scholarly journals Deciphering amphibian diversity through DNA barcoding: chances and challenges

2005 ◽  
Vol 360 (1462) ◽  
pp. 1859-1868 ◽  
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 .

scholarly journals DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sonia Trujillo-Argueta ◽  
Rafael F. del Castillo ◽  
Daniel Tejero-Diez ◽  
Carlos Alberto Matias-Cervantes ◽  
Abril Velasco-Murguía
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Trees ◽  
Cloud Forest ◽  
Phylogenetic Analyses ◽  
Universal Primers ◽  
Sign Test ◽  
Species Discrimination ◽  
P Value ◽  
Interspecific Divergence ◽  
Forest Plants

AbstractDNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these forests, from a little-explored area in Oaxaca, Mexico, applying the CBOL criteria for barcoding. We used BLASTn, genetic distance, and monophyly tree-based analyses employing neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference methods. Universal primers for rbcLa and trnH-psbA were successfully amplified and bi-directionally sequenced, but matK could not be amplified for most species. rbcLa showed the highest species discrimination in BLASTn (66.67%). trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e−16). Using NJ and ML phylogenetic trees, monophyletic species were successfully resolved (100%), differing only in support values and displaying full agreement with the most recent fern classification. ML trees showed the highest mean support value (80.95%). trnH-psbA was the only barcode that could detect the Elaphoglossoideae subfamily. Species discrimination did not increase using rbcLa + trnH-psbA. rbcLa is useful for fern barcoding, trnH-psbA is most helpful for phylogenetic analyses, and matK may not work as a universal barcoding marker.

Phylogenetic Analysis of Black Peper (Piper Spp.) Population Collected in Different Locations of Vietnam Based on the ITSU1-4 Gene Region

2021 ◽  
Author(s):  
Sonexay Rasphone ◽  
Long Thanh Dang ◽  
Hoan Nguyen ◽  
Ngoc Quang Nguyen ◽  
Oanh Thi Duong ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Ribosomal Dna ◽  
Maximum Likelihood Method ◽  
Dna Barcode ◽  
Population Expansion ◽  
Nuclear Ribosomal Dna ◽  
Likelihood Method ◽  
Gene Region ◽  
Universal Primers ◽  
Intraspecific Distance

Abstract Background: The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. To compare and find out the analysis genetic diversity difference some pepper individuals collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes were tested for their suitability as DNA barcoding regions of thirty-nine pepper individuals. Universal primers were used, and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program.Results: We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals, ranged from 0.000 to 0.155 (mean = 0.033). The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region was ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; P < 0.05, D* = -1.205; not significant, P > 0.10 and F* = -1.699; not significant, 0.10 > P > 0.05), indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value Strobeck’s S the obtained between individuals in a population is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst is shown in the pairs of groups II and III (Fst = 0.151), and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756.Conclusions: This database is an important resource for researchers working on Species of pepper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.

scholarly journals Uncovering hidden specific diversity of Andean glassfrogs of theCentrolene buckleyispecies complex (Anura: Centrolenidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5856 ◽  
Author(s):  
Luis Amador ◽  
Andrés Parada ◽  
Guillermo D’Elía ◽  
Juan M. Guayasamin
Keyword(s):  
Species Delimitation ◽  
Species Complex ◽  
Behavioral Data ◽  
Nuclear Markers ◽  
Evolutionary Significant Units ◽  
Candidate Species

The glassfrogCentrolene buckleyihas been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized asC. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in theC. buckleyispecies complex. Finally, our results support the validity ofC. venezuelense, formerly considered as a subspecies ofC. buckleyi.

scholarly journals COI-based barcoding of Chinese vipers (Reptilia: Squamata: Viperidae)

2015 ◽  
Vol 36 (4) ◽  
pp. 361-372 ◽  
Author(s):  
Qin Liu ◽  
Fei Zhu ◽  
Guanghui Zhong ◽  
Yunyu Wang ◽  
Min Fang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Intraspecific Variability ◽  
Gene Fragment ◽  
Reference Library ◽  
Threshold Method ◽  
Cytochrome Oxidase Subunit ◽  
Barcoding Gap ◽  
Putative Species ◽  
Interspecific Divergence ◽  
Identification Of Species

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.

