DNA sequences in taxonomy: Opportunities and challenges

The New Taxonomy

Volumn , Issue , 2008, Pages 95-128

  Meier, Rudolf ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85056043472     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420008562     Document Type: Chapter

References (148)

1. Armstrong, K.F. and Ball, S.L. (2005) DNA barcodes for biosecurity: Invasive species identification. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1813-1823.
2. Avise, J.C. (2000) Phylogeography: The History and Formation of Species, Harvard University Press, Cambridge, MA.
3. Avise, J.C. and Walker, D. (1999) Species realities and numbers in sexual vertebrates: Perspectives from an asexually transmitted genome. Proceedings of the National Academy of Sciences of the United States of America, 96: 992-995.
4. Backeljau, T., De Bruyn, L., De Wolf, H., Jordaens, K., Van Dongen, S. and Winnepennincks, B. (1996) Multiple UPGMA and neighbour-joining trees and the performance of some computer packages. Molecular Biology and Evolution, 13: 309-313.
5. Ball, S.L., Hebert, P.D.N., Burian, S.K. and Webb, J.M. (2005) Biological identifications of mayflies (Ephemeroptera) using DNA barcodes. Journal of the North American Benthological Society, 24, 508-524.
6. Ballard, J.W.O., Chernoff, B. and James, A.C. (2002) Divergence of mitochondrial DNA is not corroborated by nuclear DNA, morphology, or behavior in Drosophila simulans. Evolution, 56: 527-545.
7. Barrett, R.D.H. and Hebert, P.D.N. (2005) Identifying spiders through DNA barcodes. Canadian Journal of Zoology, 83: 481-491.
8. Bensasson, D., Zhang, D.-X., Hartl, D.L. and Hewitt, G.M. (2001) Mitochondrial pseudogenes:Evolution’s misplaced witnesses. Trends in Ecology and Evolution, 16: 314-321.
9. Bensch, S., Irwin, D.E., Irwin, J.H., Kvist, L. and Akesson, S. 2006. Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers. Molecular Ecology, 15: 161-171.
10. Bequaert, J.C. (1953) The Hippoboscidae or louse-flies (Diptera) of mammals and birds. Part 1. Structure, physiology and natural history. Entomologica Americana (New Series), 32: 1-209.
11. Bequaert, J.C. (1954) The Hippoboscidae or louse-flies (Diptera) of mammals and birds. Part II. Taxonomy, evolution and revision of American genera and species. Entomologica Americana (New Series), 34: 1-232.
12. Bickford, D., Lohman, D., Sodhi, N.S., Ng, P.K.L., Meier, R., Winker, K., Ingram, K. and Das, I. (2007) Cryptic species: A new window on diversity and conservation. Trends in Ecology and Evolution, 22: 148-155.
13. Birstein, V.J., Doukakis, P., Sorkin, B. and Desalle, R. (1998) Population aggregation analysis of three caviar-producing species of sturgeons and implications for the species identification of black caviar. Conservation Biology, 12: 766-775.
14. Blaxter, M. (2003) Counting angels with DNA. Nature, 421: 122-124.
15. Blaxter, M., Elsworth, B. and Daub, J. (2004) DNA taxonomy of a neglected animal phylum:An unexpected diversity of tardigrades. Proceedings of the Royal Society of London Series B-Biological Sciences, 271: S189-S192.
16. Blaxter, M., Mann, J., Chapman, T., Thomas, F., Whitton, C., Floyd, R. and Abebe, E. (2005) Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1935-1943.
17. Bond, J.E. (2004) Systematics of the Californian euctenizine spider genus Apomastus (Araneae:Mygalomorphae: Cyrtaucheniidae): The relationship between molecular and morphological taxonomy. Invertebrate Systematics, 18: 361-376.
18. Bond, J.E. and Sierwald, P. (2003) Molecular taxonomy of the Anadenobolus excisus (Diplopoda: Spirobolida: Rhinocricidae) species-group on the Caribbean island of Jamaica. Invertebrate Systematics, 17: 515-528.
19. Brower, A.V.Z. (2006) Problems with DNA barcodes for species delimitation: ‘Ten species’ of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae). Systematics and Biodiversity, 4: 127-132.
