An update on DNA barcoding: Low species coverage and numerous unidentified sequences

Cladistics

Volumn 28, Issue 6, 2012, Pages 639-644

  Kwong, Shiyang ^a   Srivathsan, Amrita ^a   Meier, Rudolf ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS; CYTOCHROME; DATA SET; DATABASE; GROWTH RATE; INSECT; METAZOAN; MOLECULAR ANALYSIS; PHYLOGENY; TAXONOMY;

ANIMALIA; AVES; HEXAPODA; LEPIDOPTERA; METAZOA; PISCES;

EID: 84869196690     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2012.00408.x     Document Type: Article

References (34)

1. Bartlett, S.E., Davidson, W.S., 1991. Identification of Thunnus tuna species by the polymerase chain reaction and direct sequence analysis of their mitochondrial cytochrome b genes. Can. J. Fish. Aquat. Sci. 48, 309-317.
2. Becker, S., Hanner, R., Steinke, D., 2011. Five years of FISH-BOL: brief status report. Mitochond. DNA 22, 3-9.
3. Bickford, D., Lohman, D.J., Sodhi, N.S., Ng, P.K.L., Meier, R., Winker, K., Ingram, K.K., Das, I., 2007. Cryptic species as a window on diversity and conservation. Trends Ecol. Evol. 22, 148-155.
4. Brower, A.V.Z., 2006. Problems with DNA barcodes for species delimitation: 'ten species' of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae). Syst. Biodiv. 4, 127-132.
5. Cameron, S., Rubinoff, D., Will, K., 2006. Who will actually use DNA barcoding and what will it cost? Syst. Biol. 55, 844-847.
6. Collins, R.A., Armstrong, K.F., Meier, R., Yi, Y., Brown, S.D.J., Cruickshank, R.H., Keeling, S., Johnston, C., 2012. Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS One 7, e28381.
7. Colwell, R.K., Coddington, J.A., 1994. Estimating terrestrial biodiversity through extrapolation. Philos. Trans. R. Soc. Lond. B. Biol. Sci 345, 101-118.
8. Federhen, S., 2011. Comment on "Birdstrikes and barcoding: can DNA methods help make the airways safer?". Mol. Ecol. 11, 937-938.
9. Gomez, A., Wright, P.J., Lunt, D.H., Cancino, J.M., Carvalho, G.R., Hughes, R.N., 2007. Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proc. R. Soc. Lond. B. Biol. Sci. 274, 199-207.
10. Gotelli, N.J., Colwell, R.K., 2001. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol. Lett. 4, 379-391.
11. Hajibabaei, M., DeWaard, J.R., Ivanova, N.V., Ratnasingham, S., Dooh, R.T., Kirk, S.L., Mackie, P.M., Hebert, P.D.N., 2005. Critical factors for assembling a high volume of DNA barcodes. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 360, 1959-1967.
12. Hebert, P.D., Gregory, T.R., 2005. The promise of DNA barcoding for taxonomy. Syst. Biol. 54, 852-859.
13. Hebert, P.D.N., Cywinska, A., Ball, S.L., deWaard, J.R., 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B. Biol. Sci. 270, 313-321.
14. Hebert, P.D., Stoeckle, M.Y., Zemlak, T.S., Francis, C.M., 2004. Identification of birds through DNA barcodes. PLoS Biol. 2, e312.
15. Kristensen, N.P., Scoble, M.J., Karsholt, O., 2007. Lepidoptera phylogeny and systematics: the state of inventorying moth and butterfly diversity. Zootaxa 1668, 699-747.
16. Lim, G.S., Balke, M., Meier, R. 2012. Determining species boundaries in a world full of rarity: singletons, species delimitation methods. Syst. Biol. 61, 165-169.
17. Little, D.P., Stevenson, D.W., 2007. A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 23, 1-21.
18. Marshall, E., 2005. Taxonomy. Will DNA bar codes breathe life into classification? Science 307, 1037.
19. Meier, R., 2008. DNA sequences in taxonomy-opportunities and challenges. In: Wheeler, Q.D. (Ed.), New Taxonomy. CRC Press, Boca Raton, FL, pp. 95-127.
20. Meier, R., Dikow, T., 2004. Significance of specimen databases from taxonomic revisions for estimating and mapping the global species diversity of invertebrates and repatriating reliable specimen data. Conserv. Biol. 18, 478-488.
21. Meier, R., Shiyang, K., Vaidya, G., Ng, P.K., 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst. Biol. 55, 715-728.
22. Meier, R., Zhang, G.Y., Ali, F., 2008. The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification. Syst. Biol. 57, 809-813.
23. Nanney, D.L., 1982. Genes and phenes in Tetrahymena. Bioscience 32, 783-788.
24. Ratnasingham, S., Hebert, P.D., 2007. BOLD: the barcode of life data system. Mol. Ecol. Notes 7, 355-364. (http://www.barcodinglife.org).
25. Ratnasingham, S., Hebert, P.D.N., 2011. BOLD's role in barcode data management and analysis: a response. Mol. Ecol. 11, 941-942.
26. Schindel, D.E., Miller, S.E., 2010. Provisional nomenclature: The on-ramp to taxonomic names. In Polaszek, A. (Ed.), Systema Naturae 250: The Linnaean Ark. CRC Press, Boca Raton, FL, pp. 109-116.
27. Sperling, F., 2003. DNA barcoding. Deus et machina. Newsl. Biol. Surv. Can. (Terrestrial Arthropods) 22, 50-53.
28. Srivathsan, A., Meier, R., 2012. On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics 28, 190-194.
29. Tan, D.S.H., Ang, Y., Lim, G.S., Ismail, M.R., Meier, R., 2010. From 'cryptic species' to integrative taxonomy: an iterative process involving DNA sequences, morphology, and behaviour leads to the resurrection of Sepsis pyrrhosoma (Sepsidae: Diptera). Zool. Scr. 39, 51-61.
30. Taylor, H.R., Harris, W.E., 2012. An emergent science on the brink of irrelevance: a review of the past 8years of DNA barcoding. Mol. Ecol. 12, 377-388.
31. Virgilio, M., Backeijau, T., Barr, N., De Meyer, M., 2008. Molecular evaluation of nominal species in the Ceratitis fasciventris, C. anonae, C. rosa complex (Diptera: Tephritidae). Mol. Phylogenet. Evol. 48, 270-280.
32. Ward, R.D., Hanner, R., Hebert, P.D., 2009. The campaign to DNA barcode all fishes, FISH-BOL. J. Fish Biol. 74, 329-356.
33. Will, K.W., Rubinoff, D., 2004. Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20, 47-55.
34. Will, K.W., Mishler, B.D., Wheeler, Q.D., 2005. The perils of DNA barcoding and the need for integrative taxonomy. Syst. Biol. 54, 844-851.