Known knowns, known unknowns, unknown unknowns and unknown knowns in DNA barcoding: A comment on Dowton et al.

Systematic Biology

Volumn 63, Issue 6, 2014, Pages 1005-1009

  Collins, Rupert A ^a   Cruickshank, Robert H ^b  

^a FEDERAL UNIVERSITY OF AMAZONAS   (Brazil)

^b LINCOLN UNIVERSITY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION; DNA BARCODING; PHYLOGENY; PROCEDURES; STANDARDS;

CLASSIFICATION; DNA BARCODING, TAXONOMIC; PHYLOGENY;

EID: 84921835442     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu060     Document Type: Article

References (43)

1. Abdo Z., Golding G.B. 2007. A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups. Syst. Biol. 56:44-56.
2. Armstrong K. F., Ball S.L. 2005. DNA barcodes for biosecurity: invasive species identification. Philos. T. Roy. Soc. B. 360:1813-1823.
3. Bauer A.M., Parham J.F., Brown R.M., Stuart B.L., Grismer L., Theodore J., Böhme W., Savage J.M., Carranza S., Grismer J.L., Wagner P., Schmitz A., Ananjeva N.B., Inger R.F. 2010. Availability of new Bayesian-delimited gecko names and the importance of character-based species descriptions. P. Roy. Soc. B. 278(1705):490-492.
4. Becker S., Hanner R., Steinke D. 2011. Five years of FISH-BOL: brief status report. Mitochondrial DNA 22 Suppl 1:3-9.
5. Bergsten J., Bilton D.T., Fujisawa T., Elliott M., Monaghan M.T., Balke M., Hendrich L., Geijer J., Herrmann J., Foster G.N., Ribera I., Nilsson A.N., Barraclough T.G., Vogler A.P. 2012. The effect of geographical scale of sampling on DNA barcoding. Syst. Biol. 61:851-869.
6. Borisenko A.V., Sones J.E., Hebert P.D.N. 2009. The front-end logistics of DNA barcoding: challenges and prospects. Mol. Ecol. Resour. 9:27-34.
7. Boykin L.M., Armstrong K., Kubatko L., De Barro P. 2012. DNA barcoding invasive insects: database roadblocks. Invertebr. Syst. 26:506-514.
8. Brown S.D.J., Collins R.A., Boyer S., Lefort M.-C., Malumbres-Olarte J., Vink C.J., Cruickshank R.H. 2012. Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Mol. Ecol. Resour. 12:562-565.
9. Collins R.A., Cruickshank R.H. 2013. The seven deadly sins of DNA barcoding. Mol. Ecol. Resour. 13:969-975.
10. Dowton M., Meiklejohn K., Cameron S.L., Wallman J. 2014. A preliminary framework for DNA barcoding, incorporating the multispecies coalescent. Syst. Biol. 63:639-644.
11. Dupuis J.R., Roe A.D., Sperling F.A.H. 2012. Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol. Ecol. 21:4422-4436.
12. Edwards S., Bensch S. 2009. Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008. Mol. Ecol. 18:2930-2933.
13. Ekrem T., Willassen E., Stur E. 2007. A comprehensive DNA sequence library is essential for identification with DNA barcodes. Mol. Phylogenet. Evol. 43:530-542.
14. Funk D.J., Omland K.E. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 34:397-423.
15. Gillett C.P.D.T., Crampton-Platt A., Timmermans M.J.T.N., Jordal B., Emerson B.C., Vogler A.P. 2014. Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Mol. Biol. Evol. 31:2223-2237.
16. Goldstein P.Z., DeSalle R. 2011. Integrating DNA barcode data and taxonomic practice: determination, discovery, and description. BioEssays 33:135-147.
17. Gregory T.R. 2005. DNA barcoding does not compete with taxonomy. Nature 434:1067.
18. Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., Francis C.M. 2004. Identification of Birds through DNA Barcodes. PLoS Biology 2:e312.
19. Hickerson M.J., Meyer C.P., Moritz C. 2006. DNA barcoding will often fail to discover newanimal species over broad parameter space. Syst. Biol. 55:729-739.
20. Karl S.A., Toonen R.J., Grant W.S., Bowen B.W. 2012. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol. Ecol. 21:4171-4189.
21. Ko H.-L., Wang Y.-T., Chiu T.-S., Lee M.-A., Leu M.-Y., Chang K.-Z., Chen W.-Y., Shao K.-T. 2013. Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. PLoS ONE 8:e53451.
