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DNA Barcoding in Marine Perspectives pp 29–41Cite as

Measurement of a Barcode’s Accuracy in Identifying Species

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Abstract

This chapter describes a workflow for measuring a barcode’s accuracy when identifying species. First, assemble a database of specimens with their marker sequences and their species binomials. The species binomials provide a “taxonomic gold standard” for species identification and should be as accurate as possible, to avoid penalizing correct species assignment. Second, select a computer algorithm for assigning species to barcode sequences. Only one algorithm (BLAST+P) has improved notably on the simple strategy of assigning specimens to the species of the database sequence(s) nearest under p-distance. Global sequence alignments (e.g., with the Needleman-Wunsch algorithm, or with multiple sequence alignment algorithms) align entire barcode sequences, using all available information, so they sometimes produce more accurate species identifications than local sequence alignments (e.g., with BLAST), particularly when BLAST produces barcode alignments of small subsequences within the sequences. Finally, consensus has settled on “the probability of correct identification” (PCI) as the appropriate measurement of species identification accuracy. The overall PCI for a data set is the average of the species PCIs, taken over all species in the data set. The chapter discusses some variant PCIs, their calculation and the estimation of their statistical sampling errors. It also discusses good practice in incorporating PCR failure and species with singleton representatives into data summaries. For software relevant to this chapter, see http://tinyurl.com/spouge-barcode.

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References

  • Albu M, Nikbakht H, Hajibabaei M, Hickey DA (2011) The DNA barcode linker. Mol Ecol Resour 11:84–88

    Article  PubMed  Google Scholar 

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Austerlitz F (2007) Comparing phylogenetic and statistical classification methods for DNA barcoding. In: The second international barcode of life conference, Taipei

    Google Scholar 

  • Austerlitz F, David O, Schaeffer B, Bleakley K, Olteanu M, Leblois R, Veuille M, Laredo C (2009) DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinform 10:1

    Article  Google Scholar 

  • Blaxter M, Mann J, Chapman T, Thomas F, Whitton C, Floyd R, Abebe E (2005) Defining operational taxonomic units using DNA barcode data. Philos Trans R Soc B Biol Sci 360:1935–1943

    Article  CAS  Google Scholar 

  • CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:12794–12797

    Article  PubMed Central  Google Scholar 

  • Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, Savolainen V (2005) Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc Lond B Biol Sci 360:1889–1895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen J, Zhao JT, Erickson DL, Xia NH, Kress WJ (2015) Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China. Mol Ecol Resour 15:337–348

    Article  PubMed  Google Scholar 

  • Collins RA (2012) Barcoding’s next top model: an evaluation of nucleotide substitution models for specimen identification. Methods Ecol Evol 3:457–465

    Article  Google Scholar 

  • Cowan RS, Chase MW, Kress JW, Savolainen V (2006) 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 55:611–616

    Article  Google Scholar 

  • DasGupa B, Konwar KM, Mandoiu II, Shvartsman AA (2005) DNA-BAR: distinguisher selection for DNA barcoding. Bioinformatics 21:3424–3426

    Article  Google Scholar 

  • Eddy SR (1995) Multiple alignment using hidden Markov models. Proc Int Conf Intell Syst Mol Biol 3:114–120

    CAS  PubMed  Google Scholar 

  • Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform 5:113

    Article  Google Scholar 

  • Efron B, Stein C (1981) The Jackknife estimate of variance. Ann Stat 9:586–596

    Article  Google Scholar 

  • Erickson DL, Spouge JL, Resch A, Weight LA, Kress JW (2008) DNA barcoding in land plants: developing standards to quantify and maximize success. Taxon 13:1304–1316

    Google Scholar 

  • Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106:645–668

    Article  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1988) Phylogenies from molecular sequences—inference and reliability. Annu Rev Genet 22:521–565

    Article  CAS  PubMed  Google Scholar 

  • Ferguson JWH (2002) On the use of genetic divergence for identifying species. Biol J Linn Soc 75:509–516

    Article  Google Scholar 

  • Ferri G, Corradini B, Ferrari F, Santunione AL, Palazzoli F, Alu M (2015) Forensic botany II, DNA barcode for land plants: which markers after the international agreement? Forensic Sci Int Genet 15:131–136

    Article  CAS  PubMed  Google Scholar 

  • Floyd R, Abebe E, Papert A, Blaxter M (2002) Molecular barcodes for soil nematode identification. Mol Ecol 11:839–850

    Article  CAS  PubMed  Google Scholar 

  • Fregin S, Haase M, Olsson U, Alstrom P (2012) Pitfalls in comparisons of genetic distances: a case study of the avian family Acrocephalidae. Mol Phylogenet Evol 62:319–328

    Article  PubMed  Google Scholar 

  • Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci USA 103:968–971

    Article  PubMed  PubMed Central  Google Scholar 

  • Hebert PD, Cywinska A, Ball SL, deWaard JR (2003a) Biological identifications through DNA barcodes. Proc Biol Sci 270:313–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hebert PD, Ratnasingham S, deWaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci 270(Suppl 1):S96–S99

