From DNA taxonomy to barcoding — How a vague idea evolved into a biosystematic tool

Zoosystematics and Evolution

Volumn 83, Issue S1, 2007, Pages 44-51

  Köhler, Frank ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

Author keywords

DNA sequences; Molecular markers; Species recognition; Taxonomy

Indexed keywords

EID: 42149128225     PISSN: 14351935     EISSN: 18600743     Source Type: Journal    
DOI: 10.1002/mmnz.200600025     Document Type: Article

References (50)

1. Altschul, S. F., Gish, W., Miller, W., Meyers, E. W. & Lipman, D. J. 1990. Basic local alignment search tool. – Journal of Molecular Biology 215: 403 –410.
2. Blaxter, M. 2003. Counting angels with DNA. – Nature 421: 122 –124.
3. Blaxter, M.2004. The promise of a DNA taxonomy. – Philosophical Transactions of the Royal Society B: Biological Sciences 359: 669 –679.
4. Blaxter, M., Mann, J., Chapman, T., Thomas, F., Whitton, C. Floyd, R. & Abebe, E. 2005. Defining operational taxonomic units using DNA barcode data. – Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1935 –1943.
5. DeSalle, R., Egan, M. G. & Siddall, M. 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding. – Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1905 –1916.
6. Felsenstein, J. 2001. The troubled growth of statistical phylogenetics. – Systematic Biology 50: 465 –467.
7. Funk, D. J. & 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.
8. Glaubrecht, M. & Köhler, F. 2004. Radiating in a river: Systematics, molecular genetics and morphological differentiation of viviparous freshwater gastropods endemic to the Kaek River, Central Thailand (Cerithioidea, Pachy-chilidae). – Biological Journal of the Linnean Society of London 82: 275 –311.
9. st Century’. – Philosophical Transactions of the Royal Society B: Biological Sciences 359: 559 –569.
10. Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. 2003. Biological identifications through DNA barcodes. – Proceedings of the Royal Society B: Biological Sciences 270: 313 –321.
11. Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S. & Francis, C. M. 2004a. Identification of birds through DNA barcodes. PloS Biology 2: c312.
12. Hebert, P. D. N., Penton, E. H., Burns, J. M. Janzen, D. H. & Hallwachs, W. 2004b. Ten species in one: DNA barcoding reveals cryptic species in the Neotropical skipper butterfly Astraptes fulgerator. – Proceedings of the Academy of Sciences of the USA 101: 14812 –14817.
13. Hillis, D. M. 1987. Molecular versus morphological approaches to systematics. – Annual Review of Ecology and Systematics 18: 23–42.
14. Janzen, D. H., Hajibabaei, M., Burns, J. M., Hallwachs, W., Remigio, E. & Hebert, P. D. N. 2004. Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. – Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1835 –1845.
15. Köhler, F. & Glaubrecht, M. 2006. A systematic revision of the southeast Asian freshwater gastropod Brotia (Cer-ithioidea: Pachychilidae). – Malacologia 48: 159 –251.
16. Köhler, F., Rintelen, T. von, Meyer, A. & Glaubrecht, M. 2004. Multiple origin of viviparity in southeast Asian gastropods (Cerithioidea: Pachychilidae) and its evolutionary implications. – Evolution 58: 2215 –2226.
17. Krause, J., Dear, P. H., Pollack, J. L., Slatkin, M., Spriggs, H., Barnes, I., Lister, A. M., Ebersberger, I., Päabo, S. & Hof-reiter, M. 2006. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 439: 724 –726.
18. Lipscomb, D., Platnick, N. & Wheeler, Q. 2003. The intellectual content of taxonomy: a comment on DNA taxonomy. – Trends in Ecology and Evolution 18: 65–66.
19. Lorenz, J. G., Jackson, W. E., Beck, J. C. & Hanner, R. 2005. The problems and promises of DNA barcodes for species diagnosis of primate biomaterials. – Proceedings of the Royal Society London B: Biological Scienes 360: 1869 –1877.
20. Mallet, J. & Willmott, K. 2003. Taxonomy: renaissance or the tower of Babel? – Trends in Ecology and Evolution 18: 57 –59.
21. Markmann, M. & 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 B: Biological Sciences 360: 1917 –1924.
22. Mayr, E. 1997. This is biology. The science of the living world. Belknap Press, Cambridge, Massachusetts.
23. Moritz, C. & Cicero, C. 2004. DNA barcoding: Promise and pitfalls. – PloS Biology 2: 1529 –1531.
24. Moritz, C. & Hillis, D. M. 1996. Molecular systematics: context and controversies. In D. M. Hillis, C. Moritz & B. K. Mable, eds., Molecular Systematics. Pp. 1 –4. Sinauer Associates, Inc., Publishers Sunderland, Massachusetts.