22. Lim G.S., Balke M., Meier R. 2012. Determining species boundaries in aworld full of rarity: singletons, species delimitation methods. Syst. Biol. 61:165-169.
23. McKay B.D., Zink R.M. 2010. The causes of mitochondrial DNA gene tree paraphyly in birds. Mol. Phylogenet. Evol. 54:647-650.
24. Meier, R. 2008. DNA Sequences in Taxonomy: Opportunities and Challenges. In Wheeler Q.D., editor, The New Taxonomy chap. 7. New York: CRC Press. pp. 95-127.
25. Meier R., Shiyang K., Vaidya G., Ng P.K.L. 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst. Biol. 55:715-728.
26. Meiklejohn K.A., Wallman J.F., Cameron S.L., Dowton M. 2012. Comprehensive evaluation of DNA barcoding for the molecular species identification of forensically important Australian Sarcophagidae (Diptera). Invertebr. Syst. 26:515-525.
27. Meiklejohn K.A., Wallman J.F., Dowton M. 2011. DNA-based identification of forensically important Australian Sarcophagidae (Diptera). Int. J. Legal Med. 125:27-32.
28. Meiklejohn K.A., Wallman J.F., Pape T., Cameron S.L., Dowton M. 2013. Utility of COI, CAD and morphological data for resolving relationships within the genus Sarcophaga (sensu lato) (Diptera: Sarcophagidae): a preliminary study. Mol. Phylogenet. Evol. 69:133-141.
29. Meyer C.P., Paulay G. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3:e422.
30. Nielsen R., Matz M. 2006. Statistical approaches for DNA barcoding. Syst. Biol. 55:162-169.
31. Puillandre N., Bouchet P., Boisselier-Dubayle M.-C., Brisset J., Buge B., Castelin M., Chagnoux S., Christophe T., Corbari L., Lambourdière J., Lozouet P., Marani G., Rivasseau A., Silva N., Terryn Y., Tillier S., Utge J., Samadi S. 2012a. New taxonomy and old collections: integrating DNA barcoding into the collection curation process. Mol. Ecol. Resour. 12:396-402.
32. Puillandre N., Lambert A., Brouillet S., Achaz G. 2012b. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol. Ecol. 21:1864-1877.
33. Ratnasingham S., Hebert P.D.N. 2013. A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS ONE 8:e66213.
34. Ross H.A. 2014. The incidence of species-level paraphyly in animals: a re-assessment. Mol. Phylogenet. Evol. 76:10-17.
35. Shokralla S., Gibson J.F., Nikbakht H., Janzen D.H., Hallwachs W., Hajibabaei M. 2014. Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Mol. Ecol. Resour. 14(5):892-901.
36. Sonet G., Jordaens K., Nagy Z.T., Breman F.C., De Meyer M., Backeljau T., Virgilio M. 2013. Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification. ZooKeys 336:329-335.
37. Taylor H.R., Harris W.E. 2012. An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol. Ecol. Resour. 12:377-388.
38. Virgilio M., Jordaens K., Breman F.C., Backeljau T., De Meyer M. 2012. Identifying insects with incomplete DNA barcode libraries, African fruit flies (Diptera: Tephritidae) as a test case. PLoS ONE 7:e31581.
39. Weitschek E., Van Velzen R., Felici G., Bertolazzi P. 2013. BLOG 2.0: a software systemfor character-based species classification with DNA Barcode sequences. What it does, how to use it. Mol. Ecol. Resour. 13:1043-1046.
40. Yang Z., Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. P. Nat. Acad. Sci. USA 107:9264-9269.
41. Zhang A.-B., Feng J., Ward R.D., Wan P., Gao Q., Wu J., Zhao W.-Z. 2012a. A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods. PLoS ONE 7:e30986.
42. Zhang A.-B., Muster C., Liang H.-B., Zhu C.-D., Crozier R., Wan P., Feng J., Ward R.D. 2012b. A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding. Mol. Ecol. 21:1848-1863.
43. Zhang A.-B., Sikes D.S., Muster C., Li S.Q. 2008. Inferring species membership using DNA sequences with back-propagation neural networks. Syst. Biol. 57:202-215.