bucklin A, Wibe PH, Smolenack SB, Copley NJ, Beaudet JG, Bonner KG, Farber-Lorda J, Pierson JJ (2007) DNA Barcodes for species identification of euphausiids (Euphausiacea, Crustacea). J Plankton Res 29:483–493CrossRefGoogle Scholar
  13. Böttger-Schnack R, Machida RJ (2011) Comparison of morphological and molecular traits for species identification and taxonomic grouping of oncaeid copepods. Hidrobiologia 666:111–125CrossRefGoogle Scholar
  14. Camacho AI, Rey I, Dorda BA (2011) Identifying cryptic speciation across ground wáter populations: first COI sequences of Bathynellidae (Crustacea, Syncarida). Graellsia. doi: 10.3989/graellsia.2011.v67.031 Google Scholar
  15. Costa FO, deWaard JR, Boutillier J, Ratnasingham S, Dooh RT, Hajibabaei M, Hebert PDN (2007) Biological identifications through DNA barcodes: the case of the Crustacea. Can J Fish Aquat Sci 64:272–295CrossRefGoogle Scholar
  16. Davolos D, Maclean N (2005) Mitochondrial COI-NC-COII sequences in talitrid amphipods (Crustacea). Nature 94:81–86Google Scholar
  17. Elías-Gutiérrez M, Martínez FJ, Ivanova NV, Valdez-Moreno M, Hebert PDN (2008) DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries. Zootaxa 1839:1–42Google Scholar
  18. Elías–Gutiérrez M, Valdez-Moreno M (2008a) A new cryptic species of Leberis Smirnov, 1989 (Crustacea, Cladocera, Chydoridae) from the Mexican semi-desert region, highlighted by DNA barcoding. Hidrobiológica 18(1):63–74Google Scholar
  19. Elías-Gutiérrez M, Valdez-Moreno M (2008b) Código de barras, una alternativa para estudiar la biodiversidad. Ciencia y Desarrollo 34(218):60–67Google Scholar
  20. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3(5):294–299Google Scholar
  21. Gollner S, Fontaneto D, Martínez-Arbizu P (2011) Molecular taxonomy confirms morphological classification of deep-sea hydrothermal vent copepods (Dirivultidae) and suggests broad physiological tolerance of species and frequent dispersal along ridges. Mar Biol 158:221–231CrossRefGoogle Scholar
  22. González-Navarro E, Saldierna-Martínez R (1997) Zooplancton de la Bahía de La Paz. In: Ramírez JU, Rodríguez MR (eds) La Bahía de La Paz, investigación y conservación. UABCS-CICIMAR-SCRIPPS, La Paz, pp 43–57Google Scholar
  23. Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, Hebert PDN (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Mol Ecol Notes 6(4):959–964CrossRefGoogle Scholar
  24. Hajibabaei M, Singer GAC, Clare EL, Hebert PDN (2007) Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biology 5:24. doi: 10.1186/1741-7007-5-24
  25. Hebert PA, Cywinska SLB, de Waard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–322CrossRefGoogle Scholar
  26. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2(10):e312. doi: 10.1371/journal.pbio.0020312 PubMedPubMedCentralCrossRefGoogle Scholar
  27. Hernández-Trujillo S, Esqueda-Escárcega GM (2002) La diversidad de copépodos marinos en México. Oceánides 17(1):57–68Google Scholar
  28. Hernández-Trujillo S, Esquivel-Herrera A (1989) Los copépodos y quetognatos del Golfo de California en la primavera de 1985. Inv Mar CICIMAR 4(2):151–164Google Scholar
  29. Hill RS, Allen LD, Bucklin A (2001) Multiplexed species-specific PCR protocol to discriminate four N. Atlantic Calanus species, with an mtCOI gene tree for ten Calanus species. Mar Biol 139:279–287CrossRefGoogle Scholar
  30. Kurtzman CP (1985) Molecular taxonomy on the fungi. In: Bennett W, Lasure LL (eds) Gene manipulation in fungi, pp 35–63Google Scholar
  31. Lavaniegos-Espejo B, González-Navarro E (1999) Cambios en la comunidad de copépodos durante el ENSO 1992–93 en el Canal de San Lorenzo, Golfo de California. Ciencias Marinas 25(2):239–265Google Scholar
  32. Machida R, Hashiguchi Y, Nishida M, Nishida S (2009) Zooplankton diversity analysis through single-gene sequencing of a community sample. BMC Genom 10:438CrossRefGoogle Scholar
  33. Matz MV, Nielsen R (2005) A likelihood ratio test for species membership based on DNA sequence data. Philos Trans R Soc Lond B Biol Sci 360:1969–1974. doi: 10.1098/rstb.2005.1728 PubMedPubMedCentralCrossRefGoogle Scholar
  34. Palomares R (1996) Estructura espacial y variación estacional de los copépodos en la Ensenada de La Paz. Oceánides 11(1):29–43Google Scholar
  35. Radulovici AE, Archambault P, Dufresne F (2010) DNA barcodes for marine biodiversity: moving fast forward? Diversity 2:450–472. doi: 10.3390/d2040450 CrossRefGoogle Scholar
  36. Ratnasingham S, Hebert PDN (2007) Barcoding bold: the barcode of life data system. Mol Ecol Notes.
  37. Raupach M, Astrin JJJ, Hannig K, Peters MK, Stoeckle MY, Wägele J-W (2010) Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes. Front Zool 7:26PubMedPubMedCentralCrossRefGoogle Scholar
  38. Razouls C, de Bovée F, Kouwenberg J, Desreumaux N (2011) 2005–2011 Diversity and geographic distribution of marine planktonic copepods. Accessed 7 Sept 2011
  39. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739Google Scholar
  40. Trewick SA (2000) Mitochondrial DNA sequences support allozyme evidence for cryptic radiation of New Zealand Peripatoides (Onychophora). Mol Ecol 9:269–281PubMedCrossRefGoogle Scholar
  41. Trivedi S, Affan R, Alessa AHA et al (2014) DNA barcoding of Red Sea fishes from Saudi Arabia—the first approach. DNA Barcodes 2:17–20.
  42. Unal E, Frost BW, Armbrust V, Kideys AE (2006) Phylogeography of Calanushelgolandicus and the Black Sea copepod Calanuseuxinus, with notes on Pseudocalanuselongatus (Copepoda, Calanoida). Deep-Sea Res II 53:1961–1975CrossRefGoogle Scholar
  43. Wilson K, Thorndyke M, Nilsen F, Rogers A, Martínez P (1995) Marine systems: moving into the genomics era. Mar Ecol 26:3–16. doi: 10.1111/j.1439-0485.2005.00041.x CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Juan Ramon Beltrán-Castro
    • 1
  • Sergio Hernández-Trujillo
    • 1
    Email author
  1. 1.Instituto Politécnico Nacional.CICIMARLa PazMexico

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