Identifying Canadian freshwater fishes through DNA barcodes

PLoS ONE

Volumn 3, Issue 6, 2008, Pages

  Hubert, Nicolas ^a   Hanner, Robert ^b   Holm, Erling ^c   Mandrak, Nicholas E ^d   Taylor, Eric ^e   Burridge, Mary ^c   Watkinson, Douglas ^f   Dumont, Pierre ^g   Curry, Allen ^h   Bentzen, Paul ⁱ   Zhang, Junbin ^b   April, Julien ^a   Bernatchez, Louis ^a  

^a UNIVERSITÉ LAVAL   (Canada)

^b UNIVERSITY OF GUELPH   (Canada)

^c DEPARTMENT OF NATURAL HISTORY   (Canada)

^d GREAT LAKES LABORATORY FOR FISHERIES AND AQUATIC SCIENCES   (Canada)

^e Department of Zoology ^*  (Canada)

^f FRESHWATER INSTITUTE   (Canada)

^g MINISTÈRE DES RESSOURCES NATURELLES ET DE LA FAUNE   (Canada)

^h UNIVERSITY OF NEW BRUNSWICK   (Canada)

ⁱ DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AQUATIC FAUNA; ARTICLE; CANADA; CONTROLLED STUDY; DNA BARCODING; DNA POLYMORPHISM; ECONOMIC ASPECT; FRESHWATER FISH; GENETIC DISTANCE; GENETIC VARIABILITY; INTRASPECIFIC VARIATION; MOLECULAR ECOLOGY; NONHUMAN; SALMON; SPECIES COMPARISON; SPECIES DIFFERENCE; SPECIES IDENTIFICATION;

ANIMALS; CANADA; DATABASES, GENETIC; DNA; DNA BARCODING, TAXONOMIC; FISHES; FRESH WATER; GENETIC VARIATION;

ACIPENSERIDAE; PISCES; VERTEBRATA;

EID: 49449115546     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002490     Document Type: Article

References (56)

1. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B 270: 313-321.
2. Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Systematic Biology 54: 852-859.
3. Ratnasingham S, Hebert PDN Bold: The barcode of life data system (www.barcodinglife.org). Molecular Ecology Notes 7: 355-364.
4. Hebert PDN, Stoekle M, Zemlak T, Francis CM (2004) Identification of birds through DNA barcodes. Plos Biology 2: 1657-1668.
5. Ball SL, Hebert PDN, Burian SK, Webb JM (2005) Biological identification of mayflies (Ephemeroptera) using DNA barcodes. Journal of the North American Benthological Society 24: 508-524.
6. Saunders G (2005) Applying DNA barcoding to red macroalgae:a preliminary appraisal holds promise for future applications. Philosophical Transactions of the Royal Society, Series B 360: 1879-1888.
7. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society, Series B 360: 1847-1857.
8. Clare EB, Lim BK, Engstrom MD, Eger JL, Hebert PDN (2006) DNA barcoding of Neotropical bats: species identification and discovery within Guyana. Molecular Ecology Notes 7: 184-190.
9. Cywinska A, Hunter FF, Hebert PDN (2006) Identifying Canadian mosquito species through DNA barcodes. Medical and Veterinary Entomology 20: 413-424.
10. Kerr KC, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, et al. (2007) Comprehensive DNA barcode coverage of North American birds. Molecular Ecology Notes doi: 10.1111/j.1471-8286.2007.01670.x.
11. Robins JH, Hingston M, Matisoo-Smith E, Ross HA (2007) Identifying Rattus species using mitochondrial DNA. Molecular Ecology Notes doi: 10.1111/j.1471-8286.2007.01752.x.
12. Siefert KA, Samson RA, deWaard JR, Houbraken J, Lévesque A, et al. (2007) Prospects for fungus identification using COI DNA barcodes with penicillium as a test case. Proceedings of the National Academy of Sciences, USA 104: 3901-3906.
13. Will KW, Rubinoff D (2004) Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20: 47-55.
14. Ebach MC, Holdredge C (2005) DNA barcoding is no subsitute for taxonomy. Nature 434: 697.
15. Pfenninger M, Cordellier M, Streit B (2006) Comparing the efficacy of morphologic and DNA-based taxonomy in the freshwater gastropod genus Radix (Basommatophora, Pulmonata). BMC Evolutionary Biology 6: 100.
16. Caterino MS, Tishechkin AK (2006) DNA identification and morphological description of the first confirmed larvae of Hetaeriinae (Coleoptera: Histeridae). Systematic Entomology 31: 405-418.
17. Pegg CG, Sinclair B, Briskey L, Aspden WJ (2006) MtDNA barcode identification of fish larvae in the southern great barrier reef, Australia. Scientia Marina 70: 7-12.
18. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences, USA 101: 14812-14817.
19. Witt J, Threloff DS, Doug L, Hebert PDN (2006) DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Molecular Ecology 15: 3073-3082.
20. Smith MA, Wood DM, Janzen DH, Hallwachs W, Hebert PDN (2007) DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists. Proceedings of the National Academy of Sciences, USA 104: 4967-4972.
21. Dawnay NR, Ogden R, McEwing R, Carvalho GR, Thorpe RS (2007) Validation of the barcoding gene COI for use in forensic genetic species identification. Forensic Science International in press..
22. Nelson LA, Wallman JF, Dowton M (2007) Using COI barcodes to identify forensically and medically important blowflies. Medical and Veterinary Entomology 21: 44-52.
23. Pfenninger MC, Nowak C, Kley D, Steinke D, Streit B (2007) Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. Molecular Ecology 16: 1957-1968.
24. Scheffer SJ, Lewis ML (2006) Mitochondrial phylogeography of the vegetable pest Liriomyza trifolii (Diptera: Agromyzidae): diverged clades and invasive populations. Annals of Entomological Society of America 99: 991-998.
25. Corin SE, Lester PJ, Abbott KL, Ritchie PA (2007) Inferring historical introduction pathways with mitochondrial DNA: the case of introduced Argentine ants (Linepithema humile) into New Zealand. Diversity and Distributions doi: 10.1111/j.1472-4642.2007.00355.x.
26. Pons J (2006) DNA-based identification of preys from non-destructive, total DNA extractions of predators using arthropod universal primers. Molecular Ecology Notes 6: 623-626.
27. Birky CW, Fuerst P, Maruyama T (1989) Organelle gene diversity under migration and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells and comparison to nuclear genes. Genetics 121: 613-627.
28. Brown WM, George M Jr, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences, USA 76: 1967-1971.
29. Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Molecular Biology and Evolution 5: 568-581.
30. Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: frequency, causes and consequences, with insights from animal mitonchondria DNA. Annual Review of Ecology, Evolution and Systematics 34: 397-423.
31. Zhang DX, Hewitt GM (1996) Nuclear integrations: challenge for mitochondria DNA markers. Trends in Ecology and Evolution 11: 247-251.
32. Hubert N, Torrico JP, Bonhomme F, Renno JF (2007) Species polyphyly and mtDNA introgression among three Serrasalmus sister-species. Molecular Phylogenetics and Evolution 46: 375-381.
33. McPhail JD, Lindsey CC (1970) Freshwater fishes of northwestern Canada and Alaska. Bulletin of the Fisheries Research Board Canada, 173.
34. Mandrak NE, Crossman EJ (1992) A checklist of Ontario freshwater fishes. Toronto, Canada: Royal Ontario Museum Publications.
35. Nelson JS, Paetz MJ (1992) The fishes of Alberta. Edmonton, Canada: University of Alberta Press.
36. Scott WB, Crossman EJ (1998) Freshwater fishes of Canada. Oakville, Canada: Galt House Publications.
37. Stewart KW, Watkinson DA (2004) The freshwater fishes of Manitoba. Winnipeg, Canada: The University of Manitoba Press.
38. Ward RD, Woodwark M, Skininski DOF (1994) A comparison of genetic diversity levels in marine, freshwater and anadromous fish. Journal of Fish Biology 44: 213-232.
39. Canadian Endangered Species Conservation Council (CESCC) (2001) Wild Species 2000: the general status ofspecies in Canada. Ottawa. Ontario: Minister of Public Works and Government Services Canada.
40. Hajibabaei M, deWaard JR, Ivanova NV, Ratnasingham S, Dooh RT, et al. (2005) Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society, Series B 360: 1959-1967.
41. Ivanova NV, deWaard J, Hebert PDN (2006) An inexpensive, automation-friendly protocol for recovering high-quality DNA. Molecular Ecology Notes 6: 998-1002.
42. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN (2007) Universal primers cocktails for fish DNA barcoding. Molecular Ecology Notes doi: 10.1111/ j.1471-8286.2007.01748.x.
43. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 15: 111-120.
44. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing evolutionary trees. Molecular Biology and Evolution 4: 406-425.
45. Statgraphic (1999) Statistical package. Los AngelesCA: Statistical Graphics Corporation.
46. Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLOS Biology 3: 2229-2238.
47. Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, et al. (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology 55: 595-606.
48. Saccone C, De Giorgi C, Cissi C, Pesole G, Reyes A (1999) Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238: 195-209.
49. Kingman JFC (1982) The coalescent. Stochastic Process and their Applications 13: 245-248.
50. Tajima F (1983) Evolutionary relationships of DNA sequences in finite populations. Genetics 105: 437-460.
51. Hickerson MJ, Meyer CP, Moritz C (2006) DNA barcoding will often fail to discover new animal species over broad parameter space. Systematic Biology 55: 729-739.
52. Meier R, Shiyang K, Vaidya C, Ng PKL (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55: 715-728.
53. Abdo A, Golding GB (2007) A step toward barcoding life: a model-based, decision-theoritic method to assign genes to preexisting species groups. Systematic Biology 56: 44-56.
54. Nielsen R, Matz M (2006) Statistical approaches for DNA barcoding. Systematic Biology 55: 162-169.
55. Bernatchez L, Wilson CC (1998) Comparative phylogeography of Neartic and Paleartic fishes. Molecular Ecology 7: 431-452.
56. Barber P, Boyce SL (2006) Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae. Proceedings of the Royal Society of London, Series B, Biological Sciences 273: 2053-2061.