DNA Barcoding: Error Rates Based on Comprehensive Sampling

By Christopher P. Meyer, Gustav Paulay. PLoS Biology, 2005

1,849 citations recorded by the source corpus.

DNA barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. We provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries). We utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. Error rates are estimated for (1) identifying samples against a well-characterized phylogeny, and (2) assisting in species discovery for partially known groups. We find that the lowest overall error for species identification is 4%. In contrast, barcoding performs poorly in incompletely sampled groups. Here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. Whereas proponents envision a “barcoding gap” between the two, we find substantial overlap, leading to minimal error rates of ~17% in cowries. Moreover, error rates double if only traditionally recognized species are analyzed. Thus, DNA barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. However, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. The promise of barcoding will be realized only if based on solid taxonomic foundations.

Subfields: Ecology, Molecular Biology, Oceanography

View Paper: https://www.semanticscholar.org/paper/24e1b181425519cebd27425dd5786244b9d57626

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Citations in the corpus

Integrative taxonomy: a multisource approach to exploring biodiversity. (2010, result): “This conclusion agrees with recent assertions that genetics may distort taxonomy when other data are neglected (15, 36, 40, 44, 65, 67).”
DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep‐sea environments (2007, background): “…the resolution of intra- and interspecific variation in DNA sequences (Hewitt 1996; Avise & Johns 1999; Hebert et al. 2003b; Moritz & Cicero 2004; Meyer & Paulay 2005) including problems associated with inherited symbionts (Hurst & Jiggins 2005), with introgression/ hybridization (e.g. Masta et…”
DNA barcoding reveals new insights into the diversity of Antarctic species of Orchomene sensu lato (Crustacea: Amphipoda: Lysianassoidea) (2011, background): “Meyer and Paulay (2005) assume that insufficient sampling on both intraspecific and interspecific levels can lead to false barcoding gaps.”
Recent advances in DNA taxonomy (2007, background): “There are now several well-documented cases where morphologically or cytologically defined taxa align closely with mtDNA clusters (Hugall et al. 2002; Hebert et al. 2003b, 2004b; Dalebout et al. 2004; Hogg and Hebert 2004; Paquin and Hedin 2004; Sharley et al. 2004; Barrett and Hebert 2005; Hebert a”
Evaluation of 10 plant barcodes in Bryophyta (Mosses) (2010, result): “Our results showed a significant difference for each locus (Table 3), although no single region exhibited clear discontinuity between inter- and intra-specific divergence like cox1 in animals (Meyer & Paulay, 2005).”
DNA Barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). (2008, methodology): “DNA barcoding studies of invertebrates indicate that the method is particularly misleading when applied to incompletely sampled and taxonomically poorly characterized groups (Meyer and Paulay, 2005; Meier et al., 2006).”
Integrative taxonomy identifies new (and old) species in the Lasioglossum (Dialictus) tegulare (Robertson) species group (Hymenoptera, Halictidae) (2009, background): “While many cases of completely non-overlapping % differences between intraspecific and interspecific divergences are known, the mere fact of evolution will result in numerous instances of overlap between them (e.g. Meyer & Paulay 2005).”
Current progress in DNA barcoding and future implications for entomology (2011, background): “Such cases may be improved by integrative taxonomic revisions that combine genetic and morphological data (Funk & Omland 2003; Dayrat 2005; Meyer & Paulay 2005; Kehlmaier & Assmann 2010).”
Cryptic species diversity in a widespread bumble bee complex revealed using mitochondrial DNA RFLPs (2008, background): “More recently, Meyer and Paulay (2005) have warned of difficulties in the use of CO1-based barcodes to differentiate among taxa when prior sampling of taxa is incomplete.”
DNA Barcoding, species delineation and taxonomy: a historical perspective (2015, neutral): “…of false positive ( i.e. a conspecific diverging by more than the threshold to the nearest species is attributed to a distinct species) and false-negative ( i.e. a heterospecific sequence diverging by less than the threshold from the nearest species is attributed to the same species) [64].”
Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals (2010, positive): “The intra-specific variations and inter-specific divergences of congeneric species in the dicotyledons, monocotyledons, gymnosperms, ferns, mosses, and animals were calculated using a K2P distance matrix, as described previously [11,31,32].”
DNA barcoding of Pacific Canada’s fishes (2009, background): “Cases of deep genetic divergence within single species often indicate overlooked cryptic species (Moritz 1994; Meyer and Paulay 2005 ).”