DNA barcode divergence among species and genera of birds and fishes

Molecular Ecology Resources

Volumn 9, Issue 4, 2009, Pages 1077-1085

  Ward, Robert D ^a  

^a CSIRO   (Australia)

Author keywords

Cox1; Cryptic species; Cytochrome c oxidase; Species identification

Indexed keywords

ANIMALIA; AVES; PISCES;

EID: 67649845828     PISSN: 1755098X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2009.02541.x     Document Type: Article

References (32)

1. Cantatore P, Roberti M, Pesole G et al 1994) Evolutionary analysis of cytochrome b sequences in some Perciformes - evidence for a slower rate of evolution than in mammals. Journal of Molecular Evolution, 39, 589 597. (Pubitemid 24379721)
2. Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270, 313 322.
3. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. Public Library of Science, Biology, 2, 1657 1663.
4. 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.
5. Hubert N, Hanner R, Holm E et al 2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS One, 3, e2490.
6. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN (2007) Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes, 7, 544 548. (Pubitemid 47035520)
7. Kelly RP, Sarkar IN, Eernisse DJ, DeSalle R (2007) DNA barcoding using chitons (genus Mopalia). Molecular Ecology Notes, 7, 177 183.
8. Kerr KCR, Stoeckle MY, Dove CJ, Weight LA, Francis CM, Hebert PDN (2007) Comprehensive DNA barcode coverage of North American birds. Molecular Ecology Notes, 7, 535 543. (Pubitemid 47035498)
9. Kimura M (1980) A simple method of estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111 120. (Pubitemid 11166431)
10. Krieger J, Fuerst PA (2002) Evidence for a slowed rate of molecular evolution in the order Acipenseriformes. Molecular Biology and Evolution, 19, 891 897. (Pubitemid 34605988)
11. Kumar S (2005) Molecular clocks: four decades of evolution. Nature Reviews Genetics, 6, 654 662. (Pubitemid 41044303)
12. Martin AP (1999) Substitution rates if organelle and nuclear genes in sharks: implicating metabolic rate (again). Molecular Biology and Evolution, 16, 996 1002. (Pubitemid 29314178)
13. Martin AP, Naylor GJP, Palumbi SR (1992) Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature, 357, 153 155.
14. Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. Public Library of Science, Biology, 3, 2229 2238.
15. Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. Public Library of Science, Biology, 2, 1529 1531.
16. Nevo E, Beiles A, Ben-Shlomo R (1984) The evolutionary significance of genetic diversity: ecological, demographic and life history correlates. In : Evolutionary Dynamics of Genetic Diversity (ed. Mani GS), pp. 13 213. Springer-Verlag, Berlin.
17. Olavarria C, Balbontin F, Bernal R, Baker CS (2006) Lack of divergence in the mitochondrial cytochrome b gene between Macruronus species (Pisces: Merluccidae) in the Southern Hemisphere. New Zealand Journal of Marine and Freshwater Research, 40, 299 304. (Pubitemid 44133785)
18. Rach J, DeSalle R, Sarkar IN, Schierwater B, Hadrys H (2008) Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proceedings of the Royal Society B: Biological Sciences, 275, 237 247. (Pubitemid 350295712)
19. Ratnasingham S, Hebert PDN (2007) BOLD: the Barcode of Life Data System (http://www.barcodinglife.org). Molecular Ecology Notes, 7, 355 364.
20. Tamura K, Dudley J, Nei M, Kumar S (2007) mega 4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. Molecular Biology and Evolution, 24, 1596 1599. (Pubitemid 47236692)
21. Tavares ES, Baker AJ (2008) Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evolutionary Biology, 8, 81.
22. Valdez-Moreno M, Ivanova NV, Elías-Gutiérrez M, Contreras-Balderas S, Hebert PDN (2009) Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes. Journal of Fish Biology, 74, 377 402.
23. Verheyen E, Salzburger W, Snoeks J, Meyer A (2003) Origin of the superflock of cichlid fishes from Lake Victoria, East Africa. Science, 300, 325 329. (Pubitemid 36433723)
24. Ward RD, Holmes BH (2007) An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes. Molecular Ecology Notes, 7, 899 907. (Pubitemid 350059273)
25. Ward RD, Costa FO, Holmes BH, 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.
26. Ward RD, Holmes BH, White WT, Last PR (2008b) DNA barcoding Australian chondrichthyans: results and potential uses in conservation. Marine and Freshwater Research, 59, 57 71. (Pubitemid 351170398)
27. Ward RD, Holmes BH, Yearsley GK (2008c) DNA barcoding reveals a likely second species of Asian seabass (barramundi) (Lates calcarifer). Journal of Fish Biology, 72, 458 463. (Pubitemid 351190161)
28. Ward RD, Holmes BH, Zemlak TS, Smith PJ (2007) DNA barcoding discriminates spurdogs of the genus Squalus. In : Descriptions of New Dogfishes of the Genus Squalus (Squaloidea: Squalidae) (eds Last PR, White WT, Pogonoski JJ), pp. 117 130. Marine and Atmospheric Research Paper 014. CSIRO, Hobart, Australia.
29. Ward RD, Skibinski DOF, Woodwark M (1992) Protein heterozygosity, protein structure, and taxonomic differentiation. Evolutionary Biology, 26, 73 159.
30. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) Barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1847 1857. (Pubitemid 44365045)
31. Weir JT, Schluter D (2008) Calibrating the avian molecular clock. Molecular Ecology, 17, 2321 2328. (Pubitemid 351623774)
32. Zhang AB, Sikes DS, Muster C, Li SQ (2008) Inferring species membership using DNA sequences with back-propagation neural networks. Systematic Biology, 57, 202 215.