A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea–Neodilsea complex and WeeksiaThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 773-789 ◽  
Author(s):  
Gary W. Saunders
Keyword(s):  
Species Diversity ◽  
Dna Barcoding ◽  
Life Histories ◽  
Dna Barcode ◽  
Genetic System ◽  
Marine Macroalgae ◽  
Accurate Identification ◽  
Additional Species ◽  
Large Numbers ◽  
Red Algal

The field of DNA barcoding is working towards generating a genetic system for the quick and accurate identification of eukaryotic species. For the more systematic minded, however, DNA barcoding offers a new approach towards screening and uniting large numbers of biological specimens in genetic groups as a first step towards assigning them to species and genera in an approach best termed “molecular-assisted alpha taxonomy”. This approach is particularly amenable in organisms with simple morphologies, a propensity for convergence, extensive phenotypic plasticity, and life histories with an alternation of heteromorphic generations. It is hard to imagine a group of organisms better defined by all of these traits than the marine macroalgae. In an effort to assess the utility of the DNA barcode (COI-5′) for testing the current concepts of biodiversity of marine macroalgae in Canada, a study to assess species diversity in the red algal family, Dumontiaceae, was initiated. Through this work I confirm the presence in Canadian waters of Dilsea californica (J. Agardh) Kuntze, Dilsea integra (Kjellman) Rosenvinge, and Neodilsea borealis (I.A. Abbott) Lindstrom of the Dilsea–Neodilsea complex, and Weeksia coccinea (Harvey) Lindstrom for the genus Weeksia . However, our work has uncovered two additional species of the former complex, Dilsea lindstromiae Saunders sp. nov. and Dilsea pygmaea (Setchell) Setchell, and an additional species of the latter, Weeksia reticulata Setchell, effectively doubling representation of these foliose dumontiacean genera in Canadian waters.

scholarly journals Beyond Bycatch: The Species Diversity of Tonguesole (Pleuronectiformes: Cynoglossidae) in Coastal Fisheries of the Tanintharyi Region, Southern Myanmar

2021 ◽  
Vol 34 (1) ◽  
Author(s):  
IRIS SEGURA-GARCIA ◽  
SABAI SOE ◽  
NYO-NYO TUN ◽  
STEPHEN BOX
Keyword(s):  
Species Diversity ◽  
Dna Barcoding ◽  
Life Histories ◽  
Dna Barcode ◽  
Common Species ◽  
Small Scale ◽  
New Information ◽  
The Family ◽  
Management Plans ◽  
Species Specific

Flatfishes in the family Cynoglossidae are an important coastal fishery in Myanmar. Due to the overlapping morphologies of multiple tonguesole species, caught both as bycatch from trawl fisheries and targeted specifically by small scale fishers, they are all marketed under a single local name, “khwayshar”. This presents a management challenge given the potential differences in the species-specific life-histories, population dynamics, fishing vulnerability and harvest rates. This study investigated the species diversity of tonguesole landings from coastal communities of the Tanintharyi Region of southern Myanmar. DNA barcoding was used to distinguish potentially 10 different species, of which five were identified to species level and five at the genus level. Unconfirmed genetic identifications were based on external morphology. The poor efficacy of DNA barcoding for tonguesole species identification resulted from the limited DNA barcode reference sequences available for the family Cynoglossidae in public databases. An asymmetric occurrence and relative abundance of the identified species in landing sites where samples were collected suggested that the most common species was Cynoglossus oligolepis (Bleeker, 1855), a new species record for Myanmar, followed by Cynoglossus lingua Hamilton, 1822. The results of the present study provide new information to characterise the tonguesole fishery as a first step in the development of management plans for the coastal fishery in Myanmar.

DNA barcoding reveals multiple overlooked Australian species of the red algal order Rhodymeniales (Florideophyceae), with resurrection of Halopeltis J. Agardh and description of Pseudohalopeltis gen. nov.

Botany ◽  
2010 ◽  
Vol 88 (7) ◽  
pp. 639-667 ◽  
Author(s):  
Gary W. Saunders ◽  
Brian McDonald
Keyword(s):  
Dna Barcode ◽  
South Australia ◽  
Sensu Stricto ◽  
Cryptic Diversity ◽  
Additional Species ◽  
Australian Species ◽  
Lord Howe Island ◽  
Red Algal ◽  
Species Groups ◽  
Genetic Species