20. Burbrink, F.T., Lawson, R. and Slowinski, J.B. (2000) Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): A critique of the subspecies concept. Evolution, 54; 2107-2118.
21. Caterino, M.S., Cho, S. and Sperling, F.A.H. (2000) The current state of insect molecular systematics: A thriving tower of Babel. Annual Review of Entomology, 45: 1-54.
22. Chu, K.H., Ho, H.Y., Li, C.P. and Chan, T.Y. (2003) Molecular phylogenetics of the mitten crab species in Eriocheir, sensu lato (Brachyura: Grapsidae). Journal of Crustacean Biology, 23: 738-746.
23. Chu, K.H., Tong, J. and Chan, T.Y. (1999) Mitochondrial cytochrome oxidase I sequence divergence in some Chinese species of Charybdis (Crustacea: Decapoda: Portunidae). Biochemical Systematics and Ecology, 27: 461-468.
24. Cracraft, J. (1992) The species of the birds of paradise Paradisaeidae. Applying the phylogenetic species concept to a complex pattern of diversification. Cladistics, 8: 1-43.
25. Davis, J.I. and Nixon, K.C. (1992) Populations, genetic variation, and the delimitation of phylogenetic species. Systematic Biology, 41: 421-435.
26. Dayrat, B. (2005) Towards integrative taxonomy. Biological Journal of the Linnean Society, 85: 407-415.
27. Deagle, B.E., Jarman, S.N., Pemberton, D. and Gales, N.J. (2005) Genetic screening for prey in the gut contents from a giant squid (Architeuthis sp.). Journal of Heredity, 96: 417-423.
28. De Ley, P., De Ley, I.T., Morris, K., Abebe, E., Mundo-Ocampo, M., Yoder, M., Heras, J., Waumann, D., Rocha-Olivares, A., Burr, A.H.J., Baldwin, J.G. and Thomas, W.K. (2005) An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1945-1958.
29. DeSalle, R., Egan, M.G. and Siddall M. (2005) The unholy trinity: Taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society (Biological Sciences), 360: 1905-1916.
30. Dunn, C.P. (2003) Keeping taxonomy based in morphology. Trends in Ecology & Evolution, 18: 270-271.
31. Ebach, M.C. and Holdrege, C. (2005) DNA barcoding is no substitute for taxonomy. Nature, 434: 697.
32. Feder, J.L., Berlocher, S.H., Roethele, J.B., Dambroski, H., Smith, J.J., Perry, W.L., Gavrilovic, V., Filchak, K.E., Rull, J. and Aluja, M. (2003) Allopatric genetic origins for sympatric host-plant shifts and race formation in Rhagoletis. Proceedings of the National Academy of Sciences of the United States of America, 100: 10314-10319.
33. Ferguson, J.W.H. (2002) On the use of genetic divergence for identifying species. Biological Journal of the Linnean Society, 75: 509-516.
34. Floyd, R., Abebe, E., Papert, A. and Blaxter, M. (2002) Molecular barcodes for soil nematode identification. Molecular Ecology, 11: 839-850.
35. Frost, D.R., Crafts, H.M., Fitzgerald, L.A. and Titus, T.A. (1998) Geographic variation, species recognition, and molecular evolution of cytochrome oxidase I in the Tropidurus spinulosus complex (Iguania: Tropiduridae). Copeia, 1998: 839-851.
36. Funk, D.J. and Omland, K.E. (2003) Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology and Systematics, 34: 397-423.
37. Gaston, K.J. and O’Neill, M.A. (2004) Automated species identification: Why not? Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 359: 655-667.
38. Gibbs, M.J., Armstrong, J.S. and Gibbs, A.J. (2005) Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared subsequences. BMC Bioinformatics, 6: 90.
39. Godfray, H.C.J. (2002) Challenges for taxonomy. Nature, 417: 17-19.
40. Godfray, H.C.J. and Knapp, S. (2004) Taxonomy for the twenty-first century-Introduction. Philosophical Transactions of the Royal Society of London B Biological Sciences, 359: 559-569.
41. Hajibabaei, M., DeWaard, J.R., Ivanova, N.V., Ratnasingham, S., Dooh, R.T., Kirk, S.L., Mackie, P.M. and Hebert, P.D.N. (2005) Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1959-1967.
