IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0030490.html
   My bibliography  Save this article

DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods

Author

Listed:
  • Robin van Velzen
  • Emanuel Weitschek
  • Giovanni Felici
  • Freek T Bakker

Abstract

Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a ‘barcode gap’ and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P

Suggested Citation

  • Robin van Velzen & Emanuel Weitschek & Giovanni Felici & Freek T Bakker, 2012. "DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-12, January.
    • Handle: RePEc:plo:pone00:0030490
    DOI: 10.1371/journal.pone.0030490
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030490
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0030490&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0030490?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. David E. Schindel & Scott E. Miller, 2005. "DNA barcoding a useful tool for taxonomists," Nature, Nature, vol. 435(7038), pages 17-17, May.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. B Eugene Smith & Mark K Johnston & Robert Lücking, 2016. "From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories," PLOS ONE, Public Library of Science, vol. 11(3), pages 1-15, March.
    2. Qian Jin & Li-Jun He & Ai-Bing Zhang, 2012. "A Simple 2D Non-Parametric Resampling Statistical Approach to Assess Confidence in Species Identification in DNA Barcoding—An Alternative to Likelihood and Bayesian Approaches," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-11, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0030490. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.