On the inappropriate use of Kimura‐2‐parameter (K2P) divergences in the DNA‐barcoding literature

Here we present evidence, based on 10 datasets comprising 5283 sequences for 200 genera, that the use of the Kimura‐2‐parameter (K2P) model in DNA‐barcoding studies is poorly justified. We demonstrate that K2P is neither expected nor confirmed to be an appropriate model for closely related COI sequences. In addition, we show that the use of uncorrected distances yields higher or similar identification success rates for neighbour‐joining trees and distance‐based identification techniques. K2P also does not widen the barcoding gap for closely related sequences. We conclude that the spread of K2P through the barcoding literature is difficult to explain, and urge the use of evidence‐based approaches to DNA barcoding.

[1]  Mark J. F. Brown,et al.  Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae) , 2010, BMC Evolutionary Biology.

[2]  A. Oskooi Molecular Evolution and Phylogenetics , 2008 .

[3]  B. W. Sweeney,et al.  Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? , 2011, Journal of the North American Benthological Society.

[4]  Amanda D. Roe,et al.  Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implications for DNA barcoding. , 2007, Molecular phylogenetics and evolution.

[5]  N. Ivanova,et al.  The Role of DNA Barcodes in Understanding and Conservation of Mammal Diversity in Southeast Asia , 2010, PloS one.

[6]  Q. Wheeler,et al.  The perils of DNA barcoding and the need for integrative taxonomy. , 2005, Systematic biology.

[7]  C. Cicero,et al.  Open access, freely available online Correspondence DNA Barcoding: Promise and Pitfalls , 2022 .

[8]  D. Posada jModelTest: phylogenetic model averaging. , 2008, Molecular biology and evolution.

[9]  P. Hebert,et al.  bold: The Barcode of Life Data System (http://www.barcodinglife.org) , 2007, Molecular ecology notes.

[10]  M. P. Cummings,et al.  PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4 , 2000 .

[11]  D. Steinke,et al.  Biodiversity of arctic marine fishes: taxonomy and zoogeography , 2011, Marine Biodiversity.

[12]  S. Pauls,et al.  DNA barcode data confirm new species and reveal cryptic diversity in Chilean Smicridea (Smicridea) (Trichoptera:Hydropsychidae) , 2010, Journal of the North American Benthological Society.

[13]  N. Baeshen,et al.  Biological Identifications Through DNA Barcodes , 2012 .

[14]  Indra Neil Sarkar,et al.  caos software for use in character‐based DNA barcoding , 2008, Molecular ecology resources.

[15]  Philip Smith,et al.  Cryptic speciation and the circumpolarity debate: A case study on endemic Southern Ocean octopuses using the COI barcode of life , 2011 .

[16]  D. Rubinoff Utility of Mitochondrial DNA Barcodes in Species Conservation , 2006, Conservation biology : the journal of the Society for Conservation Biology.

[17]  Vladimir Pavlovic,et al.  Fast Kernel Methods for SVM Sequence Classifiers , 2007, WABI.

[18]  P. Hebert,et al.  Females do count: Documenting Chironomidae (Diptera) species diversity using DNA barcoding , 2010, Organisms Diversity & Evolution.

[19]  A. Brower Problems with DNA barcodes for species delimitation: ‘Ten species’ of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae) , 2006 .

[20]  Rudolf Meier,et al.  Dna Sequences In Taxonomy: Opportunities And Challenges , 2008 .

[21]  K. Will,et al.  Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification , 2004, Cladistics : the international journal of the Willi Hennig Society.

[22]  Shilin Chen,et al.  Applying plant DNA barcodes for Rosaceae species identification , 2011, Cladistics : the international journal of the Willi Hennig Society.

[23]  R. Hanner,et al.  The campaign to DNA barcode all fishes, FISH-BOL. , 2009, Journal of fish biology.

[24]  M. Kimura A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[25]  A. Kawahara,et al.  The butterfly subfamily Pseudopontiinae is not monobasic: marked genetic diversity and morphology reveal three new species of Pseudopontia (Lepidoptera: Pieridae) , 2011 .

[26]  R. Meier,et al.  The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification. , 2008, Systematic biology.

[27]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[28]  Zhiduan Chen,et al.  Species identification of Alnus (Betulaceae) using nrDNA and cpDNA genetic markers , 2009, Molecular ecology resources.

[29]  D. Stevenson,et al.  A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms , 2007, Cladistics : the international journal of the Willi Hennig Society.

[30]  L. Weigt,et al.  Seven new species within western Atlantic Starksia atlantica, S. lepicoelia, and S. sluiteri (Teleostei, Labrisomidae), with comments on congruence of DNA barcodes and species , 2011, ZooKeys.

[31]  D. Baird,et al.  Building freshwater macroinvertebrate DNA-barcode libraries from reference collection material: formalin preservation vs specimen age , 2011, Journal of the North American Benthological Society.

[32]  A. Couloux,et al.  The actinopterygian diversity of the CEAMARC cruises: Barcoding and molecular taxonomy as a multi-level tool for new findings , 2011 .

[33]  P. Hebert,et al.  DNA barcoding Indian marine fishes , 2011, Molecular ecology resources.

[34]  C. Erséus,et al.  DNA Barcoding Reveals Cryptic Diversity in Lumbricus terrestris L., 1758 (Clitellata): Resurrection of L. herculeus (Savigny, 1826) , 2010, PloS one.

[35]  Rob DeSalle,et al.  The unholy trinity: taxonomy, species delimitation and DNA barcoding , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[36]  I. Kaczmarska,et al.  Barcoding of diatoms: nuclear encoded ITS revisited. , 2010, Protist.

[37]  Gaurav Vaidya,et al.  DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. , 2006, Systematic biology.

[38]  C. Meyer,et al.  DNA Barcoding: Error Rates Based on Comprehensive Sampling , 2005, PLoS biology.