Testing mitochondrial marker efficacy for DNA barcoding in spiders: a test case using the dwarf spider genus Oedothorax (Araneae : Linyphiidae : Erigoninae)

2014 ◽  
Vol 28 (5) ◽  
pp. 501 ◽  
Author(s):  
Lara Lopardo ◽  
Gabriele Uhl
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Analyses ◽  
Test Case ◽  
Mitochondrial Marker ◽  
Promising Candidate ◽  
Future Studies ◽  
Mitochondrial Markers ◽  
Identification Of Species ◽  
Morphological Species

The present study focusses on comparatively assessing the efficacy for DNA barcoding of the two most commonly used mitochondrial markers (cox1 and 16S) in a genus of erigonine spiders. In total, 53 specimens representing five species, including four multi-sampled species, were sampled from several European localities. Initial evaluation of species monophyly was performed through parsimony and Bayesian phylogenetic analyses. Efficacy of mitochondrial markers was tested using operational (including distance-, tree-based measures and Barcode Gap) and evolutionary criteria (using the General Mixed Yule-coalescent Model) for species delimitation. We propose that the cox1 marker can potentially overestimate analyses of biodiversity and thus might not be the preferred marker for DNA species identification and delimitation methods in Oedothorax. Instead, our results suggest that the 16S marker appears to be a promising candidate for such endeavour. Evaluating the contribution and suitability of markers to the re-identification of species, measured by their recovery of well established morphological species, is critical for future studies and for reliable results in species identification in spiders.

Use of molecular methods in identification of species, age and sex of insects useful in forensic entomology

2014 ◽  
Vol 286 ◽  
pp. 66-69
Author(s):  
Joanna Stojak ◽  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Environmental Conditions ◽  
Forensic Entomology ◽  
Sex Identification ◽  
The Body ◽  
Molecular Methods ◽  
Insect Larvae ◽  
Identification Of Species ◽  
Age And Sex

Forensic entomology uses insects to determine the time, cause and place of death. To this end, two entomological methods are used. The development-based method uses the patterns of insect larvae development under the specific thermal and environmental conditions. The succession-based method analyzes the sequence of insect succession on the body in various environmental conditions. The proper insect species identification is essential in both methods. In this article, the molecular methods of species, age and sex identification are presented such as DNA barcoding or DNA-HRM-PCR.

scholarly journals DNA barcoding unveils the first record of Andrena allosa for Italy and unexpected genetic diversity in Andrena praecox (Hymenoptera: Andrenidae)

2020 ◽  
Vol 52 (1) ◽  
pp. 71-75
Author(s):  
Maurizio Cornalba ◽  
Paolo Biella ◽  
Andrea Galimberti
Keyword(s):  
Genetic Diversity ◽  
Global Change ◽  
Dna Barcoding ◽  
Species Identification ◽  
First Record ◽  
Global Distribution ◽  
Genetic Identification ◽  
Genetic Structuring ◽  
Eastern Sector ◽  
Morphological Species

DNA barcoding is well-known to support morphological species identification and it can be helpful for unveiling unexpected populations divergence patterns, especially in the context of the impacts on species posed by global change. In this note, we provided the first Italian record of the alpine mining bee Andrena allosa Warncke, 1975, confirmed with DNA barcoding. In addition, genetic identification of a specimen of Andrena praecox (Scopoli 1753) from western Italy pointed to an unexpected intraspecific genetic structuring at COI DNA barcoding region, with sequences from the Italian and the western sector of its global distribution differing 2.22% (p-dist) from populations of the eastern sector. Given the relevance of these records and of the genetic identity of bee populations from Italy, we argue that implementing molecular surveys in bee monitoring would surely contribute to the conservation of these important pollinators.

scholarly journals Identification of species adulteration in traded medicinal plant raw drugs using DNA barcoding

Genome ◽  
2017 ◽  
Vol 60 (2) ◽  
pp. 139-146 ◽  
Author(s):  
Stalin Nithaniyal ◽  
Sophie Lorraine Vassou ◽  
Sundar Poovitha ◽  
Balaji Raju ◽  
Madasamy Parani
Keyword(s):  
Medicinal Plants ◽  
Medicinal Plant ◽  
Alternative Medicine ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Regulatory Agencies ◽  
Vernacular Names ◽  
Identification Of Species ◽  
Whole Plants

Plants are the major source of therapeutic ingredients in complementary and alternative medicine (CAM). However, species adulteration in traded medicinal plant raw drugs threatens the reliability and safety of CAM. Since morphological features of medicinal plants are often not intact in the raw drugs, DNA barcoding was employed for species identification. Adulteration in 112 traded raw drugs was tested after creating a reference DNA barcode library consisting of 1452 rbcL and matK barcodes from 521 medicinal plant species. Species resolution of this library was 74.4%, 90.2%, and 93.0% for rbcL, matK, and rbcL + matK, respectively. DNA barcoding revealed adulteration in about 20% of the raw drugs, and at least 6% of them were derived from plants with completely different medicinal or toxic properties. Raw drugs in the form of dried roots, powders, and whole plants were found to be more prone to adulteration than rhizomes, fruits, and seeds. Morphological resemblance, co-occurrence, mislabeling, confusing vernacular names, and unauthorized or fraudulent substitutions might have contributed to species adulteration in the raw drugs. Therefore, this library can be routinely used to authenticate traded raw drugs for the benefit of all stakeholders: traders, consumers, and regulatory agencies.