42. Harris, D.J. (2003) Can you bank on GenBank? Trends in Ecology & Evolution, 18: 317-319.
43. Harris, D.J. and Froufe, E. (2005) Taxonomic inflation: Species concept or historical geopolitical bias? Trends in Ecology & Evolution, 20: 6-7.
44. Hebert, P.D.N., Cywinska, A., Ball, S.L. and deWaard, J.R. (2003a) Biological identifications through DNA barcodes. Proceedings of the Royal Society (Biological Sciences Series), 270: 313-321.
45. Hebert, P.D.N. and Gregory, T.R. (2005) The promise of DNA barcoding for taxonomy. Systematic Biology, 54: 852-859.
46. Hebert, P.D.N., Penton, E.H., Burns, J.M., Janzen, D.H. and Hallwachs, W. (2004a) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America, 101: 14812-14817.
47. Hebert, P.D.N., Stoeckle, M., Zemlak, T.S. and Francis, C.M. (2004b) Identification of birds through DNA barcodes. PLoS Biology, 2: 1657-1663.
48. Hebert, P.D.N., Ratnasingham, S. and deWaard, J.R. (2003b) Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society Biological Sciences Series B, 270: S96-S99.
49. Hendrixson, B.E. and Bond, J.E. (2005) Testing species boundaries in the Antrodiaetus unicolor complex (Araneae: Mygalomorphae: Antrodiaetidae): ‘Paraphyly’ and cryptic diversity. Molecular Phylogenetics and Evolution, 36: 405-416.
50. Hennig, W. (1966) Phylogenetic Systematics, University of Illinois Press, Urbana, 280 pp.
51. Hill, D.S. (1962a) Revision of the British Ornithomyia (Diptera: Hippoboscidae). Proceedings of the Royal Entomological Society of London (Series B), 31: 11-18.
52. Hill, D.S. (1962b) A study of the distribution and host preference of three species of Ornithomyia (Diptera: Hippoboscidae) in the British Isles. Proceedings of the Royal Entomological Society of London (Series A), 37: 37-48.
53. Hill, D.S. (1963) The life history of the British species of Ornithomya (Diptera: Hippoboscidae). Transactions of the Royal Entomological Society of London, 115: 391-407.
54. Hill, D.S., Hackmann, W. and Lyneborg, L. (1964) The genus Ornithomya (Diptera: Hippoboscidae) in Fennoscandia. Denmark and Iceland, Notulae Entomologicae, 44: 33-52.
55. Hogg, I.D. and Hebert, P.D.N. (2004) Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes. Canadian Journal of Zoology, 82: 749-754.
56. Hurst, G.D.D. and Jiggins, F.M. (2005) Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: The effects of inherited symbionts. Proceedings of the Royal Society (Series B), 272: 1525-1534.
57. Hutson, A.M. (1984) Keds, flat-flies and bat-flies. Handbooks for the Identification of British Insects, 10: 1-40.
58. Janzen, D.H., Hajibabaei, M., Burns, J.M., Hallwachs, W., Remigio, E. and Hebert, P.D.N. (2005) Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philosophical Transactions of the Royal Society (Series B), 360: 1835-1845.
59. Johnsen, P. (1948) Notes on the Danish louse-flies (Diptera: Hippoboscidae). Entomologiske Meddelelser, 25: 278-298.
60. Kasper, M.L., Reeson, A.F., Cooper, S.J.B., Perry, K.D. and Austin, A.D. (2004) Assessment of prey overlap between a native (Polistes humilis) and an introduced (Vespula germanica) social wasp using morphology and phylogenetic analyses of 16S rDNA. Molecular Ecology, 13: 2037-2048.
61. Koski, L.B. and Golding, G.B. (2001) The closest BLAST hit is often not the nearest neighbour. Journal of Molecular Evolution, 52: 540-542.
62. Krzywinski, J. and Besansky, N.J. (2003) Molecular systematics of Anopheles: From subgenera to subpopulations. Annual Review of Entomology, 48: 111-139.
63. Laamanen, T.R., Petersen, F.T. and Meier, R. (2003) Kelp flies and species concepts: The case of Coelopa frigida (Fabricius, 1805) and C. nebularum Aldrich, 1929 (Diptera: Coelopidae). Journal of Zoological Systematics and Evolutionary Research, 41: 127-136.
