DNA barcoding of Cuban freshwater fishes: Evidence for cryptic species and taxonomic conflicts

Molecular Ecology Resources

Volumn 10, Issue 3, 2010, Pages 421-430

  Lara, Ariagna ^a   Ponce de León, José Luis ^a   Rodríguez, Rodet ^a   Casane, Didier ^b   Côté, Guillaume ^c   Bernatchez, Louis ^c   García Machado, Erik ^a  

^a UNIVERSITY OF HAVANA   (Cuba)

^b CNRS   (France)

^c UNIVERSITÉ LAVAL   (Canada)

Author keywords

COI; DNA barcode; Freshwater fish; Molecular taxonomy

Indexed keywords

GAMBUSIA; PISCES; RIVULUS; RIVULUS CYLINDRACEUS;

EID: 77953080088     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2009.02785.x     Document Type: Article

References (61)

1. Ayala FJ. Vagaries of the molecular clock. Proceedings of the National Academy of Sciences, USA 1997, 94:7776-7783.
2. Barber P, Boyce SL. Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae. Proc. R. Soc. B 2006, 273:2053-2061.
3. Baer CF, Miyamoto MM, Denver DR. Mutation rate variation in multicellular eukaryotes: causes and consequences. Nature Reviews Genetics 2007, 8:619-631.
4. Barus V, Wohlgemuth E. Two proposed subspecies in Girardinus microdactylus (Pisces: Poeciliidae) from isla de Cuba and isla de la Juventud. Folia Zoologica 1994, 43:245-254.
5. Barus V, Liborsvársky J, De la Cruz J. Observations on Limia vittata (Poeciliidae) from Cuba. Folia Zoologica 1980, 29:267-287.
6. Bermingham E, Avise JC. Molecular zoogeograhy of freshwater fishes in the southeastern United States. Genetics 1986, 113:939-963.
7. Bernatchez L, Wilson C. Comparative phylogeography of Neartic and Paleartic fishes. Molecular Ecology 1998, 7:431-452.
8. Blaxter ML. The promise of a DNA taxonomy. Phil. Trans. R. Soc. Lond. B 2004, 359:669-679.
9. Blaxter M, Mann J, Chapman T, Thomas F, Whitton C, Floyd R, Abebe E. Defining operational taxonomic units using DNA barcode data. Phil. Trans. R. Soc. B 2005, 360:1935-1943.
10. Briggs JC. Freshwater fishes and biogeography of Central America and the Antilles. Systematic Zoology 1984, 33:428-435.
11. Burgess GH, Franz R. Zoogeography of the Antillean freshwater fish fauna. Biogeography of the West Indies: past, present and future 1989, 263-304. Woods CA, In, ed, pp, Sand Hill Crane Press, Gainesville, Florida
12. Caterino MS, Cho S, Sperling FAH. The current state of insect molecular systematics: a thriving tower of babel. Annual Review of Entomology 2000, 45:1-54.
13. Chang YS, Huang FL, Lo TB. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. Journal of Molecular Evolution 1994, 38:138-155.
14. Chown SL, Sinclair BJ, Jansen van Vuuren B. DNA barcoding and the documentation of alien species establishment on sub-Antarctic Marion Island. Polar Biology 2008, 31:651-655.
15. Cognato AI. Standard percent DNA sequence difference for insects does not predict species boundaries. Journal of Economic Entomology 2006, 99:1037-1045.
16. de la Cruz J, Dubitsky AM. Dos nuevas especies de peces dulceacuícolas del género Rivulus, Poey (Cyprinodontidae) de Cuba e Isla de Pinos. Poeyana 1976, 155:1-6. Series A
17. Davis JI, Nixon KC. Populations, genetic variation, and the delimitation of phylogenetic species. Systematic Biology 1992, 41:421-435.
18. DeSalle R. Species discovery versus species identification in DNA barcoding efforts: Response to Rubinoff. Conservation Biology 2006, 20:1545-1547.
19. DeSalle R, Amato G. The expansion of conservation genetics. Nature Reviews Genetics 2004, 5:702-712.
20. DeSalle R, Egan MG, Siddall M. The unholy trinity: taxonomy, species delimitation, and DNA barcoding. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 2005, 360:1905-1916.
21. Doadrio I, Perea S, Alcaraz L, Hernandez N. Molecular phylogeny and biogeography of the Cuban genus Girardinus Poey, 1854 and relationships within the tribe Girardinini (Actinopterygii, Poeciliidae). Molecular Phylogenetics and Evolution 2009, 50:16-30.
22. Eigenmann CH. The fresh-water fishes of western Cuba. Bulletin of the U. S. Fish Commission 1903, 22:211-236.
23. García I, Koldenkova L. Clave pictórica para las principales especies de peces larvívoros de Cuba 1990, Instituto de Medicina Tropical Pedro Courí, Cuba
24. Hajibabaei M, Smith MA, Janzen DH, Rodríguez JJ, Whitfield JB, Hebert PDN. A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes 2006a, 6:959-964.
25. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN. DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl. Acad. Sci. USA 2006b, 103:968-971.
26. Hajibabaei M, Singer GAC, Hickey DA. Benchmarking DNA barcodes: an assessment using available primate sequences. Genome 2006c, 49:851-854.
27. Hall TA. bioedit: a user-friendly biological sequences alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 1999, 41:95-98.
28. Hamilton A. Phylogeny of Limia (Teleostei: Poecilidae) based on NADH dehydrogenase subunit 2 sequences. Molecular Phylogenetics and Evolution 2001, 19:277-289.
29. Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B: Biological Sciences 2003, 270:313-322.
30. Hebert PDN, Cywinska A, Ball SL, deWaard J. Identification of birds through DNA barcodes. PLoS Biol 2004, 2.
31. Hubert N, Hanner R, Holm E. Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE 2008, 3. 2410.1371/journal.pone.0002490, doi
32. Johns GC, Avise JC. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution 1998, 15:1481-1490.
33. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 1980, 15:111-120.
34. Krieger J, Fuerst PA. Evidence for a slowed rate of molecular evolution in the Order Acipenseriformes. Molecular Biology and Evolution 2002, 19:891-897.
35. Lee T, Foighil DO. Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex. Molecular Ecology 2004, 13:3527-3542.
36. Lucinda PHF. Family Poeciliidae. Check List of the Freshwater Fishes 2003, 556-582. Reis REKullander SOFerraris C. In, eds, pp, Porto Alegre, Edipucrs, pp
37. Meyer CP, Paulay G. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 2005, 3:e422.
38. Menéndez Z, Manso E, Castex M, Fuentes O, Hernández N, García I. Algunos aspectos ecológicos de la ictiofauna larvífaga presente en Cayo Santa María, Cuba. Rev. Cubana Med. Trop 2007, 3.
39. Murphy WJ, Thomerson JE, Collier GE. Phylogeny of the Neotropical Killifish Family Rivulidae (Cyprinodontiformes, Aplocheiloidei) inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 1999, 13:289-301.
40. Nelson LA, Wallman JF, Dowton M. Using COI barcodes to identify forensically and medically important blowflies. Medical and Veterinary Entomology 2007, 21:44-52.
41. Pfenninger M, Nowak C, Kley C, Steinke D, Streit B. Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. Molecular Ecology 2007, 16:1957-1968.
42. Rauchenberger M. Systematics and biogeography of the genus Gambusia (Cyprinodontiformes: Poecilidae). American Museum Novitates 1989, 2951:1-74.
43. Rivas LR. Contributions to the study of the Poecilid fishes of Cuba. I. Descriptions of six new species of the subfamily Gambusiinae. Proceedings of the New England Zool. Club 1944, 23:41-53.
44. Rivas LR. The origin, evolution, dispersal and geographical distribution of the Cuban poeciliid fishes of the tribe Girardinini. The American Philisophical Society 1958, 102:281-320.
45. Robins CR, Ray GC. A Field Guide to Atlantic Coast Fishes of North America 1986, Houghton Mifflin Company, Boston, MA, USA, pp
46. Rodríguez J, González E, Hernández N, Capó V, García I. Comparación morfológica e histológica del tubo digestivo de Gambusia puncticulata y Girardinus metallicus, peces utilizados en el control biológico de mosquitos. Rev. Cubana Med. Trop. 2004, 56:73-76.
47. Rosen DE, Bailey RM. Middle-American poeciliid fishes of the genera Carlhubbsia and Phallichthys, with descriptions of two new species. Zoological 1959, 44:1-44.
48. Rosen DE, Bailey RM. The poecilid fishes (Cyprinodontiformes), their structure, zoogeography and systematics. Bulletin of the American Museum of Natural History 1963, 126:1-176.
49. Rubinoff D. Utility of mitochondrial DNA barcodes in species conservation. Conservation Biology 2006, 20:1026-1033.
50. Saitou N, Nei M. The Neighbor-Joining method for reconstructing phylogenetic trees. Molecular Biology and Evolution 1987, 4:406-425.
51. Smith MA, Poyarkov NA, Hebert PDN. CO1 DNA barcoding amphibians: take the chance, meet the challenge. Molecular Ecology Notes 2007, 7:235-246.
52. Stoeckle M. Taxonomy, DNA and the bar code of life. BioScience 2003, 53:2-3.
53. Tamura K, Dudley J, Nei M, Kumar S. mega4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 2007, 24:1596-1599.
54. Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP. A plea for DNA taxonomy. Trends Ecol. Evol. 2003, 18:70-74.
55. Tavares ES, Baker AJ. Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evolutionary Biology 2008, 8:81.
56. Vales MA, Álvarez MA, Montes L, Ávila A. Estudio nacional sobre la diversidad biológica en la República de Cuba 1998, PNUMA, Centro Nacional de Biodiversidad, Instituto de Ecología y Sistemática, CITMA, La Habana, Cuba, pp
57. Vences M, Thomas M, Van der Meijden A, Chiari Y, Vieites DR. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front. Zool. 2005, 2:1-12.
58. Vergara RR. Principales características de la ictiofauna dulceacuícola cubana 1992, Editorial Academia, La Habana, Cuba, pp
59. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. DNA barcoding Australia's fish species. Proceedings of Royal Society, Series B 2005, 360:1847-1857.
60. Waugh J, Huynen L, Millar C, Lambert D. DNA barcoding of animal species - response to DeSalle. BioEssays 2007, 30:92-93.
61. Yancy HF, Zemlak TS, Mason JA, Washington JD, Tenge BJ, Nguyen NL, Barnett JD, Savary WE, Hill WE, Moore MM, Fry FS, Randolph SC, Rogers PL, Hebert PDN. Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia. J. Food Prot. 2008, 71:210-217.