DNA Barcoding: Promise and Pitfalls

Moritz, Craig; Cicero, Carla

doi:10.1371/journal.pbio.0020354

Cited by 839 publications

(721 citation statements)

References 31 publications

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“…There is no single optimal method to determine the resolving power of DNA barcodes for all taxa (Austerlitz et al., 2009; Casiraghi et al., 2010; Collins & Cruickshank, 2013; Meyer & Paulay, 2005; Moritz & Cicero, 2004; Ross et al., 2008). Different approaches exist for matching an unknown query sequence with sequences in a reference database or library and tend to be based on ad hoc criteria which may include the frequency of the highest hits, percentage sequence similarity, bootstrapping, BLAST scores or tree‐based clustering assessment (Kress et al., 2009; Wilson et al.…”

Section: Discussionmentioning

confidence: 99%

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

Hosein

Austin

Maharaj

et al. 2017

Ecology and Evolution

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The islands of the Caribbean are considered to be a “biodiversity hotspot.” Collectively, a high level of endemism for several plant groups has been reported for this region. Biodiversity conservation should, in part, be informed by taxonomy, population status, and distribution of flora. One taxonomic impediment to species inventory and management is correct identification as conventional morphology‐based assessment is subject to several caveats. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species. In this study, the ability of DNA barcoding to confirm the identities of 14 endangered endemic vascular plant species in Trinidad was assessed using three DNA barcodes (matK, rbcL, and rpoC1). Herbarium identifications were previously made for all species under study. matK, rbcL, and rpoC1 markers were successful in amplifying target regions for seven of the 14 species. rpoC1 sequences required extensive editing and were unusable. rbcL primers resulted in cleanest reads, however, matK appeared to be superior to rbcL based on a number of parameters assessed including level of DNA polymorphism in the sequences, genetic distance, reference library coverage based on BLASTN statistics, direct sequence comparisons within “best match” and “best close match” criteria, and finally, degree of clustering with moderate to strong bootstrap support (>60%) in neighbor‐joining tree‐based comparisons. The performance of both markers seemed to be species‐specific based on the parameters examined. Overall, the Trinidad sequences were accurately identified to the genus level for all endemic plant species successfully amplified and sequenced using both matK and rbcL markers. DNA barcoding can contribute to taxonomic and biodiversity research and will complement efforts to select taxa for various molecular ecology and population genetics studies.

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Section: Discussionmentioning

confidence: 99%

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

Hosein

Austin

Maharaj

et al. 2017

Ecology and Evolution

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“…We obtained data for 184 specimens (see supplementary on-line Appendix S1) comprising 33 of the 41 described 235 species (>80%: 2/2 Ceroptres, 6/6 Saphonecrus, 23/30 Synergus, 2/3 Synophrus; Csóka et al, 10 2005;Sadeghi et al, 2006). Because the ability of DNA barcodes to assign individuals to species requires adequate sampling of intraspecific as well as interspecific variation (Moritz & Cicero, 2004;Morando et al, 2003), where possible we incorporated samples from multiple refugial centres of intraspecific diversity (Rokas et al, 2003b) Specimens were identified by Melika and Pujade-Villar, recognised experts in the field of morphological cynipid taxonomy and the authors of the existing keys (Pujade-Villar et al, 2003). Due to difficulties in morphological identification, some individual specimens were 255 assigned >1 morphospecies name (see Appendix S1).…”

Section: Taxon Samplingmentioning

confidence: 99%

“…The latter hypothesis predicts a mismatch between specimen groupings based on mitochondrial sequence data and those 515 based on nuclear sequence data. There are many reasons to expect such a mismatch (Hudson 21 & Turelli, 2003;Machado and Hey, 2003;Moritz & Cicero, 2004;Hurst & Jiggins, 2005). In particular, coalescent theory predicts that species can share coxI barcodes through incomplete sorting of ancestral polymorphism (Hickerson et al, 2006;Knowles & Carstens, 2007), and many species are polyphyletic rather than monophyletic for mitochondrial genes (Johnson & 520 Cicero 2002;Funk & Omland, 2003;Meyer & Paulay, 2005).…”