64. Lee, C.E. (2000) Global phylogeography of a cryptic copepod species complex and reproductive isolation between genetically proximate ‘populations’. Evolution, 54: 2014-2027.
65. Lee, M.S.Y. (2004) The molecularization of taxonomy. Invertebrate Systematics, 18: 1-6.
66. Mallet, J., Isaac, N.J.B. and Mace, G.M. (2005) Response to Harris and Froufe, and Knapp et al.: Taxonomic inflation. Trends in Ecology & Evolution, 20: 8-9.
67. Markmann, M. and Tautz, D. (2005) Reverse taxonomy: An approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Philosophical Transactions of the Royal Society of London (Series B), 360: 1917-1924.
68. Marshall, S. (2003) The real costs of insect identification. Newsl. Biol. Surv. Can. (Terrestrial Arthropods), Opin. Page, 22: 1-4.
69. Mayr, E. (2000) The biological species concept. In Species Concepts and Phylogenetic Theory:A Debate (eds Q.D. Wheeler and R. Meier), Columbia University Press, New York, pp. 17-29.
70. Meier, R. and Dikow, T. (2004) Significance of specimen databases from taxonomic revisions for estimating and mapping the global species diversity of invertebrates and repatriating reliable and complete specimen data. Conservation Biology, 18: 478-488.
71. Meier, R., Kwong, S., Vaidya, G. and Ng, P.K.L. (2006) DNA barcoding and taxonomy in Diptera: A tale of high intraspecific variability and low identification success. Systematic Biology, 55: 715-728.
72. Meier, R. and Willmann, R. (2000) The Hennigian species concept. In Species Concepts and Phylogenetic Theory: A Debate (eds Q.D. Wheeler and R. Meier), Columbia University Press, New York, pp. 30-43.
73. Memon, N., Meier, R., Mannan, A. and Su Feng-Yi, K. (2006) On the use of DNA sequences for determining the species limits of a polymorphic new species in the stink bug genus Halys (Heteroptera: Pentatomidae) from Pakistan. Systematic Entomology, 31: 703-710.
74. Meyer, C.P. and Paulay, G. (2005) DNA barcoding: Error rates based on comprehensive sampling. PLoS Biology, 3: 2229-2238.
75. Mishler, B. and Theriot, E. (2000) The phylogenetic species concept sensu Mishler and Theriot:Monophyly, apomorphy, and phylogenetic species concepts. In Species Concepts and Phylogenetic Theory: A Debate (eds Q.D. Wheelerand R. Meier), Columbia University Press, New York, pp. 44-54.
76. Mishler, B.D. and Brandon, R.N. (1987) Individuality, pluralism, and the phylogenetic species concept. Biology and Philosophy, 2: 397-414.
77. Monaghan, M.T., Balke, M., Gregory, T.R. and Vogler, A.P. (2005) DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1925-1933.
78. Moore, W.S. (1995) Inferring phylogenies from mtDNA variation: Mitochondrial-gene trees versus nuclear-gene trees. Evolution, 49: 718-726.
79. Moritz, C. and Cicero, C. (2004) DNA barcoding: Promise and pitfalls. PLoS Biology, 2: 1529-1531.
80. Muir, C.C., Galdikas, B.M.F., Beckenbach, A.T. and Arnason, U. (1998) Is there sufficient evidence to elevate the orangutan of Borneo and Sumatra to separate species? (and reply). Journal of Molecular Evolution, 46: 378-381.
81. Murray, R. and Stackebrandt, E. (1995) International Journal of Systematic Bacteriology, 45: 186-187.
82. Nilsson, R.H., Larsson, K.H. and Ursing, B.M. (2004) Galaxie-CGI scripts for sequence identification through automated phylogenetic analysis. Bioinformatics, 20: 1447-1452.
83. Nixon, K.C. and Wheeler, Q.D. (1990) An amplification of the phylogenetic species concept. Cladistics, 6: 211-224.
84. Ødegaard, F. (2000) How many species of arthropods? Erwin’s estimate revised. Biological Journal of the Linnean Society, 71: 583-597.
