scholarly journals DNA barcode identification of commercial fish sold in Mexican markets

Genome ◽  
2018 ◽  
Vol 61 (6) ◽  
pp. 457-466 ◽  
Author(s):  
Stephanie Sarmiento-Camacho ◽  
Martha Valdez-Moreno
Keyword(s):  
Conservation Status ◽  
Dna Barcode ◽  
Common Species ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Commercial Fish ◽  
Sphyrna Lewini ◽  
Pangasianodon Hypophthalmus ◽  
Makaira Nigricans ◽  
The Status

The substitution of high-value fish species for those of lower value is common practice. Although numerous studies have addressed this issue, few have been conducted in Mexico. In this study, we sought to identify fresh fillets of fish, sharks, and rays using DNA barcodes. We analyzed material from “La Viga” in Mexico City, and other markets located on the Gulf and Caribbean coasts of Mexico. From 134 samples, we obtained sequences from 129, identified to 9 orders, 28 families, 38 genera, and 44 species. The most common species were Seriola dumerili, Pangasianodon hypophthalmus, Carcharhinus falciformis, Carcharhinus brevipinna, and Hypanus americanus. Pangasianodon hypophthalmus was most commonly used as a substitute for higher-value species. The substitution rate was 18% of the total. A review of the conservation status of the specimens identified against the IUNC list enabled us to establish that some species marketed in Mexico are threatened: Makaira nigricans, Lachnolaimus maximus, Hyporthodus flavolimbatus, and Isurus oxyrinchus are classified as vulnerable; Lopholatilus chamaeleonticeps and Sphyrna lewini are endangered; and the status of Hyporthodus nigritus is critical. These results will demonstrate to the Mexican authorities that DNA barcoding is a reliable tool for species identification, even when morphological identification is difficult or impossible.

Efferia okanagana, a new species of robber fly (Diptera: Asilidae) from the grasslands of southern British Columbia, Canada, with notes on taxonomy, biology, distribution, and conservation status

2011 ◽  
Vol 143 (6) ◽  
pp. 578-593 ◽  
Author(s):  
Robert A. Cannings
Keyword(s):  
British Columbia ◽  
Conservation Status ◽  
Dna Barcode ◽  
Species Group ◽  
Flight Period ◽  
Species At Risk ◽  
Key To Species ◽  
Male And Female ◽  
The Status ◽  
A New Species

AbstractEfferia okanagana sp. nov. is described from specimens collected in the grasslands of the southern Interior of British Columbia, Canada, mainly the Okanagan Valley. The male and female genitalia are described and illustrated. The existing key to species of Efferia Coquillett is modified to enable identification of male and female E. okanagana. The species belongs to the E. arida species group and perhaps is most closely related to E. arida (Williston) and E. pinali Wilcox. Efferia coulei Wilcox is the closest sympatric relative. Sequences of the cytochrome oxidase I gene (DNA barcode) for E. okanagana and E. coulei show distinct clusters for each species that are approximately 7.0% divergent (uncorrected p distance). Efferia okanagana has an early flight period (May and June) and lives in low-elevation grasslands dominated by bluebunch wheatgrass (Pseudoroegneria spicata (Pursh) Á. Löve) (Poaceae), especially where the soil is gravelly. It is considered a potential species at risk by the Committee on the Status of Endangered Wildlife in Canada.

Identity of some recently described Lepidoptera from France—re-assessed with DNA barcodes and morphology

Zootaxa ◽  
2021 ◽  
Vol 4941 (3) ◽  
pp. 301-337
Author(s):  
PETER HUEMER ◽  
ERIK J. VAN NIEUKERKEN
Keyword(s):  
Related Species ◽  
Dna Barcode ◽  
Molecular Data ◽  
Integrative Analysis ◽  
Type Material ◽  
Dna Barcodes ◽  
Closely Related Species ◽  
Diagnostic Characters ◽  
The Status

