A test of the utility of DNA barcoding in the radiation of the freshwater stingray genus Potamotrygon (Potamotrygonidae, Myliobatiformes)

Genetics and Molecular Biology

Volumn 31, Issue 1 SUPPL. 1, 2008, Pages 324-336

  Toffoli, Daniel ^a   Hrbek, Tomas ^a,b   de Araújo, Maria Lúcia Góes ^a   de Almeida, Maurício Pinto ^c   Charvet Almeida, Patricia ^d   Farias, Izeni Pires ^a  

^a FEDERAL UNIVERSITY OF AMAZONAS   (Brazil)

^b UNIVERSITY OF PUERTO RICO   (Puerto Rico)

^c FEDERAL UNIVERSITY OF PARÁ   (Brazil)

^d FEDERAL UNIVERSITY OF PARAÍBA   (Brazil)

Author keywords

Barcoding; COI; mtDNA; Phylogenetics; Potamotrygon; Radiation

Indexed keywords

CYTOCHROME C OXIDASE; CYTOCHROME C OXIDASE 1;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DNA BARCODING; DNA SEQUENCE; FISH; FISH GENETICS; FRESHWATER SPECIES; GENETIC DISTANCE; HAPLOTYPE; MYLIOBATIFORMES; NEW GENUS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POTAMOTRYGON; POTAMOTRYGON MOTORO; POTAMOTRYGON ORBIGNYI; POTAMOTRYGON SCOBINA; POTAMOTRYGONIDAE; SPECIES DIFFERENTIATION; STINGRAY; TAXONOMY;

MYLIOBATIFORMES; POTAMOTRYGON; POTAMOTRYGON MOTORO; POTAMOTRYGON ORBIGNYI; POTAMOTRYGONIDAE;

EID: 46649119311     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/s1415-47572008000200028     Document Type: Article

References (74)