85. Oren, A. (2004) Prokaryote diversity and taxonomy: Current status and future challenges. Philosophical Transactions of the Royal Society of London (Series B), 359: 623-638.
86. Paetkau, D. (1999) Using genetics to identify intraspecific conservation units: A critique of current methods. Conservation Biology, 13: 1507-1509.
87. Page, T.J., Choy, S.C. and Hughes, J.M. (2005) The taxonomic feedback loop: Symbiosis of morphology and molecules. Biology Letters, 1: 139-142.
88. Palumbi, S.R. and Cipriano, F. (1998) Species identification using genetic tools: The value of nuclear and mitochondrial gene sequences in whale conservation. Journal of Heredity, 89: 459-464.
89. Paquin, P. and Hedin, M. (2004) The power and perils of ‘molecular taxonomy’: A case study of eyeless and endangered Cicurina (Araneae: Dictynidae) from Texas caves. Molecular Ecology, 13: 3239-3255.
90. Paterson, H.E.H. (1985) The recognition species concept of species. In Transvaal Museum Monograph (ed E. Vrba), Transvaal Museum, Pretoria, pp. 21-29.
91. Pennisi, E. 2003a. Modernizing the tree of life. Science, 300: 1692-1697.
92. Pennisi, E. 2003b. Systems biology: Tracing life’s circuitry. Science, 302: 1646-1649.
93. Pestano, J., Brown, R.P., Suarez, N.M. and Baez, M. (2003) Diversification of sympatric Sapromyza (Diptera: Lauxaniidae) from Madeira: Six morphological species but only four mtDNA lineages. Molecular Phylogenetics and Evolution, 27: 422-428.
94. Petersen, F.T., Damagaard, J. and Meier, R. (2007a) How many DNA sequences are needed for solving a taxonomic problem? The case of two parapetic species of house flies (Diptera:Hippoboscidae: Ornithomya Latreille, 1802). Arthropod Systematics & Phylogeny, 65: 111-117.
95. Petersen, F.T., Meier, R., Kutty, S.N. and Wiegmann, B.M. (2007b) The phylogeny and evolution of host choice in the Hippoboscoidea (Diptera) as reconstructed using four molecular markers. Molecular Phylogenetics and Evolution, 45: 111-122.
96. Ponder, W. and Lunney, D. (1999) The Other 99%-The Conservation and Biodiversity of Invertebrates, Royal Zoological Society of New South Wales, Sydney, 462 pp.
97. Pozhitkov, A.E. and Tautz, D. (2002) An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification. BMC Bioinformatics, 3: 1-7.
98. Prendini, L. (2005) Comment on ‘Identifying spiders through DNA barcodes’. Canadian Journal of Zoology, 83: 498-504.
99. Pryce, T.M., Palladino, S., Kay, I.D. and Coombs, G.W. (2003) Rapid identification of fungi by sequencing the ITSI and ITS2 regions using an automated capillary electrophoresis system. Medical Mycology, 41: 369-381.
100. Puorto, G., da Graca Salomao, M., Theakston, R.D.G., Thorpe, R.S., Warrell, D.A. and Wuster, W. (2001) Combining mitochondrial DNA sequences and morphological data to infer species boundaries: Phylogeography of lanceheaded pitvipers in the Brazilian Atlantic forest, and the status of Bothrops pradoi (Squamata: Serpentes: Viperidae). Journal of Evolutionary Biology, 14: 527-538.
101. Quicke, D.L.J. (2004) The world of DNA barcoding and morphology-Collision or synergism and what of the future? The Systematist-Newsletter of the Systematics Association, 8-12: 90. (www.systass.org/newsletter/)
102. Ratnasingham, S. and Hebert, P.D.N. (2007) BOLD: The barcode of life data system (www.barcodinglife.org). Molecular Ecology Notes, 7: 355-364.
103. Roberts, L. (2001) Controversial from the start. Science, 291: 1182-1188.
104. Roe, A.D. and Sperling, F.A.H. (2007) Population structure and species boundary delimitation of cryptic Dioryctria moths: An integrative approach. Molecular Ecology, 16: 3617-3633.