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hogg ID, Hebert PDN (2004) Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes. Can J Zool (Revue Canadienne De Zoologie) 82:749–754

    Article  Google Scholar 

  • Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Chase MW, Cowan RS, Erickson DL, Fazekas AJ, Graham SW, James KE, Kim K-J, Kress WJ, Schneider H, van AlphenStahl J, Barrett SCH, van den Berg C, Bogarin D, Burgessk KS, Cameron KM, Carine M, Chacón J, Clark A, Clarkson JJ, Conrad F, Devey DS, Ford CS, Hedderson TAJ, Hollingsworth ML, Husband BC, Kellya LJ, Kesanakurti PR, Kim JS, Kim Y-D, Lahaye R, Lee H-L, Long DG, Madriñán S, Maurin O, Meusnier I, Newmaster SG, Park C-W, Percy DM, Petersen G, Richardson JE, Salazar GA, Savolainene V, Seberg O, Wilkinson MJ, Yi D-K, Little DP (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:12794–12797

    Article  CAS  PubMed Central  Google Scholar 

  • Huang D, Meier R, Todd PA, Chou LM (2008) Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J Mol Evol 66:167–174

    Article  CAS  PubMed  Google Scholar 

  • Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl Acids Res 30:3059–3066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kress WJ, Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proc Natl Acad Sci USA 105:2761–2762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102:8369–8374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuksa P, Pavlovic V (2009) Efficient alignment-free DNA barcode analytics. BMC Bioinform 10:S9

    Article  Google Scholar 

  • Kwong S, Srivathsan A, Vaidya G, Meier R (2012) Is the COI barcoding gene involved in speciation through intergenomic conflict? Mol Phylogenet Evol 62:1009–1012

    Article  CAS  PubMed  Google Scholar 

  • Lambert DM, Baker A, Huynen L, Haddrath O, Hebert PDN, Millar CD (2005) Is a large-scale DNA-based inventory of ancient life possible? J Hered 96:279–284

    Article  CAS  PubMed  Google Scholar 

  • Little DP (2011) DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability. PLoS ONE 6(8):e20552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Little DP, Stevenson DW (2007) A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 23:1–27

    Article  Google Scholar 

  • Liu C, Liang D, Gao T, Pang X, Song J, Yao H, Han J, Liu Z, Guan X, Jiang K, Li H, Chen S (2011) PTIGS-IdIt, a system for species identification by DNA sequences of the psbA-trnH intergenic spacer region. BMC Bioinform 12:1

    Google Scholar 

  • Lorenz JG, Jackson WE, Beck JC, Hanner R (2005) The problems and promise of DNA barcodes for species diagnosis of primate biomaterials. Philos Trans R Soc B Biol Sci 360:1869–1877

    Article  CAS  Google Scholar 

  • Meier R, Shiyang K, Vaidya G, Ng PK (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol 55:715–728

    Article  PubMed  Google Scholar 

  • Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3:e422

    Article  PubMed  PubMed Central  Google Scholar 

  • Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R (2008) Statistical assignment of DNA sequences using Bayesian phylogenetics. Syst Biol 57:750–757

    Article  PubMed  Google Scholar 

  • Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453

    Article  CAS  PubMed  Google Scholar 

  • Pang X, Liu C, Shi L, Liu R, Liang D, Li H, Cherny SS, Chen S (2012) Utility of the trnH-psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis. PLoS ONE 7:e48833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ratnasingham S, Hebert PD (2007) BOLD: the barcode of life data system, Mol Ecol Notes 7:355–364. http://www.barcodinglife.org

  • Saitou N, Nei M (1987) The neighbor-joining method—a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sarkar IN, Planet PJ, Desalle R (2008) CAOS software for use in character-based DNA barcoding. Mol Ecol Resour 8:1256–1259

    Article  CAS  PubMed  Google Scholar 

  • Saunders GW (2005) Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos Trans R Soc B Biol Sci 360:1879–1888