25. Murphy, W. J, Eizirik, E., Johnson, W. E., Zhang, Y. P., Ryder, O. A. & O’Brien, S. J. 2001. Molecular phylogenetics and the origins of placental mammals. – Nature 409: 614 –618.
26. Nei, M. & Kumar, S., 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
27. Pennisi, E. 2003. Modernizing the tree of life. – Science 300: 1692 –1696.
28. Plötner, J., Köhler, F., Uzzell, T. & Beerli, P. 2007. Molecular Systematics of Amphibians. In: Heatwole, H. (ed.), Amphibian Biology, Vol. 7. Systematics. (in press).
29. Poinar, H. N., Schwarz, C., Qi, J., Shapiro, B., Macphee, R. D., Buigues, B., Tikhonov, A., Huson, D. H., Tomsho, L. P., Auch, A., Rampp, M., Miller, W. & Schuster, S. C. 2006. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. – Science 311: 392 –394.
30. Rintelen, T., Wilson, A. B., Meyer, A. & Glaubrecht, M. 2004. Escalation and trophic specialization drive adaptive radiation of freshwater gastropods in ancient lakes on Sulawesi, Indonesia. – Proceedings of the Royal Society London B: Biological Scienes 271: 2541 –2549.
31. Saitou, N. & Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. – Molecular Biology and Evolution 4: 406 –425.
32. San Mauro, D. Vences, M. Alcobendas, M., Zardoya, R. and Meyer, A., 2005. Initial diversification of living amphibians predated the breakup of Pangaea. – The American Naturalist 165: 590 –599.
33. Savolainen, V., Cowan, R. S., Vogler, A. P., Roderick, G. K. & Lane, R. 2005. Towards writing the encyclopaedia of life: An introduction to DNA barcoding. – Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1805 –1811.
34. Schander, C. & Willassen, E. 2005. What can biological barcoding do for marine biology? – Marine Biology Research 1: 79–83.
35. Seberg, O., Humphries, C. J., Knapp, S., Stevenson, D. W., Petersen, G., Scharff, N. & Andersen, N. M. 2003. Shortcuts in systematics? A commentary on DNA-based taxonomy. – Trends in Ecology and Evolution 18: 63–65.
36. Service, R. F. 2006. The race for the 1000 genome. – Science 311: 1544 –1546.
37. Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCut-cheon, J. P., Rosenbaum A. M., Wang, M. D., Zhang, K., Mitra, R. D. & Church, G. M. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. – Science 309: 1728 –1732.
38. Steinke, D., Vences, M., Salzburger, W. & 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.
39. Tautz, D., Arctander, P., Minelli, A., Thomas, R. H. & Vogler, A. P. 2002. DNA points the way ahead in taxonomy. – Nature 418: 479.
40. Tautz, D., Arctander, P., Minelli, A., Thomas, R. H. & Vogler, A. P. �2003. A plea for DNA taxonomy. – Trends in Ecology and Evolution 18: 70–74.
41. Thomaz, D., Guiller, A. & Clarke, B. 1996. Extreme divergence of mitochondrial DNA within species of pulmonate land snails. – Proceedings of the Royal Society B: Biological Sciences 263: 363 –368.
42. Veith, M., Kosuch, J. & Feldmann, R. 2000. A test for correct species declaration of frog legs imports from Indonesia into the European Union. – Biodiversity and Conservation 9: 333 –341.
43. Vences, M., Thomas, M., Bonett, R. M. & 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.
44. Vences, M., Thomas, M., Van der Meijden, A., Chiari, Y. & Vieites, D. R. 2005b. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. – Frontiers in Zoology 2: 5.
45. Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y. & Smith, H. O. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. – Science 304: 66–74.
46. Verheyen, E., Salzburger, W., Snoeks, J. & Meyer, A. 2003. The origin of the superflock of cichlid fishes from Lake Victoria, East Africa. – Science 300: 325 –329.
47. Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R. & Hebert, P. D. N. 2005. DNA barcoding Australia’s fish species. – Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1847 –1857.
48. Wheeler, Q. D. 2004. Taxonomic traige and the poverty of phylogeny. – Philosophical Transactions of the Royal Society B: Biological Sciences 359: 571 –583.
49. Wilson, E. O. 2004. Taxonomy as a fundamental discipline. – Philosophical Transactions of the Royal Society B: Biological Sciences 359: 739.
50. Zhang, P., Zhou, H., Chen, Y.-Q., Liu, Y.-F. and Qu, L.-H., 2005. Mitogenomic perspectives on the origin and phylogeny of living amphibians. – Systematic Biology, 54: 391 –400.