105. Ruedas, L.A., Salazar-Bravo, J., Dragoo, J.W. and Yates, T.L. (2000) The importance of being earnest: What, if anything, constitutes a ‘specimen examined’? Molecular Phylogenetics and Evolution, 17: 129-132.
106. Sanders, K.L., Malhotra, A. and Thorpe, R.S. (2006) Combining molecular, morphological and ecological data to infer species boundaries in a cryptic tropical pit viper. Biological Journal of the Linnean Society, 87: 343-364.
107. Schindel, D.E. and Miller, S.E. (2005) DNA barcoding useful for taxonomists. Nature, 435: 17.
108. Scoble, M.J. (2004) Unitary or unified taxonomy? Philosophical Transactions of the Royal Society of London (Series B), 359: 699-710.
109. Scotland, R., Hughes, C., Donovan, B. and Wortley, A. (2003) The Big Machine and the much-maligned taxonomist. Systematics and Biodiversity, 1: 139-143.
110. Seberg, O. (2004) The future of systematics: Assembling the Tree of Life. The Systematist-Newsletter of the Systematics Association, 2-8: 23. (www.systass.org/newsletter)
111. Sharpe, R.G., Harbach, R.E. and Butlin, R.K. (2000) Molecular variation and phylogeny of members of the Minimus group of Anopheles subgenus Cellia (Diptera: Culicidae). Systematic Entomology, 25: 263-272.
112. Shih, H.-T., Ng, P.K.L. and Chang, H.-W. (2004) The systematics of the genus Geothelphusa (Crustacea, Decapoda, Brachyura, Potamidae) from southern Taiwan: A molecular appraisal. Zoological Studies, 43: 561-570.
113. Sites, J.W., Jr. and Marshall, J.C. (2003) Delimiting species: A Renaissance issue in systematic biology. Trends in Ecology & Evolution, 18: 462-470.
114. Smith, M.A., Fisher, B.L. and Hebert, P.D.N. (2005) DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: The ants of Madagascar. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1825-1834.
115. Smith, V.S. (2005) DNA barcoding: Perspectives from a ‘Partnerships for Enhancing Expertise in Taxonomy’ (PEET) debate. Systematic Biology, 54: 841-844.
116. Sodhi, N.S., Koh, L.P., Brook, B.W. and Ng, P.K.L. (2004) Southeast Asian biodiversity: An impending disaster. Trends in Ecology & Evolution, 19: 654-660.
117. Sperling, F. (2003) DNA barcoding. Deus ex machina. Newsl. Biol. Surv. Can. (Terrestrial Arthropods) Opin. Page, 22: 50-53.
118. Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont, P., Kampfer, P., Maiden, M., Nesme, X., Rossello-Mora, R., Swings, J., Truper, H.G., Vauterin, L., Ward, A.C. and Whitman, W.B. (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. International Journal of Systematic and Evolutionary Microbiology, 52: 1043-1047.
119. Steinke, D., Vences, M., Salzburger, W. and Meyer, A. (2005) TaxI: A software tool for DNA barcoding using distance methods. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1975-1980.
120. Stoeckle, M. (2003) Taxonomy, DNA and the Bar Code of Life. BioScience, 53: 796-797.
121. Summerbell, R.C., Levesque, C.A., Seifert, K.A., Bovers, M., Fell, J.W., Diaz, M.R., Boekhout, T., de Hoog, G.S., Stalpers, J. and Crous, P.W. (2005) Microcoding: The second step in DNA barcoding. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1897-1903.
122. Sun, H.Y., Zhou, K. and Yang, X.J. (2003) Phylogenetic relationships of the mitten crabs inferred from mitochondrial 16S rDNA partial sequences (Crustacean, Decapoda). Acta Zoologica Sinica, 49: 592-599.
123. Takezaki, N. (1998) Tie trees generated by distance methods of phylogenetic reconstruction. Molecular Biology and Evolution, 15: 727-737.
124. Tang, B., Zhou, K., Song, D., Yang, G. and Dai, A. (2003) Molecular systematics of the Asian mitten crabs, genus Eriocheir (Crustacea: Brachyura). Molecular Phylogenetics and Evolution, 29: 309-316.
125. Tautz, D., Arctander, P., Minelli, A., Thomas, R.H. and Vogler, A.P. (2003) A plea for DNA taxonomy. Trends in Ecology & Evolution, 18: 70-74.