1. Achenbach GM and Acbenbach SVM (1976) Notas acerca de algunas especies de raya fluvial (Batoidei, Potamotrygonidae), que frecuentam el sistema hidrografico del Rio Parana medioen el departamento La Capital. Com Mus Prov Cien Nat "Florentino Ameghino" 8:3-34.
2. Almeida MP (2003) Pesca, policromatismo e aspectos sistemáticos de Potamotrygon scobina, Garman 1913 (Chondrichthyes, Potamotrygonidae) da região da Ilha de Colares da IIha de Marajó, Pará. M.Sc. Thesis, Universidade Federal do Pará and Museu Paraense Emílio Goeldi, Belém.
3. Araújo MLG (1998) Biologia reprodutiva e pesca de Potamotrygon sp. C (Chondrichthyes, Potamotrygonidae), no médio rio Negro, Amazonas. M.Sc. Thesis, Universidade Federal do Amazonas and Instituto Nacional de Pesquisas da Amazônia, Manaus.
4. Avise JC (1990) Flocks of African fishes. Nature 347:512-513.
5. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, 384 pp.
6. Baldwin BG and Sanderson MJ (1998) Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc Natl Acad Sci USA 95:9402-9406.
7. Bromham L, Rambaut A, Fortey R, Cooper A and Penny D (1998) Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proc Natl Acad Sci USA 95:12386-12389.
8. Cameron S, Rubinoff D and Will K (2006) Who will actually use DNA barcoding andwhatwill it cost? Syst Biol 55:844-847.
9. Carvalho MR (2001) Review of: Freshwater Stingrays from South America. Copeia 4:1167-1169.
10. Carvalho MR, Lovejoy NR and Rosa RS (2003) Family Potamotrygonidae (river stingrays). In: Reis RE, Kullander SO and Ferraris CJ (eds) Check List of the Freshwater Fishes of South and Central America. EDIPUCRS, Porto Alegre, pp 22-28.
11. Castex MN (1964) Estado actual de los estudios sobre la raya fluvial neotropical. In: Cincuentenario del Museo Provincial de Ciencias Naturales "Florentino Ameghino". Museo Provincial de Ciencias Naturales "Florentino Ameghino", Santa Fé, pp 9-49.
12. Castex MN, Maciel I and Achenbach GM (1963) Acerca de la raya fluvial P. labradori. Neotropica 9:117-121.
13. Charvet-Almeida P (2001) Ocorrência, biologia e uso das raias de água doce na baía de Marajó (Pará, Brasil), com ênfase na biologia de Plesiotrygon iwamae (Chondrichthyes, Potamotrygonidae). MSc Thesis, Universidade Federal do Pará and Museu Paraense Emílio Goeldi, Belém.
14. Charvet-Almeida P (2006) Historia natural e conservação das raias de água doce (Chondrichthyes, Potamotrygonidae) no médio Rio Xingu, área de influência do projeto hidrelétrico de Belo Monte (Pará, Brasil). PhD Thesis, Universidade Federal da Paraíba.
15. Charvet-Almeida P (2004) Sub-Estudo Elasmobrânquios. Relatório Técnico agosto de 2004. Estudo Estratégico n. 8, Bases Científicas para a Conservação da Várzea: Identificação e Caracterização de Zonas Biogeográficas. Pro Várzea/IBA-MA, Manaus.
16. Conway-Morris S (1999) The Crucible of Creation: The Burgess Shale and the Rise of Animals. Oxford University Press, New York, 276 pp.
17. Coyne JA and Orr HA (2004) Speciation. Sinauer Associates, Inc., Sunderland, 545 pp.
18. DeSalle R (2006) Species discovery vs. species identification in DNA barcoding efforts: Response to Rubinoff. Conserv Biol 20:1545-1547.
19. Duda Jr TF and Rolán E (2005) Explosive radiation of Cape Verde Conus, a marine species flock. Mol Ecol 14:267-272.
20. Dunn KA, McEachran JD and Honeycutt RL (2003) Molecular phylogenetics of myliobatiform fishes (Chondrichthyes, Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood. Mol Phylogenet Evol 27:259-270.
21. Funk DJ and Omland KE (2003) Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Syst34:397-423.
22. García-Moreno J and Mindell DP (2000) Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): A case study using avian CHD. Mol Biol Evol 17:1826-1832.
23. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W and Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci USA 103:968-971.
24. Hall T (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
25. Hebert PDN, Cywinska A, Ball SL and deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc London B 270:313-321.
26. Hebert PDN, Stoeckle MY, Zemlak TS and Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:1657-1663.
27. Hey J (2001) Genes, Categories and Species: The Evolutionary and Cognitive Causes of the Species Problem. Oxford University Press, New York, 217 pp.
28. Hillis DM, Huselsenbeck JP and Cunningham CW (1994) Application and accuracy of molecular phylogenies. Science 264:671-677.
29. Hrbek T, Keivany Y and Coad BW (2006) New species of Aphanius (Teleostei, Cyprinodontidae) from Isfahan province of Iran and a reanalysis of other Iranian species. Copeia 2006:244-255.
30. Huelsenbeck JP and Hillis DM (1993) Success of phylogenetic methods in the four-taxon case. Syst Biol 42:247-264.
31. Huelsenbeck JP and Rannala B (1997) Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276:227-232.
32. Jackman TR, Larson A, de Queiroz K and Losos JB (1999) Phylogenetic relationships and tempo of early diversification in Anolis lizards. Syst Biol 48:254-285.
33. Johnson NK and Cicero C (2004) New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds. Evolution 58:1122-1130.
34. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120.
35. Kishino H and Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170-179.
36. Kishino H, Miyata T and Hasegawa M (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol 30:151-160.
