DNA BARCODING: CO1 DNA barcoding amphibians: take the chance, meet the challenge

Smith, M. Alex; Poyarkov, N.A.; Hebert, Paul D. N.

doi:10.1111/j.1471-8286.2007.01964.x

Cited by 167 publications

(157 citation statements)

References 69 publications

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“…There are multiple copies of mtDNA compared to nDNA, making it easier to amplify by polymerase chain reaction (PCR). The CO1 gene has been used as the main barcoding target gene for species identification of many organisms (Rock et al, 2008;Smith et al, 2008), but this gene is also useful in phylogeographic studies within a single species (DeBoer et al, 2008;Li et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Genetic differentiation of octopuses from different habitats near the Korean Peninsula and eastern China based on analysis of the mDNA cytochrome C oxidase 1 gene

Kang

Park²,

Choi

2012

Genet. Mol. Res.

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ABSTRACT. Distributed along the coastal waters of Korea and China, Octopus minor is found in various habitats, including the mud flats in the southern and western coasts of the Korean Peninsula and the rocky areas around Jeju Island; however, the genetic relationships among the different populations are unknown and have not been studied. We compared 630-nucleotide sequences of the CO1 gene from O. minor specimens collected from five regions around the Korean Peninsula and three regions from eastern China in order to determine population structure and genetic relationships. Based on the sequences at 12 polymorphic sites in this region, 11 haplotypes were identified from 85 specimens. Individuals from Jeju Island had unique haplotypes, including two haplotypes not found in the other populations. Nucleotide and haplotype diversity for all populations ranged from 0.03-0.37 and 0.20-0.64, respectively. Pairwise F ST values indicated significant genetic differences in populations from Korea and China. An UPGMA dendrogram showed separation of the eight populations into three clusters; one included only the Jeju population, another included the rest of the Korean populations and some from Dalian, China; a third cluster consisted of two other populations from China. We conclude that there are discrete genetic differences in O. minor from the different habitats, suggesting that the populations should be considered as management units in the ongoing recovery program.

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Section: Introductionmentioning

confidence: 99%

Genetic differentiation of octopuses from different habitats near the Korean Peninsula and eastern China based on analysis of the mDNA cytochrome C oxidase 1 gene

Kang

Park²,

Choi

2012

Genet. Mol. Res.

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“…Smith et al 2006Smith et al , 2008, including some groups of helminths (Ferri et al 2009;Moszczynska et al 2009). The aim of this study is to test the performance of partial sequences of cox1 in the discrimination of Table I.…”

Section: Introductionmentioning

confidence: 99%

Evidence of new species ofHaematoloechus(Platyhelminthes: Digenea) using partialcox1sequences

León‐Régàgnon

2010

Mitochondrial DNA

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To cite this article: Virginia León-Règagnon (2010) Evidence of new species of Haematoloechus (Platyhelminthes: Digenea) using partial cox1 sequences, Mitochondrial DNA, 21:sup1, 12-17, DOI: 10.3109/19401736.2010.523700 To link to this article: https://doi.org/10. 3109/19401736.2010.523700 Abstract Background and aims. Haematoloechus, digeneans parasites of amphibians, is a species-rich genus with more than 50 species around the globe. Establishing an accurate taxonomy for this group has been difficult due to high intraspecific variability. Nuclear DNA sequences have given independent information about species validity and phylogeny of the group.Materials and methods. In this paper, I test the performance of partial sequences of the mitochondrial cytochrome c oxidase subunit I (cox1) gene in the differentiation of recognized species of the genus and in the detection of potential new taxa. Samples from 13 nominal species were sequenced, plus four samples that could not be assigned to any described species based on morphology.Results. Parsimony analysis of the amplified 360 bp fragment resulted in six most parsimonious trees showing the same grouping of samples, differing in the samples' arrangement within those groups. All 13 species were recovered on the trees, and five potential new species are shown.Conclusion. Additional sampling and sequencing is necessary to support this hypothesis, but with this preliminary information the search for diagnostic characters that allow the description of the new taxa is less difficult.

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“…To confirm the quality and quantity of DNA in the samples from 2010, six randomly selected toe clips and eight FTA cards were selected and tested by PCR for DNA from the amphibian mitochondrial gene cytochrome oxidase I (CO1), using primers LepF1 and LepR1 (Smith et al, 2008).…”

Section: Methodsmentioning

confidence: 99%

LOW DETECTION OF RANAVIRUS DNA IN WILD POSTMETAMORPHIC GREEN FROGS, RANA (LITHOBATES) CLAMITANS, DESPITE PREVIOUS OR CONCURRENT TADPOLE MORTALITY

Forzán

Wood

2013

Journal of Wildlife Diseases

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ABSTRACT:Ranavirus (Iridoviridae) infection is a significant cause of mortality in amphibians. Detection of infected individuals, particularly carriers, is necessary to prevent and control outbreaks. Recently, the use of toe clips to detect ranavirus infection through PCR was proposed as an alternative to the more frequently used lethal liver sampling in green frogs (Rana [Lithobates] clamitans). We attempted reevaluate the use of toe clips, evaluate the potential use of blood onto filter paper and hepatic fine needle aspirates (FNAs) as further alternatives, and explore the adequacy of using green frogs as a target-sampling species when searching for ranavirus infection in the wild. Samples were obtained from 190 postmetamorphic ($1-yr-old) green frogs from five ponds on Prince Edward Island (PEI), Canada. Three of the ponds had contemporary or recent tadpole mortalities due to Frog Virus 3 (FV3) ranavirus. PCR testing for ranavirus DNA was performed on 190 toe clips, 188 blood samples, 72 hepatic FNAs, and 72 liver tissue samples. Only two frogs were ranavirus-positive: liver and toe clip were positive in one, liver only was positive in the other; all blood and FNAs, including those from the two positive frogs, were negative. Results did not yield a definitive answer on the efficacy of testing each type of sample, but resemble what is found in salamanders infected with Ambystoma tigrinum (rana)virus. Findings indicate a low prevalence of FV3 in postmetamorphic green frogs on PEI (#2.78%) and suggest that green frogs are poor reservoirs (carriers) for the virus.

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DNA BARCODING: CO1 DNA barcoding amphibians: take the chance, meet the challenge

Cited by 167 publications

References 69 publications

Genetic differentiation of octopuses from different habitats near the Korean Peninsula and eastern China based on analysis of the mDNA cytochrome C oxidase 1 gene

Genetic differentiation of octopuses from different habitats near the Korean Peninsula and eastern China based on analysis of the mDNA cytochrome C oxidase 1 gene

Evidence of new species ofHaematoloechus(Platyhelminthes: Digenea) using partialcox1sequences

LOW DETECTION OF RANAVIRUS DNA IN WILD POSTMETAMORPHIC GREEN FROGS, RANA (LITHOBATES) CLAMITANS, DESPITE PREVIOUS OR CONCURRENT TADPOLE MORTALITY

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