Section: Mismatches Between Morphological Taxonomy and Motu Membershimentioning

confidence: 99%

“…Coalescent theory predicts that both intraspecific sequence diversity and the probability of shared barcode sequences among discrete biological species will be 130 sensitive to population demography, particularly species age and past effective population size (Moritz & Cicero 2004;Meyer & Paulay 2005;Hickerson et al 2006;Nielsen & Matz 2006;Knowles & Carstens 2007). Young species with large effective population sizes are predicted not to be monophyletic for their barcode sequence, and where past population sizes vary substantially within a group of taxa, a single threshold divergence is unlikely to separate 135 6 intraspecific variation from varation among species -in other words, there may be no barcoding gap (Funk & Omland 2003;DeSalle et al, 2005;Meyer & Paulay, 2005;Cognato 2006; Vogler & Monaghan, 2006;Rubinoff, 2006).…”

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Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic

Ács

Challis

Bihari

et al. 2010

Molecular Phylogenetics and Evolution

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The NERC and CEH trade marks and logos ('the Trademarks') are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner. We examine phylogenetic relationships within the Synergus complex of herbivorous 50 inquiline gallwasps associated with (Hymenoptera; Cynipidae; Synergini) associated with cynipid host galls on oak, a biologically diverse group whose genus-level morphological taxonomy has long been considered stable but whose species level taxonomy is problematic.We incorporate data for over 80% of recognised Western Palaearctic species in 5 morphology-based genera (Ceroptres, Saphonecrus, Synergus, Synophrus, Ufo), comprising 55 sequence for two mitochondrial two mitochondrial loci (coxI, cytb) and one nuclear locus (28S D2). In particular, we assess the evidence for monophyly of two long-established, morphology-defined sections within the genus Synergus that differ in a range of biological traits between-generation polymorphism and impact on the host gall inducer (lethal versus non-lethal). To aid analyses of ecological interactions within oak cynipid communities, we 60 also consider the utility of cytochrome oxidase I (coxI) DNA barcodes in the oak inquilines.In this assessment, we do not assume that species are delineated at a single threshold value of sequence divergence for a single gene, but examine concordance in the composition of molecular operational Taxonomic units (MOTUs) across a range of sequence divergences in each gene and across genes. We also assess the impact of sampling effort on MOTU stability. 65Phylogenetic reconstructions for all three loci support monophyly for Synergus and Synophrus, but reject monophyly for Saphonecrus and for the two sections within Synergus.The suites of traits associated with the two sections of the genus Synergus are thus homoplasious. All three loci also reject monophyly for three Synergus species (S. hayneanus, S. pallipes, S. umbraculus). Sequences for each locus identify robust MOTUs that are largely 70 concordant across loci for a range of cut-off values. Though many MOTU's correspond to recognised Linnean species, there is significant, multigene disagreement between groupings supported by morphology and sequence data, with both allocation of different morphospecies to the same MOTU and allocation of the same morphospecies to multiple MOTUs, regardless 3 of cutoff value. Our results imply that while DNA barcoding has considerable utility within 75 this group, morphology-based identification needs major revision at both genus and species levels. Further, lifehistory traits currently attributed to single morphospecies probably confound attributes of multiple lineages. Revealing patterns of character state evolution in Synergus requires collection of new host association and life history data explicitly linked to DNA barcode data for the specimens concerned. 80

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“…For exam-ple, in the Hyalospheniidae, SSU rRNA does not allow to discriminating among closely related taxa (Lara et al 2008) while COI does (Kosakyan et al 2012(Kosakyan et al , 2013. The COI-based metabarcoding approach allows discrimination among taxa that are generally interpreted as biological species, for Metazoa (Hebert et al 2003;Ratnasingham and Hebert 2007) (but see Meyer and Paulay 2005;Moritz and Cicero 2004) and our recent work on Hyalospheniidae also supports this view Kosakyan et al 2013).…”

Section: Discussionmentioning

confidence: 97%

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

Kosakyan

Mulot

Mitchell

et al. 2015

European Journal of Protistology

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Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.

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DNA Barcoding: Promise and Pitfalls

Cited by 839 publications

References 31 publications

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

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