37. Kumar S and Gadagkar SR (2000) Efficiency of the neighbour-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. J Mol Evol 51:544-553.
38. Kumar S, Tamura K and Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings Bioinfor 5:150-163.
39. Li W-H (1997) Molecular Evolution. Sinauer Associates, Sunderland, 487 pp.
40. Lovejoy NR (1996) Systematics of myliobatoid elasmobranchs: With emphasis on the phylogeny and historical biogeography of neotropical freshwater stingrays (Potamotrygonidae, Rajiformes). Zool J Linn Soc 117:207-257.
41. Lovejoy NR, Bermingham E and Martin AP (1998) Marine incursion into South America. Nature 396:421-422.
42. Marques FPL (2000) Evolution of neotropical freshwater stingrays and their parasites: Taking into account space and time. Ph.D. Thesis, University of Toronto, Toronto.
43. McDonald JH and Kreitman M (1991) Adaptive protein evolution at Adh locas in Drosophila. Nature 351:652-654.
44. McEachran JD, Dunn KA and Miyake T (1996) Interrelationships within the batoid fishes (Chondrichthyes, Batoidea). In: Stiassny MLJ, Parenti LR and Johnson GD (eds) Interrelationship of Fishes. Academic Press, New York, pp 63-84.
45. Meyer CP and Paulay G (2005) DNA barcoding: Error rates based on comprehensive sampling. PLoS Biol 3:2229-2238.
46. Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC and Yuri T (1999) Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst Biol 48:138-152.
47. Moritz C and Cicero C (2004) DNA barcoding: Promises and pitfalls. PLoS Biol 2:1529-1534.
48. Quijada CCD (2003) Relações filogenéticas intergenéricas de raias neotropicais de água doce (Chondricthyies, Potamotrigonidae). M.Sc. Thesis, Universidade Estadual da Paraiba, João Pessoa.
49. Palumbi SR and Benzie J (1991) Large mitochondrial DNA differences between morphologically similar Penaeid shrimp. Mol Mar Biol Biotech 1:27-34.
50. Philippe H, Chenuil A and Adoutte A (1994) Can the Cambrian explosion be inferred through molecular phylogeny? Development 1994(suppl):15-25.
51. Posada D and Crandall KA (1998) MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817-818.
52. Reis RE, Kullander SO and Ferraris CJ (2003) Check List of the Freshwater Fishes of South and Central America. EDIPUCRS, Porto Alegre, 734 pp.
53. Rincon GF (2006) Aspectos taxonômicos, alimentação e reproduçãdo da raia deágua doce Potamotrygon orbignyi (Castetnau) (Elasmobranchii, Potamotrygonidae) no rio Paranã-Tocantins. Ph.D. Thesis, Universidade Estadual Paulista "Julio de Mesquita Filho", Rio Clam.
54. Rodriguez FJ, Oliver JL, Marin A and Medina JR (1990) The general stochastic model of nucleotide substitution. J Theor Biol 142:485-501.
55. Ronquist F and Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
56. Rosa RS (1985) A systematic revision of the South American freshwater stingrays (Chondrichthyes, Potamotrygonidae). Ph.D. Thesis, The College of William and Mary, Williamsburg.
57. Rosa RS and Carvalho MRd (2007) Família Potamotrygonidae. In: Buckup PA, Menezes NA and Ghazzi MSA (eds) Catálogo das Espécies de Peixes de Água Doce do Brasil. Museu Nacional, Rio de Janeiro, pp 17-18.
58. Rozas J, Sánchez-DelBarrio JC, Messenguer X and Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
59. Rubinoff D (2006a) Utility of mitochondrial DNA barcodes in species conservation. Conserv Biol 20:1026-1033.
60. Rubinoff D (2006b) DNA barcoding evolves into the familiar. Conserv Biol 20:1548-1549.
61. Sambrook J, Fritsch EF and Maniatis T (1989) Molecular Cloning: A Laboratory Manual. v. 1. 2nd ed. Cold Springs Harbor Laboratory Press, Cold Springs Harbor.
62. Sanderson M (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol 14:1218-1231.
63. Sanderson MJ (2002) Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol Biol Evol 19:101-109.
64. Schluter D (2000) The Ecology of Adaptive Radiation. Oxford University Press, Oxford, 288 pp.
65. Shimodaira H and Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114-1116.
66. Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), Beta Version 4b10. Sinauer Associates. Sunderland.
67. Thompson JD, Higgins DG and Gibson TJ (1996) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
68. Thorne JL and Kishino H (2002) Divergence time and evolutionary rate estimation with multilocus data. Syst Biol 51:689-702.
69. Thorson TB, Brooks DM and Mayes MA (1983) The evolution of freshwater adaptation in stingrays. Nat Geo Soc Res Reports 15:663-694.
70. Toffoli D (2006) História evolutiva de espécies do gênero Potamotrygon Garman, 1877 (Potamotrygonidae) na Bacia Amazônica. M.Sc. Thesis, Instituto Nacional de Pesquisas da Amazônia and Universidade Federal do Amazonas, Manaus.
71. Turner GF, Seehausen O, Knight ME, Allender CJ and Robinson RL (2001) How many species of cichlid fishes are there in African lakes? Mol Ecol 10:793-806.
72. Verheyen E, Salzburger W, Snoeks J and Meyer A (2003) Origin of the superflock of cichlid fishes from Lake Victoria, East Africa. Science 300:325-329.
73. Vinson C, Gomes G, Schneider H and Sampaio I (2004) Sciaenidae fish of the Caeté River estuary, Northern Brazil: Mitochondrial DNA suggests explosive radiation for the Western Atlantic assemblage. Genet Mol Biol 27:174-180.
74. Ward RD, Zemlak TS, Innes BH, Last PR and Hebert PDN (2005) DNA barcoding Australia's fish species. Phil Trans R Soc Lond B, Biol Sci 360:1-11.