Testing the Effectiveness of DNA Barcoding for Biodiversity Assessment of Moths from Nigeria

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 85
Author(s):  
Lotanna Micah Nneji ◽  
Adeniyi Charles Adeola ◽  
Yun-Yu Wang ◽  
Adeyemi Mufutau Ajao ◽  
Okorie Anyaele ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Molecular Data ◽  
Population Divergence ◽  
Biodiversity Assessment ◽  
Taxonomic Methods ◽  
Future Work

Comprehensive biodiversity assessment of moths in Nigeria rely greatly on accurate species identification. While most of the Nigerian moths are identified effortlessly using their morphological traits, some taxa are morphologically indistinguishable, which makes it difficult for taxon diagnosis. We investigated the efficiency of the DNA barcode, a fragment of the mitochondrial Cytochrome C oxidase subunit I, as a tool for the identification of Nigerian moths. We barcoded 152 individuals comprising 18 morphospecies collected from one of the remaining and threatened rainforest blocks of Nigeria – the Cross River National Park. Phenetic neighbor-joining tree and phylogenetic Maximum Likelihood approach were employed for the molecular-based species identification. Results showed that DNA barcodes enabled species-level identification of most of the individuals collected from the Park. Additionally, DNA barcoding unraveled the presence of at least six potential new and yet undescribed species—Amnemopsyche sp., Arctia sp., Deinypena sp., Hodebertia sp., Otroeda sp., and Palpita sp. The phylogenetic Maximum Likelihood using the combined dataset of all the newly assembled sequences from Nigeria showed that all species formed unique clades. The phylogenetic analyses provided evidence of population divergence in Euchromia lethe, Nyctemera leuconoe, and Deinypena lacista. This study thus illustrates the efficacy of DNA barcoding for species identification and discovery of potential new species, which demonstrates its relevance in biodiversity documentation of Nigerian moths. Future work should, therefore, extend to the creation of an exhaustive DNA barcode reference library comprising all species of moths from Nigeria to have a comprehensive insight on the diversity of moths in the country. Finally, we propose integrated taxonomic methods that would combine morphological, ecological, and molecular data in the identification and diversity studies of moths in Nigeria.

DNA barcoding as an aid for species identification in austral black flies (Insecta: Diptera: Simuliidae)

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 348-357 ◽  
Author(s):  
Luis M. Hernández-Triana ◽  
Fernanda Montes De Oca ◽  
Sean W.J. Prosser ◽  
Paul D.N. Hebert ◽  
T. Ryan Gregory ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Black Flies ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
Species Groups

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%–4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.

scholarly journals The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huili Li ◽  
Wenjun Xiao ◽  
Tie Tong ◽  
Yongliang Li ◽  
Meng Zhang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Plant Species ◽  
Phylogenetic Analyses ◽  
Germplasm Conservation ◽  
Germplasm Resources ◽  
Chloroplast Genes ◽  
Accurate Identification ◽  
Saturation State ◽  
Relationship Analysis

AbstractDNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identification of Orchids not only contributes to the safe utilization of these plants, but also it is essential to the protection and utilization of germplasm resources. In this study, the DNA barcoding of 4 chloroplast genes (matK, rbcL, ndhF and ycf1) were used to provide theoretical basis for species identification, germplasm conservation and innovative utilization of orchids. By comparing the nucleotide replacement saturation of the single or combined sequences among the 4 genes, we found that these sequences reached a saturation state and were suitable for phylogenetic relationship analysis. The phylogenetic analyses based on genetic distance indicated that ndhF and ycf1 sequences were competent to identification at genus and species level of orchids in a single gene. In the combined sequences, matK + ycf1 and ndhF + ycf1 were qualified for identification at the genera and species levels, suggesting the potential roles of ndhF, ycf1, matK + ycf1 and ndhF + ycf1 as candidate barcodes for orchids. Based on the SNP sites, candidate genes were used to obtain the specific barcode of orchid plant species and generated the corresponding DNA QR code ID card that could be immediately recognized by electronic devices. This study provides innovative research methods for efficient species identification of orchids. The standardized and accurate barcode information of Orchids is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Orchidaceae germplasm resources.

DNA barcoding of Antarctic marine zooplankton for species identification and recognition

2014 ◽  
Vol 24 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Fangping CHENG ◽  
Minxiao WANG ◽  
Song SUN ◽  
Chaolun LI ◽  
Yongshan ZHANG
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Marine Zooplankton ◽  
Antarctic Marine

scholarly journals Molecular analysis of the mitochondrial markers COI, 12S rDNA and 16S rDNA for six species of Iranian scorpions

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Parisa Soltan-Alinejad ◽  
Javad Rafinejad ◽  
Farrokh Dabiri ◽  
Piero Onorati ◽  
Olle Terenius ◽  
...  
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Coi Gene ◽  
Diagnostic Tools ◽  
Morphological Identification ◽  
Species Determination ◽  
Important Species ◽  
Mitochondrial Markers ◽  
12S Rdna ◽  
Rdna Sequences

Abstract Objectives Annually, 1.2 million humans are stung by scorpions and severely affected by their venom. Some of the scorpion species of medical importance have a similar morphology to species with low toxicity. To establish diagnostic tools for surveying scorpions, the current study was conducted to generate three mitochondrial markers, Cytochrome Oxidase I (COI gene), 12S rDNA and 16S rDNA for six species of medically important Iranian scorpions: Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus, M. eupeus, Odontobuthus doriae, and Scorpio maurus. Results Phylogenetic analyses of the obtained sequences corroborated the morphological identification. For the first time, 12S rDNA sequences are reported from Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus and M. eupeus and also the 16S rDNA sequence from Hottentotta saulcyi. We conclude that the mitochondrial markers are useful for species determination among these medically important species of scorpions.

Sign in / Sign up

Export Citation Format

Share Document