Seventy-three species of Lepidoptera described from France since 2000, particularly by Jacques Nel and Thierry Varenne, are re-assessed from largely unpublished molecular data. We tried to obtain DNA barcode sequences from 62 holotypes, supplemented by paratypes of eight species and on one case by non-type material, whereas one previously synonymized species was not sequenced. Altogether we obtained 78 DNA barcode sequences for 65 nominal taxa while sequencing failed for six holotypes. An integrative analysis from molecular data and morphology supports the validity of the majority of species but also resulted in the re-assessment of several taxa. The following 13 new synonymies are established: Stigmella cyrneorolandi Nel & Varenne, 2013 syn. nov. of Stigmella rolandi van Nieukerken, 1990; Stigmella thibaulti Varenne & Nel, 2019 syn. nov. of Stigmella nivenburgensis (Preissecker, 1942) (Nepticulidae); Nemapogon peslieri Varenne & Nel, 2017 syn. nov. of Nemapogon inexpectata Varenne & Nel, 2017 (Tineidae); Phyllonorycter acericorsica Varenne & Nel, 2015 syn. nov. of Phyllonorycter ochreojunctella (Klimesch, 1942) (Gracillariidae); Ancylis paraobtusana Varenne, Nel, & Peslier, 2020 syn. nov. of Ancylis comptana (Frölich, 1828) (Tortricidae); Celypha paludicolella Varenne & Nel, 2017 syn. nov. of Celypha doubledayana (Barrett, 1872) (Tortricidae); Cydia oxytropidana Nel & Varenne, 2016 syn. nov. of Cydia oxytropidis (Martini, 1912) (Tortricidae); Sorhagenia orocorsa Varenne & Nel, 2016 syn. nov. of Sorhagenia janiszewskae Riedl, 1962 (Cosmopterigidae); Chionodes cerdanica Peslier, Nel & Varenne, 2020 syn. nov. of Chionodes distinctella (Zeller, 1839) (Gelechiidae); Elachista bidentata Varenne & Nel, 2019 syn. nov. of Elachista orstadii Palm, 1943; Elachista karsticola Varenne & Nel, 2018 syn. nov. of Elachista maculosella Chrétien, 1896 (Elachistidae); Scythris chablaisensis Delmas, 2018 syn. nov. of Scythris laminella ([Denis & Schiffermüller], 1775) (Scythrididae); Epermenia pumila (Buvat & Nel, 2000) syn. nov. of Epermenia profugella (Stainton, 1856) (Epermeniidae). Finally, the status of some taxa still remains unclear due to the lack of DNA barcodes of closely related species and the absence of convincing diagnostic characters in morphology. 

scholarly journals A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1138
Author(s):  
Shamila Weerakoon Abeynayake ◽  
Sonia Fiorito ◽  
Adrian Dinsdale ◽  
Mark Whattam ◽  
Bill Crowe ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Pcr Amplification ◽  
Cost Effective ◽  
Diagnostic Methods ◽  
Coi Gene ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Accurate Identification ◽  
Invertebrate Pests ◽  
Barcode Sequencing

The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based identification and morphological identification of both large (>0.5 mm in length) and small (<0.5 mm in length) invertebrate specimens intercepted at the Australian border. DNA barcode sequencing results supported the morphological identification in most cases and enabled immature stages of invertebrates and their eggs to be identified more confidently. Results also showed that sequencing the COI barcode region using the ONT rapid sequencing principle is a cost-effective and field-adaptable approach for the rapid and accurate identification of invertebrate pests. Overall, the results suggest that MinION sequencing of DNA barcodes offers a complementary tool to the existing morphological diagnostic approaches and provides rapid, accurate, reliable and defendable evidence for identifying invertebrate pests at the border.

Dendropsophus minutus (Anura: Hylidae) of the Guiana Shield:  using DNA barcodes to assess identity and diversity

Zootaxa ◽  
2007 ◽  
Vol 1540 (1) ◽  
pp. 61-67 ◽  
Author(s):  
MONTY A. HAWKINS ◽  
JACK W. SITES ◽  
BRICE P. NOONAN
Keyword(s):  
Genetic Variation ◽  
Dna Barcode ◽  
Guiana Shield ◽  
Dna Barcodes ◽  
Present Evidence ◽  
Geographic Structure ◽  
Preliminary Examination ◽  
The Status ◽  
Current Sampling ◽  
The Guianas

Herein we discuss the geographic structure of genetic variation of the widely distributed lesser treefrog (Dendropsophus minutus) from the Guianas in a preliminary examination of the status of Guianan populations referred to this taxon. Current sampling is insufficient to determine the status of all lineages of this complex within South America, but our results do indicate the presence of cryptic species within this relatively small portion of the ‘species’ range. Our findings reveal a geographic discontinuity of genetic structure within this region that appears to be correlated with elevation. We also present evidence that supports previous assertions that the conventional DNA barcode locus (COI) is not suitable for amphibians.

A molecular framework for the identification of planthopper vectors (Hemiptera: Delphacidae) of central Argentina

2015 ◽  
Vol 105 (6) ◽  
pp. 754-762
Author(s):  
E.B. Argüello Caro ◽  
A.D. Dumón ◽  
M.F Mattio ◽  
V. Alemandri ◽  
G. Truol
Keyword(s):  
Species Identification ◽  
Regional Scale ◽  
Dna Barcode ◽  
Restriction Enzymes ◽  
Common Species ◽  
Molecular Techniques ◽  
Coi Gene ◽  
Morphological Identification ◽  
Accurate Identification ◽  
Central Argentina

