INVITED TECHNICAL REVIEW
An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding
H. R. TAYLOR,
W. E. HARRIS,
H. R. TAYLOR
Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, PO Box 600 Wellington, New Zealand
School of Science and the Environment, Manchester Metropolitan University, Oxford Road, Manchester M1 5GD, UK
Search for more papers by this authorW. E. HARRIS
School of Science and the Environment, Manchester Metropolitan University, Oxford Road, Manchester M1 5GD, UK
Search for more papers by this author
H. R. TAYLOR,
W. E. HARRIS,
H. R. TAYLOR
Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, PO Box 600 Wellington, New Zealand
School of Science and the Environment, Manchester Metropolitan University, Oxford Road, Manchester M1 5GD, UK
Search for more papers by this authorW. E. HARRIS
School of Science and the Environment, Manchester Metropolitan University, Oxford Road, Manchester M1 5GD, UK
Search for more papers by this author
Helen Taylor, Fax: +64 4 463 5331; E-mail: [email protected]
Abstract
DNA barcoding has become a well-funded, global enterprise since its proposition as a technique for species identification, delimitation and discovery in 2003. However, the rapid development of next generation sequencing (NGS) has the potential to render DNA barcoding irrelevant because of the speed with which it generates large volumes of genomic data. To avoid obsolescence, the DNA barcoding movement must adapt to use this new technology. This review examines the DNA barcoding enterprise, its continued resistance to improvement and the implications of this on the future of the discipline. We present the consistent failure of DNA barcoding to recognize its limitations and evolve its methodologies, reducing the usefulness of the data produced by the movement and throwing into doubt its ability to embrace NGS.
References
- Avise JC (2010) Perspective: conservation genetics enters the genomics era. Conservation Genetics, 11, 665–669.
- Ball SL, Hebert PDN, Burian SK, Webb JM (2005) Biological identifications of mayflies (Ephemeroptera) using DNA barcodes. Journal of the North American Benthological Society, 24, 508–524.
- Barber P, Boyce SL (2006) Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae. Proceedings of the Royal Society of London Series B-Biological Sciences, 273, 2053–2061.
- Barbuto M, Galimberti A, Ferri E et al. (2010) DNA barcoding reveals fraudulent substitutions in shark seafood products: the Italian case of “palombo” (Mustelus spp.). Food Research International, 43, 376–381.
- Begerow D, Nilsson H, Unterseher M, Maier W (2010) Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Applied Microbiology and Biotechnology, 87, 99–108.
- Bellemain E, Carlsen T, Brochmann C et al. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology, 10, 189.
- Bergmann T, Hadrys H, Breves G, Schierwater B (2009) Character-based DNA barcoding: a superior tool for species classification. Berliner Und Munchener Tierarztliche Wochenschrift, 122, 446–450.
- Blaxter M (2003) Molecular systematics – counting angels with DNA. Nature, 421, 122–124.
- Blaxter M, Mann J, Chapman T et al. (2005) Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 360, 1935–1943.
- Bonnet X, Shine R, Lourdais O (2002) Taxonomic chauvinism. Trends in Ecology & Evolution, 17, 1–3.
- Borisenko AV, Lim BK, Ivanova NV, Hanner RH, Hebert PDN (2008) DNA barcoding in surveys of small mammal communities: a field study in Suriname. Molecular Ecology Resources, 8, 471–479.
- Borisenko AV, Sones JE, Hebert PDN (2009) The front-end logistics of DNA barcoding: challenges and prospects. Molecular Ecology Resources, 9, 27–34.
- Bottrill MC, Joseph LN, Carwardine J et al. (2008) Is conservation triage just smart decision making? Trends in Ecology & Evolution, 23, 649–654.
- Bruns TD, White TJ, Taylor JW (1991) Fungal molecular systematics. Annual Review of Ecology and Systematics, 22, 525–564.
- Bucklin A, Wiebe PH, Smolenack SB et al. (2007) DNA barcodes for species identification of euphausiids (Euphausiacea, Crustacea). Journal of Plankton Research, 29, 483–493.
- Casiraghi M, Labra M, Ferri E, Galimberti A, De Mattia F (2010) DNA barcoding: a six-question tour to improve users’ awareness about the method. Briefings in Bioinformatics, 11, 440–453.
- Clare EL, Lim BK, Engstrom MD, Eger JL, Hebert PDN (2007) DNA barcoding of Neotropical bats: species identification and discovery within Guyana. Molecular Ecology Notes, 7, 184–190.
- Clark JA, May RM (2002) Taxonomic bias in conservation research. Science, 297, 191–192.
- Clarkston BE, Saunders GW (2010) A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthora timburtonii sp nov. Botany-Botanique, 88, 119–131.
