DNA BARCODING: Barcoding corals: limited by interspecific divergence, not intraspecific variation

DNA barcoding seeks to assemble a standardized reference library for rapid and unambiguous identification of species, and can be used to screen for potentially cryptic species. The 5′ region of cytochrome oxidase subunit I (COI), which is a mitochondrial DNA (mtDNA) gene fragment, has been proposed as a universal marker for this purpose among animals. However, DNA barcoding of reptiles is still supported only by few datasets compared with other groups. We investigated the utilization of COI to discriminate 34 putative species of vipers, representing almost 92% of the recorded species in China. Based on a total of 241 sequences, our results indicated that the average degree of intraspecific variability (0.0198) tends to be one-sixth the average of interspecific divergence (0.0931), but no barcoding gap was detected between them. The threshold method, BLOG analyses and tree-based methods all can identify species with a high success rate. These results consistently suggested the usefulness and reliability of the DNA barcoding approach in Chinese vipers.

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Morphology and DNA barcodes reveal the presence of the non-native land planarian Obama marmorata (Platyhelminthes : Geoplanidae) in Europe

Invertebrate Systematics ◽

10.1071/is14033 ◽

2015 ◽

Vol 29 (1) ◽

pp. 12 ◽

Cited By ~ 9

Author(s):

Domingo Lago-Barcia ◽

Fernando A. Fernández-Álvarez ◽

Lisandro Negrete ◽

Francisco Brusa ◽

Cristina Damborenea ◽

...

Keyword(s):

Dna Barcoding ◽

Geographic Origin ◽

Original Description ◽

Neotropical Region ◽

Morphological Evidence ◽

Intraspecific Divergence ◽

Interspecific Divergence ◽

Allochthonous Species ◽

First Time ◽

Land Planarian

We report for the first time the occurrence of Obama marmorata in the Iberian Peninsula as an introduced species from the Neotropical Region. The species is also reported for the first time in Argentina. The identification was made on the basis of morphological evidence. The divergence levels of a fragment of the mitochondrial cytochromec oxidaseI gene from Argentinean and Iberian samples were studied. The morphology of samples from the two regions was the same and matched the original description of the species. A DNA barcoding matrix was constructed using new sequences from O. marmorata and sequences of related species taken from GenBank. Among the Geoplanidae, interspecific divergence ranged between 3.3 and 14.4%, while intraspecific divergence percentages were 0–1.2%, signalling the presence of a DNA barcoding gap. All O. marmorata sequences, irrespective of their geographic origin, form a well supported clade with an intraspecific divergence of 0–0.9 (average = 0.4%). These results indicate the utility of DNA barcoding to discover allochthonous species in this group of organisms.

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Identifying Chinese species of Gammarus (Crustacea: Amphipoda) using DNA barcoding

Current Zoology ◽

10.1093/czoolo/55.2.158 ◽

2009 ◽

Vol 55 (2) ◽

pp. 158-164 ◽

Cited By ~ 22

Author(s):

Zhong-e Hou ◽

Zhu Li ◽

Shu-qiang Li

Keyword(s):

Cryptic Species ◽

Dna Barcoding ◽

Cytochrome C Oxidase ◽

Neighbor Joining ◽

Cytochrome C Oxidase I ◽

Widespread Species ◽

Intraspecific Divergence ◽

Gammarus Lacustris ◽

Interspecific Divergence ◽

Identification Of Species

Abstract Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21. 9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection.

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Deciphering amphibian diversity through DNA barcoding: chances and challenges

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2005.1717 ◽

2005 ◽

Vol 360 (1462) ◽

pp. 1859-1868 ◽

Cited By ~ 272

Author(s):

Miguel Vences ◽

Meike Thomas ◽

Ronald M Bonett ◽

David R Vieites

Keyword(s):

Dna Barcoding ◽

Single Locus ◽

Universal Primers ◽

Nuclear Markers ◽

Amphibian Species ◽

Interspecific Divergence ◽

Candidate Species ◽

Mitochondrial Population ◽

Tremendous Amount ◽

Definition Of

Amphibians globally are in decline, yet there is still a tremendous amount of unrecognized diversity, calling for an acceleration of taxonomic exploration. This process will be greatly facilitated by a DNA barcoding system; however, the mitochondrial population structure of many amphibian species presents numerous challenges to such a standardized, single locus, approach. Here we analyse intra- and interspecific patterns of mitochondrial variation in two distantly related groups of amphibians, mantellid frogs and salamanders, to determine the promise of DNA barcoding with cytochrome oxidase subunit I ( cox1 ) sequences in this taxon. High intraspecific cox1 divergences of 7–14% were observed (18% in one case) within the whole set of amphibian sequences analysed. These high values are not caused by particularly high substitution rates of this gene but by generally deep mitochondrial divergences within and among amphibian species. Despite these high divergences, cox1 sequences were able to correctly identify species including disparate geographic variants. The main problems with cox1 barcoding of amphibians are (i) the high variability of priming sites that hinder the application of universal primers to all species and (ii) the observed distinct overlap of intraspecific and interspecific divergence values, which implies difficulties in the definition of threshold values to identify candidate species. Common discordances between geographical signatures of mitochondrial and nuclear markers in amphibians indicate that a single-locus approach can be problematic when high accuracy of DNA barcoding is required. We suggest that a number of mitochondrial and nuclear genes may be used as DNA barcoding markers to complement cox1 .