DNA barcoding ofCryptosporidium

Parasitology ◽  
2017 ◽  
Vol 145 (5) ◽  
pp. 574-584 ◽  
Author(s):  
JAN ŠLAPETA
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Whole Genome ◽  
Species Identity ◽  
Dna Taxonomy ◽  
Host Diversity ◽  
Clinical Evaluations ◽  
Definition Of ◽  
Outstanding Question ◽  
Metagenomic Approach

SUMMARYCryptosporidiumspp. (Apicomplexa) causing cryptosporidiosis are of medical and veterinary significance. The genusCryptosporidiumhas benefited from the application of what is considered a DNA-barcoding approach, even before the term ‘DNA barcoding’ was formally coined. Here, the objective to define the DNA barcode diversity ofCryptosporidiuminfecting mammals is reviewed and considered to be accomplished. Within theCryptosporidiumliterature, the distinction between DNA barcoding and DNA taxonomy is indistinct. DNA barcoding and DNA taxonomy are examined using the latest additions to the growing spectrum of namedCryptosporidiumspecies and within-species and between-species identity is revisited. Ease and availability of whole-genome DNA sequencing of the relatively smallCryptosporidiumgenome offer an initial perspective on the intra-host diversity. The opportunity emerges to apply a metagenomic approach to purified field/clinicalCryptosporidumisolates. The outstanding question remains a reliable definition ofCryptosporidiumphenotype. The complementary experimental infections and metagenome approach will need to be applied simultaneously to addressCryptosporidiumphenotype with carefully chosen clinical evaluations enabling identification of virulence factors.

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

2015 ◽  
Vol 29 (1) ◽  
pp. 12 ◽  
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.

Controlled heterozygosity in livestock

1955 ◽  
Vol 144 (915) ◽  
pp. 192-203 ◽  
Keyword(s):  
Single Locus ◽  
Common Method ◽  
Dominance Relations ◽  
Livestock Breeding ◽  
Definition Of

The word heterozygosity appears in the title of this paper in preference to heterosis for three reasons. First, heterosis has different usages and might be misleading. A simple illustration is provided by the colours of Shorthorn cattle which are determined by a pair of alleles. The heterozygotes, which are roan, may fairly be described as intermediate between the red and the white of the two homozygotes, and thus show no dominance and therefore no heterosis. Since, however, breeders prefer roans, they are maintained in breeding herds at a frequency greater than 0·5 (Rendel 1952).* On Dobzhansky’s (1952) definition of heterosis, this would be an example of single-locus heterosis and over-dominance. A similar situation obtains in respect of the white saddle of Wessex Saddleback pigs (Donald 1951). for neither the cattle nor the pigs is there evidence that breeders’ preferences for heterozygotes lead to higher production of meat or milk. Second, too little is known about metrical bias and scaling (Mather 1946) which are basic to a proper onception of the dominance relations involved; and third, heterosis in any current sense is not sufficiently comprehensive to describe the uses which controlled heterozygosity has or might have in livestock breeding. One simple and common method of increasing heterozygosity is to mate animals rawn from two distinct breeds. As may be judged from their appearance and their ross-bred progeny, many of these breeds differ substantially in genotype. The ncrease in heterozygosity consequent on crossing them has the assured merit of Adapting the progeny to market demands and the probable merit of improving Performance through heterosis.

scholarly journals Amplification and Analysis of Cytocrome Oxidase I of Polypedates leucomystax from Bogor Agricultural University Area

2017 ◽  
Vol 3 (1) ◽  
pp. 13-19
Author(s):  
Perkasa Arian ◽  
I Made Artika ◽  
Syamsul Falah
Keyword(s):  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Genetic Identification ◽  
Coi Gene ◽  
Morphological Identification ◽  
Amphibian Species ◽  
Bufo Melanostictus ◽  
Polypedates Leucomystax

DNA barcoding has become a useful tool for identifying and confirming of species within a known taxonomic framework. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I (COI). This study was aimed to use DNA barcoding technique to identify and confirm species of Polypedates leucomystax and to analyze their phylogenetic relationship. Samples of Polypedates leucomystax were collected from Campus Area of Bogor Agricultural University. The cytochrome oxidase I gene of 600-700 nucleotides were amplified and observed in agarose gel electrophoresis. Forward sequence (604 base pairs) of COI gene was used for phylogenetic analyses. BLAST analysis against BOLD System database showed 95.75% identity with sequences of Polypedates leucomystax. The pairwise genetic distances of Polypedates leucomystax with Rhacophorus schlegelii, Limnonectes fujianensis, Fejervarya cancrivora, and Bufo melanostictus were 0.274, 0.352, 0.339, 0.339, 0.393, respectively. These results illustrated that the genetic identification is congruence with the morphological identification. Phylogenetic tree analysis showed that the samples were in one clade with other tree frogs. The DNA barcoding technique based on the sequence of COI gene can therefore be used to identify and confirm species of Polypedates leucomystax.

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