- Creer S, Fonseca VG, Porazinska DL et al. (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology, 19, 4–20.
- Davis JI, Nixon KC (1992) Populations, genetic variation and the delimitation of phylogenetic species. Systematic Biology, 41, 421–435.
- DeSalle R (2006) Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conservation Biology, 20, 1545–1547.
- DeSalle R (2007) Phenetic and DNA taxonomy; a comment on Waugh. Bioessays, 29, 1289–1290.
- DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society B-Biological Sciences, 360, 1905–1916.
- deWaard JR, Landry JF, Schmidt BC et al. (2009) In the dark in a large urban park: DNA barcodes illuminate cryptic and introduced moth species. Biodiversity and Conservation, 18, 3825–3839.
- Dove CJ, Rotzel NC, Heacker M, Weigt LA (2008) Using DNA barcodes to identify bird species involved in birdstrikes. Journal of Wildlife Management, 72, 1231–1236.
- Eberhardt U (2010) A constructive step towards selecting a DNA barcode for fungi. New Phytologist, 187, 266–268.
- Eggert LS, Rasner CA, Woodruff DS (2002) The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers. Proceedings of the Royal Society of London Series B-Biological Sciences, 269, 1993–2006.
- Elias-Gutierrez M, Jeronimo FM, Ivanova NV, Valdez-Moreno M, Hebert PDN (2008) DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries. Zootaxa, 1839, 1–42.
10.11646/zootaxa.1839.1.1 Google Scholar
- Ellegren H (2008) Sequencing goes 454 and takes large-scale genomics into the wild. Molecular Ecology, 17, 1629–1631.
- Floyd R, Abebe E, Papert A, Blaxter M (2002) Molecular barcodes for soil nematode identification. Molecular Ecology, 11, 839–850.
- Foottit RG, Maw HEL, Havill NP, Ahern RG, Montgomery ME (2009) DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea). Molecular Ecology Resources, 9, 188–195.
- Forister ML, Nice CC, Fordyce JA, Gompert Z, Shapiro AM (2008) Considering evolutionary processes in the use of single-locus genetic data for conservation, with examples from the Lepidoptera. Journal of Insect Conservation, 12, 37–51.
- Gile GH, Stern RF, James ER, Keeling PJ (2010) DNA barcoding of chlorarachniophytes using nucleomorph ITS sequences. Journal of Phycology, 46, 743–750.
- Goldstein PZ, DeSalle R (2011) Integrating DNA barcode data and taxonomic practice: determination, discovery, and description. Bioessays, 33, 135–147.
- Gomez A, Wright PJ, Lunt DH et al. (2007) Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proceedings of the Royal Society of London Series B-Biological Sciences, 274, 199–207.
- Gompert Z, Nice CC, Fordyce JA, Forister ML, Shapiro AM (2006) Identifying units for conservation using molecular systematics: the cautionary tale of the Karner blue butterfly. Molecular Ecology, 15, 1759–1768.
- Gossner MM, Hausmann A (2009) DNA barcoding enables the identification of caterpillars feeding on native and alien oak (Lepidoptera: Geometridae). Mitteilungen Muenchener Entomologischen Gesellschaft, 99, 135–140.
- Hajibabaei MHM, Shokralla S, Zhou X, Singer GAC, Baird DJ (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE, 6, e17497.
- Hebert PDN, Barrett RDH (2005) Reply to the comment by L. Prendini on “Identifying spiders through DNA barcodes”. Canadian Journal of Zoology-Revue Canadienne De Zoologie, 83, 505–506.
- Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003a) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences, 270, 313–321.
- Hebert PDN, Ratnasingham S, deWaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London Series B-Biological Sciences, 270, S96–S99.
- Hebert PDN, Penton EH, Burns JM, Janzen DH, 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.
- Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004b) Identification of birds through DNA barcodes. Plos Biology, 2, 1657–1663.
- Hollingsworth PM, Forrest LL, Spouge JL et al. (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America, 106, 12794–12797.
- Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS ONE, 6, e19254.
- Holmes BH, Steinke D, Ward RD (2009) Identification of shark and ray fins using DNA barcoding. Fisheries Research, 95, 280–288.
- Hubert N, Hanner R, Holm E et al. (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE, 3, e2490.
- Humphries EM, Winker K (2011) Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds. Molecular Ecology, 20, 573–583.
- Janzen DH (2004) Now is the time. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 359, 731–732.
- Johnson SB, Waren A, Vrijenhoek RC (2008) DNA barcoding of Lepetodrilus limpets reveals cryptic species. Journal of Shellfish Research, 27, 43–51.
- Kelly RP, Sarkar IN, Eernisse DJ, Desalle R (2007) DNA barcoding using chitons (genus Mopalia). Molecular Ecology Notes, 7, 177–183.