The DNA barcode (COI-5P) was used to investigate cryptic diversity among Rhodymenia spp. in southern Australia. Whereas eight species are currently recognized, we uncovered ca. 20 genetic species groups, phylogenetically assigned to four genera in two families. Procumbent specimens with molecular and anatomical signatures of the Fryeellaceae are assigned to Pseudohalopeltis tasmanensis gen. et sp. nov. Collections from Lord Howe Island recorded in the field as Rhodymenia / Fauchea sp. are assigned to the poorly known genus Microphyllum as Microphyllum robustum sp. nov. A cluster of species with distinct molecular and anatomical attributes is included in a resurrected Halopeltis J.G. Agardh, including Halopeltis australis (J. Agardh) comb. nov. (type species); Halopeltis austrina (Womersley) comb. nov.; Halopeltis cuneata (Harvey) comb. nov. [including Rhodymenia halymenioides (J. Agardh) Womersley]; Halopeltis gracilis sp. nov.; Halopeltis prostrata sp. nov.; and Halopeltis verrucosa (Womersley) comb. nov. Four additional species of Halopeltis from Lord Howe Island (LH1, LH2), Tasmania (TAS), and Western Australia are not characterized further. For Rhodymenia sensu stricto, similar levels of cryptic diversity were noted. Samples tentatively field-identified as “ Rhodymenia sonderi ,” but having affiliations to Rhodymenia rather than Halopeltis, are referred to Rhodymenia novahollandica sp. nov. Collections field-identified as R. obtusa are genetically distinct from that species and are assigned to Rhodymenia wilsonis (Sonder) comb. nov. Two highly divergent species currently identified as Rhodymenia leptophylla (LH from Lord Howe Island; TAS from Tasmania), as well as two additional cryptic previously unnamed taxa from South Australia (SA) and Victoria (VIC), are not characterized further.

Research Paper DNA barcode identification of fish products from Guiyang markets in southwest China

2022 ◽  
Author(s):  
Qian Tang ◽  
Qi Luo ◽  
Qian Duan ◽  
Lei Deng ◽  
Renyi Zhang
Keyword(s):  
Dna Barcoding ◽  
Molecular Identification ◽  
Fish Consumption ◽  
Southwest China ◽  
Dna Barcode ◽  
Guizhou Province ◽  
Accurate Identification ◽  
Continuous Growth ◽  
Fish Products ◽  
Fresh Frozen

Nowadays, the global fish consumption continues to rise along with the continuous growth of the population, which has led to the dilemma of overfishing of fishery resources. Especially high-value fish that are overfished are often replaced by other fish. Therefore, the accurate identification of fish products in the market is a problem worthy of attention. In this study, full-DNA barcoding (FDB) and mini-DNA barcoding (MDB) used to detect the fraud of fish products in Guiyang, Guizhou province in China. The molecular identification results showed that 39 of the 191 samples were not consistent with the labels. The mislabelling of fish products for fresh, frozen, cooked and canned were 11.70%, 20.00%, 34.09% and 50.00%, respectively. The average kimura 2 parameter distances of MDB within species and genera were 0.27% and 5.41%, respectively; while average distances of FDB were 0.17% within species and 6.17% within genera. In this study, commercial fraud is noticeable, most of the high-priced fish were replaced of low-priced fish with a similar feature. Our study indicated that DNA barcoding is a valid tool for the identification of fish products and that it allows an idea of conservation and monitoring efforts, while confirming the MDB as a reliable tool for fish products.

scholarly journals An Integrated Approach for Efficient and Accurate Medicinal Cuscutae Semen Identification

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1410
Author(s):  
Inkyu Park ◽  
Sungyu Yang ◽  
Goya Choi ◽  
Byeong Cheol Moon ◽  
Jun-Ho Song
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Northeast Asia ◽  
Herbal Medicines ◽  
Integrated Approach ◽  
Rbcl Gene ◽  
Accurate Identification ◽  
Diagnostic Characteristics ◽  
Microscopic Techniques ◽  
Cuscuta Species

To guarantee the safety and efficacy of herbal medicines, accurate identification and quality evaluation are crucial. The ripe dried seeds of Cuscuta australis R.Br. and C. chinensis Lam. are known as Cuscutae Semen (CS) and are widely consumed in Northeast Asia; however, the seeds of other species can be misidentified as CS owing to morphological similarities, leading to misuse. In this report, we propose a multilateral strategy combining microscopic techniques with statistical analysis and DNA barcoding using a genus-specific primer to facilitate the identification and authentication of CS. Morphology-based identification using microscopy revealed that the useful diagnostic characteristics included general shape, embryo exudation, hairiness, and testa ornamentation, which were used to develop an effective identification key. In addition, we conducted DNA barcoding-based identification to ensure accurate authentication. A novel DNA barcode primer was produced from the chloroplast rbcL gene by comparative analysis using Cuscuta chloroplast genome sequences, which allowed four Cuscuta species and adulterants to be discriminated completely. Therefore, this investigation overcame the limitations of universal DNA barcodes for Cuscuta species with high variability. We believe that this integrated approach will enable CS to be differentiated from other species, thereby improving its quality control and product safety in medicinal markets.