    Article  CAS  Google Scholar 

  • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Bolchacova E, Voigt K, Crous PW, Miller AN, Wingfield MJ, Aime MC, An KD, Bai FY, Barreto RW, Begerow D, Bergeron MJ, Blackwell M, Boekhout T, Bogale M, Boonyuen N, Burgaz AR, Buyck B, Cai L, Cai Q, Cardinali G, Chaverri P, Coppins BJ, Crespo A, Cubas PP, Cummings C, Damm U, de Beer ZW, de Hoog GS, Del-Prado R, Dentinger B, Dieguez-Uribeondo J, Divakar PK, Douglas B, Duenas M, Duong TA, Eberhardt U, Edwards JE, Elshahed MS, Fliegerova K, Furtado M, Garcia MA, Ge ZW, Griffith GW, Griffiths K, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Guo LD, Hagen F, Hambleton S, Hamelin RC, Hansen K, Harrold P, Heller G, Herrera G, Hirayama, K, Hirooka Y, Ho HM, Hoffmann K, Hofstetter V, Hognabba F, Hollingsworth PM, Hong SB, Hosaka K, Houbraken J, Hughes K, Huhtinen S, Hyde KD, James T, Johnson EM, Johnson JE, Johnston PR, Jones EB, Kelly LJ, Kirk PM, Knapp DG, Koljalg U, Kovacs GM, Kurtzman CP, Landvik S, Leavitt SD, Liggenstoffer AS, Liimatainen K, Lombard L, Luangsa-Ard JJ, Lumbsch HT, Maganti H, Maharachchikumbura SS, Martin MP, May TW, McTaggart AR, Methven AS, Meyer W, Moncalvo JM, Mongkolsamrit S, Nagy LG, Nilsson RH, Niskanen T, Nyilasi I, Okada G, Okane I, Olariaga I, Otte J, Papp T, Park D, Petkovits T, Pino-Bodas R, Quaedvlieg W, Raja HA, Redecker D, Rintoul T, Ruibal C, Sarmiento-Ramirez JM, Schmitt I, Schussler A, Shearer C, Sotome K, Stefani FO, Stenroos S, Stielow B, Stockinger H, Suetrong S, Suh SO, Sung GH, Suzuki M, Tanaka K, Tedersoo L, Telleria MT, Tretter E, Untereiner WA, Urbina H, Vagvolgyi C, Vialle A, Vu TD, Walther G, Wang QM, Wang Y, Weir BS, Weiss M, White MM, Xu J, Yahr R, Yang, ZL, Yurkov A, Zamora JC, Zhang N, Zhuang WY, Schindel D, Fungal Barcoding C (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109:6241–6246

    Google Scholar 

  • Smith MA, Fisher BL, Hebert PDN (2005) DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philos Trans R Soc B Biol Sci 360:1825–1834

    Article  CAS  Google Scholar 

  • Smith MA, Woodley NE, Janzen DH, Hallwachs W, Hebert PDN (2006) DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). Proc Natl Acad Sci USA 103:3657–3662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147:195–197

    Article  CAS  PubMed  Google Scholar 

  • Smith TF, Waterman MS, Fitch WM (1981) Comparative biosequence metrics. J Mol Evol 18:38–46

    Article  CAS  PubMed  Google Scholar 

  • Spouge JL, Mariño-Ramírez L (2012) The practical evaluation of DNA barcode efficacy. Methods Mol Biol 858:365–377

    Article  PubMed  PubMed Central  Google Scholar 

  • Suwannasai N, Martin MP, Phosri C, Sihanonth P, Whalley AJS, Spouge JL (2013) Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon Genera. PLoS ONE 8:e54529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weitschek E, Fiscon G, Felici G (2014) Supervised DNA barcodes species classification: analysis, comparisons and results. Biodata Min 7:1

    Article  Google Scholar 

  • Weitschek E, Van Velzen R, Felici G, Bertolazzi P (2013) BLOG 2.0: a software system for character-based species classification with DNA barcode sequences. What it does, how to use it. Mol Ecol Resour 13:1043–1046

    PubMed  Google Scholar 

  • Wilson EB (1927) Probable inference, the law of succession, and statistical inference. J Am Stat Assoc 22:209–212

    Article  Google Scholar 

  • Wouters MA, Husain A (2001) Changes in zinc ligation promote remodeling of the active site in the zinc hydrolase superfamily. J Mol Biol 314:1191–1207

    Article  CAS  PubMed  Google Scholar 

  • Zalasiewicz J et al (2000) Are we now living in the Anthropocene? GSA Today 18:4–8

    Article  Google Scholar 

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Acknowledgments

This research was supported in part by the Intramural Research Program of the NIH, NLM, NCBI.

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Authors and Affiliations

  1. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA

    John L. Spouge

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  1. John L. Spouge
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Correspondence to John L. Spouge .

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Editors and Affiliations

  1. Department of Biology, Faculty of Sci., University of Tabuk Department of Biology, Faculty of Sci., Tabuk, Saudi Arabia

    Subrata Trivedi

  2. University of Tabuk, Tabuk, Saudi Arabia

    Abid Ali Ansari

  3. Department of Biotechnology, Assam University Department of Biotechnology, Assam, India

    Sankar K. Ghosh

  4. Department of Biology, University of Tabuk Faculty of Science, Tabuk, Saudi Arabia

    Hasibur Rehman

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Spouge, J.L. (2016). Measurement of a Barcode’s Accuracy in Identifying Species. In: Trivedi, S., Ansari, A., Ghosh, S., Rehman, H. (eds) DNA Barcoding in Marine Perspectives. Springer, Cham. https://doi.org/10.1007/978-3-319-41840-7_2

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