AbstractPlanthoppers are important worldwide crop pests as well as vectors of numerous diseases. Different species transmit Mal de Río Cuarto virus, which causes the most economically important corn disease in central Argentina. Epidemiological studies rely on the accurate identification of the species present in the field. Presently, morphological identification of planthoppers requires taxonomic expertise and there are no taxonomic keys for females and nymphs. Nevertheless, no molecular protocols are available for accurate species identification of most frequent delphacid species from central Argentina. In this context, the aim of this study was to evaluate the utility of the cytochrome oxidase I gene (COI) as a DNA barcode and its digestion with restriction enzymes (Restriction Fragment Length Polymorphism, RFLP) for the identification of the most common species of planthoppers in central Argentina. We amplified and sequenced a 843 bp fragment of the COI gene of taxonomically identified specimens and evaluated its use as a DNA barcode. Restriction enzymes were also selected for digesting the COI fragment via RFLP. The high interspecific variability (20.79%; ± 2.32%) and low intraspecific divergence (0.12%; ± 0.17%) observed in the studied species, demonstrate the effectiveness of the COI gene for species identification of major vector delphacids affecting corn crops in Argentina. Moreover, the digestion of this COI gene fragment with Bfa I and Apo I enzymes allows a fast and cost-effective species identification method when numerous specimens need to be processed. Both molecular techniques developed here, allow the accurate identification of planthopper species at regional scale. These new tools would assist traditional identification of these insects, especially for aiding non-experts in morphological taxonomy.

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

scholarly journals A Systematic Study on DNA Barcoding of Medicinally Important Genus Epimedium L. (Berberidaceae)

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 637 ◽  
Author(s):  
Mengyue Guo ◽  
Yanqin Xu ◽  
Li Ren ◽  
Shunzhi He ◽  
and Xiaohui Pang
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Identification Accuracy ◽  
Dna Barcodes ◽  
Success Rates ◽  
Data Set ◽  
Herba Epimedii ◽  
Potential Risks ◽  
Medicinal Properties ◽  
Species Being

Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species’ morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we tested the applicability of four single loci, namely, rbcL, psbA-trnH, internal transcribed spacer (ITS), and ITS2, and their combinations as DNA barcodes to identify 37 Epimedium species on the basis of the analyses, including the success rates of PCR amplifications and sequencing, specific genetic divergence, distance-based method, and character-based method. Among them, character-based method showed the best applicability for identifying Epimedium species. As for the DNA barcodes, psbA-trnH showed the best performance among the four single loci with nine species being correctly differentiated. Moreover, psbA-trnH + ITS and psbA-trnH + ITS + rbcL exhibited the highest identification ability among all the multilocus combinations, and 17 species, of which 12 are medicinally used, could be efficiently discriminated. The DNA barcode data set developed in our study contributes valuable information to Chinese resources of Epimedium. It provides a new means for discrimination of the species within this medicinally important genus, thus guaranteeing correct and safe usage of Herba Epimedii.

scholarly journals Ground beetles (Carabidae) of field margin habitats

Biologia ◽  
2020 ◽  
Vol 75 (10) ◽  
pp. 1631-1641
Author(s):  
Janina Bennewicz ◽  
Tadeusz Barczak
Keyword(s):  
Conservation Status ◽  
Ground Beetle ◽  
Abundant Species ◽  
Ground Beetles ◽  
Field Margin ◽  
Poecilus Cupreus ◽  
The Status ◽  
Beetle Assemblages ◽  
Anchomenus Dorsalis ◽  
Pterostichus Melanarius

Abstract The aim of this study was to identify the role of field margin habitats in preserving the diversity and abundance of ground beetle assemblages, including potentially entomophagous species and those with conservation status in Poland. Research material was collected in 2006–2007 in four types of margin habitats – a forest, bushes, ditches and in two arable fields. Insects were captured into pitfalls, without preservation liquid or bait added to the traps. Traps were inspected twice a week, between May and August, and one sample was a weekly capture. In field margin habitats the most abundant species were Limodromus assimilis, Anchomenus dorsalis, Pterostichus melanarius and Carabus auratus. A lower abundance of species was noted on fields, with dominant Poecilus cupreus and P. melanarius. The group of zoophagous carabids found in our study includes 30 species from field margin habitats, i.e. 37.5% of all captured Carabidae taxa and 58.3% of all specimens. The share of aphidophagous species was 84.9% among bushes, 86.7% near ditches, and 88.0% in the forest habitat. Several species captured during the study are under protection in Poland. These include the partly protected Carabus convexus, which also has the status of near threatened species, the partly protected Calosoma auropunctatum, and Broscus cephalotes. Considering all the investigated field margin habitats, ground beetles were most numerous in the oak-hornbeam habitat, defined as bushes, formed predominantly by Prunus spinosa, Crataegus leavigata, Sambucus nigra and Rosa canina. Thus, this habitat was the most important reservoir/refugium for the ground beetles.

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

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