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Description of a new species of the genus Maua Distant (Hemiptera, Cicadidae) from China

Zootaxa ◽

10.11646/zootaxa.4949.3.8 ◽

2021 ◽

Vol 4949 (3) ◽

pp. 582-588

Author(s):

JIALI WANG ◽

JOANNES P. DUFFELS ◽

CONG WEI

Keyword(s):

New Species ◽

Dna Barcoding ◽

Intraspecific Variation ◽

Male Genitalia ◽

Morphological Characters ◽

Coi Gene ◽

Morphological Observation ◽

Mitochondrial Coi ◽

Mitochondrial Coi Gene ◽

A New Species

A new species, Maua squeala sp. nov., is described from China. This species is similar to M. affinis Distant, 1905 and M. palawanensis Duffels, 2009, but can be distinguished by the shorter and more slender body of the new species, the lateral fasciae on the mesonotum and the shape of the male genitalia. The intraspecific variation of this species is discussed based on morphological observation combined with sequences of partial mitochondrial COI gene (DNA barcoding) of individuals exhibiting different morphological characters.

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Comparative larval morphology in Madagascan frogs of the genus Mantella (Amphibia: Mantellidae)

Zootaxa ◽

10.11646/zootaxa.2124.1.2 ◽

2009 ◽

Vol 2124 (1) ◽

pp. 21-37 ◽

Cited By ~ 2

Author(s):

OLGA JOVANOVIC ◽

JULIAN GLOS ◽

FRANK GLAW ◽

ROGER-DANIEL RANDRIANIAINA ◽

MIGUEL VENCES

Keyword(s):

Parental Care ◽

Dna Barcoding ◽

Species Identification ◽

Intraspecific Variation ◽

Phylogenetic Relationships ◽

Species Group ◽

Larval Morphology ◽

Oral Disc ◽

Tree Hole ◽

First Time

We describe and compare the tadpole morphology of nine species of frogs of the endemic Madagascan genus Mantella based upon specimens identified through DNA barcoding or captive bred. The tadpole morphology of M. crocea/ milotympanum-hybrids, M. madagascariensis, M. pulchra, M. viridis, M. baroni, M. bernhardi and M. betsileo is described for the first time. In general, Mantella have small and generalized tadpoles with a uniform dark colouration. The oral disc is elliptical, emarginated, and positioned anteroventrally. In M. laevigata the oral disc is rounded, not emarginated, and positioned ventrally; eyes are positioned and directed dorsally, while in other species they are directed dorsolaterally. Labial tooth row formulas of Mantella tadpoles differ among some species, and in M. aurantiaca and M. crocea/milotympanum they also show intraspecific variation. Species identification is difficult when considering only morphometric variables. Tadpoles within each species group of the genus do not cluster together (except for some clustering of species belonging to the M. madagascariensis group), confirming that the larval morphology in closely related Mantella species is not suitable for determining phylogenetic relationships. Mantella laevigata, distinguished by tree-hole breeding and parental care, shows the most distinguished larval morphology.

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DNA barcoding of forensically important flies in the Western Cape, South Africa

Genome ◽

10.1139/gen-2018-0054 ◽

2018 ◽

Vol 61 (12) ◽

pp. 823-828 ◽

Cited By ~ 2

Author(s):

Tenielle Cooke ◽

Kyle Kulenkampff ◽

Marise Heyns ◽

Laura Jane Heathfield

Keyword(s):

South Africa ◽

Dna Barcoding ◽

Dna Sequences ◽

The Body ◽

Western Cape ◽

Accurate Identification ◽

Intraspecific Divergence ◽

Post Mortem Interval ◽

Interspecific Divergence

Forensic entomology aids the determination of post mortem interval based on arthropods associated with a deceased body. This relies on the accurate identification of insects that visit the body, particularly first colonisers such as Calliphoridae (Diptera). Traditional species identification though morphological keys can be challenging as immature or closely related specimens can look similar. Some of these challenges have been overcome through “DNA barcoding”, which involves the sequencing of informative regions within a species’ DNA and comparison to a database of reference sequences. However, reference DNA sequences of blow fly species in South Africa is currently limited. In this study, adult blow flies representing four species common to the Western Cape, South Africa (Chrysomya chloropyga, Chrysomya albiceps, Chrysomya marginalis, Lucilia sericata) were examined using morphological keys and DNA barcoding of two regions: COI and ITS2. These DNA sequences were then used as references for the successful identification of seven unknown immature specimens. Intraspecific divergence showed a maximum of 0.36% and 2.25% for COI and ITS2, respectively; interspecific divergence showed a minimum of 6.14% and 64.6% for COI and ITS2, respectively. According to these results, COI and ITS2 have sufficient discriminatory power for species-level identification for the four species studied.

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