- Kerr KCR, Stoeckle MY, Dove CJ et al. (2007) Comprehensive DNA barcode coverage of North American birds. Molecular Ecology Notes, 7, 535–543.
- Kerr KCR, Lijtmaer DA, Barreira AS, Hebert PDN, Tubaro PL (2009) Probing evolutionary patterns in neotropical birds through DNA barcodes. PLoS ONE, 4, e4379.
- Kircher M, Kelso J (2010) High-throughput DNA sequencing – concepts and limitations. Bioessays, 32, 524–536.
- Kress WJ, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE, 2, e508.
- Kress WJ, Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences of the United States of America, 105, 2761–2762.
- Kucera H, Saunders GW (2008) Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding. Botany-Botanique, 86, 1065–1079.
- Lane CE, Lindstrom SC, Saunders GW (2007) A molecular assessment of northeast Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding. Molecular Phylogenetics and Evolution, 44, 634–648.
- Locke SA, McLaughlin JD, Marcogliese DJ (2010) DNA barcodes show cryptic diversity and a potential physiological basis for host specificity among Diplostomoidea (Platyhelminthes: Digenea) parasitizing freshwater fishes in the St. Lawrence River, Canada. Molecular Ecology, 19, 2813–2827.
- Lowenstein JH, Amato G, Kolokotronis SO (2009) The real maccoyii: identifying tuna sushi with DNA barcodes – contrasting characteristic attributes and genetic distances. PLoS ONE, 4, e7866.
- Lowenstein JH, Burger J, Jeitner CW et al. (2010) DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers. Biology Letters, 6, 692–695.
- Lucking R (2008) Taxonomy: a discipline on the brink of extinction are DNA barcode scanners the future of biodiversity research? Archives Des Sciences, 61, 75–88.
- Magnacca KN, Brown MJF (2010) Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae). BMC Evolutionary Biology, 10.
- Mallet J, Willmott K (2003) Taxonomy: renaissance or Tower of Babel? Trends in Ecology & Evolution, 18, 57–59.
- May RM, Harvey PH (2009) Species uncertainties. Science, 323, 687.
- McDevit DC, Saunders GW (2009) On the utility of DNA barcoding for species differentiation among brown macroalgae (Phaeophyceae) including a novel extraction protocol. Phycological Research, 57, 131–141.
- Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. Plos Biology, 3, 2229–2238.
- Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B (2011) How many species are there on earth and in the ocean? Plos Biology, 9, e1001127.
- Moulton MJ, Song H, Whiting MF (2010) Assessing the effects of primer specificity on eliminating numt coamplification in DNA barcoding: a case study from Orthoptera (Arthropoda: Insecta). Molecular Ecology Resources, 10, 615–627.
- Moura CJ, Harris DJ, Cunha MR, Rogers AD (2008) DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep-sea environments. Zoologica Scripta, 37, 93–108.
- Nanney DL (1982) Genes and phenes in tetrahymena. BioScience, 32, 783–788.
- Neigel J, Domingo A, Stake J (2007) DNA barcoding as a tool for coral reef conservation. Coral Reefs, 26, 487–499.
- Packer L, Grixti JC, Roughley RE, Hanner R (2009) The status of taxonomy in Canada and the impact of DNA barcoding. Canadian Journal of Zoology-Revue Canadienne De Zoologie, 87, 1097–1110.
- Pauls SU, Blahnik RJ, Zhou X, Wardwell CT, Holzenthal RW (2010) DNA barcode data confirm new species and reveal cryptic diversity in Chilean Smicridea (Smicridea) (Trichoptera:Hydropsychidae). Journal of the North American Benthological Society, 29, 1058–1074.
- Peterson AT, Moyle RG, Nyari AS et al. (2007) The need for proper vouchering in phylogenetic studies of birds. Molecular Phylogenetics and Evolution, 45, 1042–1044.
- Prendini L (2005) Comment on “Identifying spiders through DNA barcodes”. Canadian Journal of Zoology-Revue Canadienne De Zoologie, 83, 498–504.
- Puillandre N, Lambert A, Brouillet S, Achaz G (2011) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology, doi: 10.1111/j.1365-294X.2011.05239.x.
- 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 of London Series B-Biological Sciences, 275, 237–247.
- Ragupathy S, Newmaster SG, Murugesan M, Balasubramaniam V (2009) DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India. Molecular Ecology Resources, 9, 164–171.
- Rasmussen RS, Morrissey MT, Hebert PDN (2009) DNA barcoding of commercially important salmon and trout species (Oncorhynchus and Salmo) from North America. Journal of Agricultural and Food Chemistry, 57, 8379–8385.
- Robba L, Russell SJ, Barker GL, Brodie J (2006) Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta). American Journal of Botany, 93, 1101–1108.