scholarly journals DNA barcoding to resolve the confusion in identifying Tribolium confusum and Tribolium castaneum

2019 ◽  
Vol 47 (2) ◽  
pp. 333-342
Author(s):  
Abu Faiz Md Aslam ◽  
Sharmin Sultana ◽  
Sumita Rani Das ◽  
Abdul Jabber Howlader
Keyword(s):  
Dna Barcoding ◽  
Tribolium Castaneum ◽  
Life Stage ◽  
Dna Barcode ◽  
Tribolium Confusum ◽  
Likelihood Method ◽  
Coi Gene ◽  
Pest Species ◽  
Stored Grain ◽  
Accurate Identification

Tribolium confusum and Tribolium castaneum (Coleoptera: Tenebrionidae) are two very confusing pest species while identification is done on the basis of morphology only. Such pests are discovered in stored grain as immature stages, which further complicates the identification process. Accurate identification of these pests is urgently required for integrated pest management. In this research, DNA barcoding was used to identify these pests accurately at any life stage. A 658 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was analyzed. DNA barcode dataset of T. confusum (GeneBank Acc. no. MK120453.1) and T. castaneum (Acc. no. MK411585.1) were constructed. The nucleotide composition reveals that average AT contents (59.9%) were higher than the GC contents (38.6%). Phylogenetic analysis by maximum likelihood method showed that both the species were originated from a common major clade. About 17.13% nucleotide differences were noted between the CO1 sequences by multiple sequence alignment. The interspecies nucleotide genetic distance (0.200) was calculated using Kimura 2 parameter. Haplotype analysis showed high genetic diversity (112 mutaional steps) among them. Bangladesh J. Zool. 47(2): 333-342, 2019

scholarly journals DNA Barcoding of Mosquitoes from the Pantanos de Centla Biosphere Reserve, Southeastern Mexico

2021 ◽  
Vol 37 (4) ◽  
pp. 198-207
Author(s):  
Aldo I. Ortega-Morales ◽  
Luis M. Hernández-Triana ◽  
Rahuel J. Chan-Chable ◽  
Javier A. Garza-Hernández ◽  
Vicente H. González-Álvarez ◽  
...  
Keyword(s):  
Mosquito Control ◽  
Mosquito Species ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Biosphere Reserve ◽  
Similar Species ◽  
Accurate Identification ◽  
Molecular Approaches ◽  
Species Complexes ◽  
Large Numbers

ABSTRACT Accurate identification of mosquito species is essential to support programs that involve the study of distribution and mosquito control. Numerous mosquito species are difficult to identify based only on morphological characteristics, due to the morphological similarities in different life stages and large numbers of some species that are members of morphologically similar species complexes. In the present study, the mosquitoes collected in the Pantanos de Centla Biosphere Reserve, southeastern Mexico, were evaluated using a combination of morphological and molecular approaches (mitochondrial cytochrome c oxidase subunit I [COI] DNA barcode). A total of 1,576 specimens of 10 genera and 35 species, mostly adult stages, were collected. A total of 225 COI DNA barcode sequences were analyzed; most species formed well-supported groups in the neighbor joining, maximum likelihood, and Bayesian inference trees. The intraspecific Kimura 2-parameter (K2P) genetic distance averaged 1.52%. An intraspecific K2P distance of 6.20% was observed in Anopheles crucians s.l., while a deep split was identified in Culex erraticus and Cx. conspirator. This study showed that COI DNA barcodes offer a reliable approach to support mosquito species identification in Mexico.

scholarly journals Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

2022 ◽  
Vol 2022 ◽  
pp. 1-19
Author(s):  
Sarfraz Ahmed ◽  
Muhammad Ibrahim ◽  
Chanin Nantasenamat ◽  
Muhammad Farrukh Nisar ◽  
Aijaz Ahmad Malik ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Elongation Factor ◽  
Species Level ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bacterial Strains ◽  
Accurate Identification ◽  
Bisphosphate Carboxylase ◽  
Parallel Acquisition ◽  
Invertebrate Animal

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

Systematic revision of Brachypelma red-kneed tarantulas (Araneae : Theraphosidae), and the use of DNA barcodes to assist in the identification and conservation of CITES-listed species

