Biological identifications through DNA barcodes

Hebert, Paul D. N.; Cywinska, A.; Ball, Shelley L.; deWaard, Jeremy R

doi:10.1098/rspb.2002.2218

Cited by 10,962 publications

(9,812 citation statements)

References 36 publications

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“…Although the COI was used earlier as a population genetics tool in this way, the barcode concept itself was substantially forged in the 21st century (Hebert et al 2003).…”

Section: T H E M T D N a C O I B A R C O D Ementioning

confidence: 99%

DNA barcoding mosquitoes: advice for potential prospectors

Beebe

2018

Parasitology

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S U M M A R YMosquitoes' importance as vectors of pathogens that drive disease underscores the importance of precise and comparable methods of taxa identification among their species. While several molecular targets have been used to study mosquitoes since the initiation of PCR in the 1980s, its application to mosquito identification took off in the early 1990s. This review follows the research's recent journey into the use of mitochondrial DNA (mtDNA) cytochrome oxidase 1 (COI or COX1) as a DNA barcode target for mosquito species identification -a target whose utility for discriminating mosquitoes is now escalating. The pros and cons of using a mitochondrial genome target are discussed with a broad sweep of the mosquito literature suggesting that nuclear introgressions of mtDNA sequences appear to be uncommon and that the COI works well for distantly related taxa and shows encouraging utility in discriminating more closely related species such as cryptic/sibling species groups. However, the utility of COI in discriminating some closely related groups can be problematic and investigators are advised to proceed with caution as problems with incomplete lineage sorting and introgression events can result in indistinguishable COI sequences appearing in reproductively independent populations. In these -if not all -cases, it is advisable to run a nuclear marker alongside the mtDNA and thus the utility of the ribosomal DNAand in particular the internal transcribed spacer 2 -is also briefly discussed as a useful counterpoint to the COI.

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“…Although the COI was used earlier as a population genetics tool in this way, the barcode concept itself was substantially forged in the 21st century (Hebert et al 2003).…”

Section: T H E M T D N a C O I B A R C O D Ementioning

confidence: 99%

DNA barcoding mosquitoes: advice for potential prospectors

Beebe

2018

Parasitology

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“…COI markers can also take advantage of “barcode” databases (Hebert, Cywinska, Ball, & deWaard, 2003; Ratnasingham & Hebert, 2007). However, as COI is a protein‐coding gene, “third codon wobble” increases the chance of primer mismatches when targeting genetically diverse taxonomic groups.…”

Section: Introductionmentioning

confidence: 99%

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

Clarke

Beard

Swadling

et al. 2017

Ecology and Evolution

169

193

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DNA metabarcoding is a promising approach for rapidly surveying biodiversity and is likely to become an important tool for measuring ecosystem responses to environmental change. Metabarcoding markers need sufficient taxonomic coverage to detect groups of interest, sufficient sequence divergence to resolve species, and will ideally indicate relative abundance of taxa present. We characterized zooplankton assemblages with three different metabarcoding markers (nuclear 18S rDNA, mitochondrial COI, and mitochondrial 16S rDNA) to compare their performance in terms of taxonomic coverage, taxonomic resolution, and correspondence between morphology‐ and DNA‐based identification. COI amplicons sequenced on separate runs showed that operational taxonomic units representing >0.1% of reads per sample were highly reproducible, although slightly more taxa were detected using a lower annealing temperature. Mitochondrial COI and nuclear 18S showed similar taxonomic coverage across zooplankton phyla. However, mitochondrial COI resolved up to threefold more taxa to species compared to 18S. All markers revealed similar patterns of beta‐diversity, although different taxa were identified as the greatest contributors to these patterns for 18S. For calanoid copepod families, all markers displayed a positive relationship between biomass and sequence reads, although the relationship was typically strongest for 18S. The use of COI for metabarcoding has been questioned due to lack of conserved primer‐binding sites. However, our results show the taxonomic coverage and resolution provided by degenerate COI primers, combined with a comparatively well‐developed reference sequence database, make them valuable metabarcoding markers for biodiversity assessment.

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“…With no agreement on the process of speciation but with a pressing need to inventory biodiversity, molecular biologists have sought a means to identity species using DNA sequences – the so‐called DNA barcoding (Hebert et al. 2003a; Kress et al. 2014).…”

Section: Introductionmentioning

confidence: 99%

“…The sorting of animal species by COX1 genotype is enabled by a barcode gap whereby individuals in a species are more similar to each other in COX1 sequence than they are to individuals in any other species (Hebert et al. 2003a; Bucklin et al. 2011).…”

Section: Introductionmentioning

confidence: 99%

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

Hill

2016

Ecology and Evolution

149

178

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Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population‐specific mitonuclear coadaptations create between‐population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.

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Biological identifications through DNA barcodes

Cited by 10,962 publications

References 36 publications

DNA barcoding mosquitoes: advice for potential prospectors

DNA barcoding mosquitoes: advice for potential prospectors

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

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