126. Teletchea, F., Maudet, C. and Hanni, C. (2005) Food and forensic molecular identification:Update and challenges. Trends in Biotechnology, 23: 359-366.
127. Templeton, A.R. (1989) The meaning of species and speciation: A genetic perspective. In Speciation and Its Consequences (eds D. Otte and J. Endler), Sinauer, Sunderland, MA, pp. 3-27.
128. Thalmann, O., Hebler, J., Poinar, H.N., Pääbo, S. and Vigilant, L. (2004) Unreliable mtDNA data due to nuclear insertions: A cautionary tale from analysis of humans and other great apes. Molecular Ecology, 13: 321-335.
129. Theodor, O. and Oldroyd, H. (1964) Hippoboscidae, E. Schweizerbart’sche Verlagsbuchhandlung, Stuttgart, Germany, 126 pp.
130. Tong, J.G., Chan, T.Y. and Chu, K.H. (2000) A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda: Penaeidae) based on mitochondrial DNA sequences of selected species from the Indo West Pacific. Journal of Crustacean Biology, 20: 541-549.
131. Vences, M., Thomas, M., Bonett, R.M. and Vieites, D.R. (2005a) Deciphering amphibian diversity through DNA barcoding: Chances and challenges. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1859-1868.
132. Vences, M., Thomas, M., Van der Meijden, A., Chiari, Y. and Vieites, D.R. (2005b) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Frontiers in Zoology, 2: 5.
133. Vilgalys, R. (2003) Taxonomic misidentification in public DNA databases. New Phytologist, 160: 4-5.
134. Vogler, A.P. and Monaghan, M.T. (2007) Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research, 45: 1-10.
135. Walter, D.E. and Winterton, S. (2007) Keys and the crisis in taxonomy: Extinction or reinvention? Annual Review of Entomology, 52: 193-208.
136. Ward, R.D., Zemlak, T.S., Innes, B.H., Last, P.R. and Hebert, P.D.N. (2005) DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1847-1857.
137. Wheeler, Q.D. (2004) Taxonomic triage and the poverty of phylogeny. Philosophical Transactions of the Royal Society of London B Biological Sciences, 359: 571-583.
138. Wheeler, Q.D. (2005) Losing the plot: DNA ‘barcodes’ and taxonomy. Cladistics, 21: 405-407.
139. Wheeler, Q.D. and Meier, R., eds (2000) Species Concepts and Phylogenetic Theory: A Debate, Columbia University Press, New York, 256 pp.
140. Wheeler, Q.D., and Platnick, N.I. (2000) The phylogenetic species concept sensu Wheeler and Platnick. In Species Concepts and Phylogenetic Theory: A Debate (eds Q.D. Wheeler and R. Meier), Columbia University Press, New York, pp. 55-69.
141. Wheeler, Q.D., Raven, P.H. and Wilson, E.O. (2004) Taxonomy: Impediment or expedient? Science, 303: 285.
142. Wiens, J.J. and Penkrot, T.A. (2002) Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Systematic Biology, 51: 69-91.
143. Will, K.W. and Rubinoff, D. (2004) Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics, 20: 47-55.
144. Will, K.W., Mishler, B.D. and Wheeler, Q.D. (2005) The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology, 54: 844-851.
145. Willmann, R. and Meier, R. (2000) A critique from the Hennigian species perspective. In Species Concepts and Phylogenetic Theory: A Debate (eds Q.D. Wheeler and R. Meier), Columbia University Press, New York, pp. 101-118.
146. Wilson, E.O. (2003) The encyclopedia of life. Trends in Ecology & Evolution, 18: 77-80.
147. Xu, X. and Arnason, U. (1996) The mitochondrial DNA molecule of Sumatran orangutan and a molecular proposal for two (Bornean and Sumatran) species of orangutan. Journal of Molecular Evolution, 43: 431-437.
148. Zhi, L., Karesh, W.B., Janczewski, D.N., Frazier-Taylor, H., Sajuthi, D., Gombek, F., Andau, M., Martenson, J.S. and O’Brien, S.J. (1996) Genomic differentiation among natural populations of orangutan (Pongo pygmaeus). Current Biology, 6: 1326-1336.