2017 ◽  
Vol 31 (2) ◽  
pp. 157 ◽  
Author(s):  
Jorge Mendoza ◽  
Oscar Francke
Keyword(s):  
Dna Barcoding ◽  
Environmental Conservation ◽  
Molecular Evidence ◽  
Accurate Identification ◽  
Systematic Revision ◽  
Human Interactions ◽  
Large Numbers ◽  
New Synonym ◽  
In Captivity ◽  
Morphological Differences

Mexican red-kneed tarantulas of the genus Brachypelma are regarded as some of the most desirable invertebrate pets, and although bred in captivity, they continue to be smuggled out of the wild in large numbers. Species are often difficult to identify based solely on morphology, therefore prompt and accurate identification is required for adequate protection. Thus, we explored the applicability of using COI-based DNA barcoding as a complementary identification tool. Brachypelma smithi (F. O. Pickard-Cambridge, 1897) and Brachypelma hamorii Tesmongt, Cleton & Verdez, 1997 are redescribed, and their morphological differences defined. Brachypelma annitha is proposed as a new synonym of B. smithi. The current distribution of red-kneed tarantulas shows that the Balsas River basin may act as a geographical barrier. Morphological and molecular evidence are concordant and together provide robust hypotheses for delimiting Mexican red-kneed tarantula species. DNA barcoding of these tarantulas is further shown to be useful for species-level identification and for potentially preventing black market trade in these spiders. As a Convention on International Trade in Endangered Species (CITES) listing does not protect habitat, or control wildlife management or human interactions with organisms, it is important to support environmental conservation activities to provide an alternative income for local communities and to avoid damage to wildlife populations.

scholarly journals Identification of Nepeta olgae Regel and phylogenetic status of some genera in subtribe Nepetinae (Lamiaceae) using DNA markers

2021 ◽  
Vol 38 ◽  
pp. 00087
Author(s):  
Elena Nikitina ◽  
Abdurashid Rakhmatov
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Biodiversity Monitoring ◽  
Reference Library ◽  
Accurate Identification ◽  
Unknown Species ◽  
Phylogenetic Status ◽  
Nuclear Its

The species level diversity is the reference unit for biodiversity accounting, should be systematized and include full information about the species. Reliable identification of any species is critical for a large-scale biodiversity monitoring and conservation. A DNA barcode is a DNA sequence that identifies a species by comparing the sequence of an unknown species with barcodes of a known species sequence database. Accurate identification of important plants is essential for their conservation, inventory. The species diversity assessing exampled on the subtribe Nepetinae (Lamiaceae) representatives, growing in Uzbekistan is given, using DNA barcoding method. The study was aimed to identify indigenous important plants with the nuclear (ITS) and plastid (matK, rbcL, trnL-F) genomes. This work demonstrates the phylogenetic relationships of some genera within the subtribe Nepetinae Coss. & Germ. (Lamiaceae), based on ITS locus gene. All results indicate that the DNA barcoding tool can be successfully used to reliably identify important plants, to inventory the botanical resources of Uzbekistan and to create a reference library of DNA barcodes. So, the combination of three-four locus gene is a good candidate for this approach.

scholarly journals DNA Barcoding of Mullets (Family Mugilidae) from Pakistan Reveals Surprisingly High Number of Unknown Candidate Species

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 232
Author(s):  
Ariba Hasan ◽  
Pirzada Jamal Ahmed Siddiqui ◽  
Shabir Ali Amir ◽  
Jean-Dominique Durand
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Morphological Examination ◽  
Operational Taxonomic Units ◽  
Phylogenetic Studies ◽  
Management Measures ◽  
Morphological Criteria ◽  
Candidate Species

The mullets are a widespread group of ecologically and economically important fishes of disputed taxonomy due to their uniform external morphology. Barcoding and phylogenetic studies from various locations around the world largely highlighted the species diversity underestimation using morphological criteria used to establish the taxonomy of the family. Here, we investigated the mullet species diversity from Pakistan, a biogeographic area where nearly no mullet species were genetically characterized. Morphological examination of 40 mullets reveals 6 known species (Planiliza macrolepis, P. klunzingeri, P. subviridis, Crenimugil seheli, Ellochelon vaigiensis, and Mugil cephalus). Using a references DNA barcode library, the DNA barcode-based species identification flagged eight molecular operational taxonomic units (MOTUs) belonging to five genera (Crenimugil, Ellochelon, Mugil, Osteomugil, and Planiliza). Among these MOTUs, only one was already present in Barcode of Life Data system, all other representing new Barcode Index Numbers (BIN). These results emphasize the importance of the recognition of cryptic species and the necessity to re-evaluate the overall diversity by the genetic characterization of different species of this family. DNA barcoding is an effective tool to reveal cryptic species that need to be considered in conservation and management measures of fisheries in Pakistan.

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