- Rubinoff D (2006a) DNA barcoding evolves into the familiar. Conservation Biology, 20, 1548–1549.
- Rubinoff D (2006b) Utility of mitochondrial DNA barcodes in species conservation. Conservation Biology, 20, 1026–1033.
- Rubinoff D, Cameron S, Will K (2006) Are plant DNA barcodes a search for the Holy Grail? Trends in Ecology & Evolution, 21, 1–2.
- Sarkar IN, Trizna M (2011) The Barcode of Life Data Portal: bridging the biodiversity informatics divide for DNA barcoding. PLoS ONE, 6, e14689.
- Sarkar IN, Planet PJ, Desalle R (2008) CAOS software for use in character-based DNA barcoding. Molecular Ecology Resources, 8, 1256–1259.
- Sarkar IN, Thornton JW, Planet PJ, Figurski DH, Schierwater B, DeSalle R (2002) An automated phylogenetic key for classifying homeoboxes. Molecular Phylogenetics and Evolution, 24, 388–399.
- Saunders GW (2008) A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea-Neodilsea complex and Weeksia. Botany-Botanique, 86, 773–789.
- Savolainen V, Cowan RS, Vogler AP, Roderick GK, 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.
- Scicluna SM, Tawari B, Clark CG (2006) DNA barcoding of Blastopystis. Protist, 157, 77–85.
- Seifert KA (2009) Progress towards DNA barcoding of fungi. Molecular Ecology Resources, 9, 83–89.
- Seifert KA, Samson RA, deWaard JR et al. (2007) Prospects for fungus identification using C01 DNA barcodes, with Penicillium as a test case. Proceedings of the National Academy of Sciences of the United States of America, 104, 3901–3906.
- Shapiro B, Sibthorpe D, Rambaut A et al. (2002) Flight of the dodo. Science, 295, 1683.
- Smith MA, Poyarkov NA Jr, Hebert PDN (2008) CO1 DNA barcoding amphibians: take the chance, meet the challenge. Molecular Ecology Resources, 8, 235–246.
- Stoeck T, Bass D, Nebel M et al. (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology, 19, 21–31.
- Stribling JB (2006) Environmental protection using DNA barcodes or taxa? BioScience, 56, 878–879.
- Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2003) A plea for DNA taxonomy. Trends in Ecology & Evolution, 18, 70–74.
- Tautz D, Ellegren H, Weigel D (2010) Next generation molecular ecology. Molecular Ecology, 19, 1–3.
- Valentini A, Pompanon F, Taberlet P (2009) DNA barcoding for ecologists. Trends in Ecology & Evolution, 24, 110–117.
- Van Bers NEM, Van Oers K, Kerstens HHD et al. (2010) Genome-wide SNP detection in the great tit Parus major using high throughput sequencing. Molecular Ecology, 19, 89–99.
- Vences M, Thomas M, Bonett RM, Vieites DR (2005) Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philosophical Transactions of the Royal Society B-Biological Sciences, 360, 1859–1868.
- Vogler A (2006) Will DNA barcoding advance efforts to conserve biodiversity more efficiently than traditional taxonomic methods? Reply. Frontiers in Ecology and the Environment, 4, 272–273.
- Vogler AP, Monaghan MT (2007) Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research, 45, 1–10.
- Ward RD, Holmes BH, O’Hara TD (2008) DNA barcoding discriminates echinoderm species. Molecular Ecology Resources, 8, 1202–1211.
- Webster J (1997) Fungal biodiversity – foreword. Biodiversity and Conservation, 6, 657.
- Wiemers M, Fiedler K (2007) Does the DNA barcoding gap exist? – a case study in blue butterflies (Lepidoptera: Lycaenidae). Frontiers in Zoology, 4, doi: 10.1186/1742-9994-4-8.
- Will KW, Rubinoff D (2004) Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics-the International Journal of the Willi Hennig Society, 20, 47–55.
- Wilson DE, Reeder DAM (2005) Mammal Species of the World: A Taxonomic and Geographic Reference. Johns Hopkins University Press, Baltimore, MA.
10.56021/9780801882210 Google Scholar
- Witt JDS, Threloff DL, Hebert PDN (2006) DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Molecular Ecology, 15, 3073–3082.
- Wong EHK, Hanner RH (2008) DNA barcoding detects market substitution in North American seafood. Food Research International, 41, 828–837.
- Yoo HS, Eah J-Y, Kim JS et al. (2006) DNA barcoding Korean birds. Molecules and Cells, 22, 323–327.
- Zhang AB, Muster C, Liang HB et al. (2011) A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding. Molecular Ecology, doi: 10.1111/j.1365-294X.2011.05235.x.
