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.

DNA barcodes reveal cryptic genetic diversity within the blackfly subgenus Trichodagmia Enderlein (Diptera: Simuliidae: Simulium) and related taxa in the New World

Zootaxa ◽  
2012 ◽  
Vol 3514 (1) ◽  
pp. 43 ◽  
Author(s):  
LUIS MIGUEL HERNÁNDEZ-TRIANA ◽  
JAMES LEE CRAINEY ◽  
ANDY HALL ◽  
FARRAH FATIH ◽  
JACQUELINE MACKENZIE-DODDS ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Genetic Divergence ◽  
New World ◽  
Distinct Species ◽  
Good Resolution ◽  
Dna Barcodes ◽  
Species Complexes ◽  
Taxonomic Concept ◽  
Species Groups

In this paper we investigate the utility of the COI DNA barcoding region for species identification and for revealing hidden diversity within the subgenus Trichodagmia and related taxa in the New World. In total, 24 morphospecies within the current expanded taxonomic concept of Trichodagmia were analyzed. Three species in the subgenus Aspathia and 10 species in the subgenus Simulium s.str. were also included in the analysis because of their putative phylogenetic relationship with Trichodagmia. In the Neighbour Joining analysis tree (NJ) derived from the DNA barcodes most of the specimens grouped together according to species or species groups as recognized by other morphotaxonomic studies. The interspecific genetic divergence averaged 11.2% (range 2.8–19.5%), whereas intraspecific genetic divergence within morphologically distinct species averaged 0.5% (range 0–1.2%). Higher values of genetic divergence (3.2–3.7%) in species complexes suggest the presence of cryptic diversity. The existence of well defined groups within S. piperi, S. duodenicornium, S. canadense and S. rostratum indicate the possible presence of cryptic species within these taxa. Also, the suspected presence of a sibling species in S. tarsatum and S. paynei is supported. DNA barcodes also showed that specimens from species that were taxonomically difficult to delimit such as S. hippovorum, S. rubrithorax, S. paynei, and other related taxa (S. solarii), grouped together in the NJ analysis, confirming the validity of their species status. The recovery of partial barcodes from specimens in collections was time consuming and PCR success was low from specimens more than 10 years old. However, when a sequence was obtained, it provided good resolution for species identification. Larvae preserved in ‘weak’ Carnoy’s solution (9:1 ethanol:acetic acid) provided full DNA barcodes. Adding legs directly to the PCR mix from recently collected and preserved adults was an inexpensive, fast methodology to obtain full barcodes. In summary, DNA barcoding combined with a sound morphotaxonomic framework provides an effective approach for the delineation of species and for the discovery of hidden diversity in the subgenus Trichodagmia.

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 ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Juha Salokannel ◽  
Kyung Min Lee ◽  
Aki Rinne ◽  
Marko Mutanen
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Distinct Species ◽  
Present Species ◽  
Cryptic Diversity ◽  
Weak Support ◽  
Genomic Scale ◽  
Group Species

Abstract Large-scale global efforts on DNA barcoding have repeatedly revealed unexpected patterns of variability in mtDNA, including deep intraspecific divergences and haplotype sharing between species. Understanding the evolutionary causes behind these patterns calls for insights from the nuclear genome. While building a near-complete DNA barcode library of Finnish caddisflies, a case of barcode-sharing and some cases of deep intraspecific divergences were observed. In this study, the Apatania zonella (Zetterstedt, 1840) group and three Limnephilus Leach, 1815 species were studied using double digest RAD sequencing (ddRAD-seq), morphology, and DNA barcoding. The results support the present species boundaries in the A. zonella group species. A morphologically distinct but mitogenetically nondistinct taxon related to parthenogenetic Apatania hispida (Forsslund, 1930) got only weak support for its validity as a distinct species. The morphology and genomic-scale data do not indicate cryptic diversity in any of the three Limnephilus species despite the observed deep intraspecific divergences in DNA barcodes. This demonstrates that polymorphism in mtDNA may not reflect cryptic diversity, but mitonuclear discordance due to other evolutionary causes.

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.

Species Delimitation of Scavenger Flies in the Valley of Mexico

2021 ◽  
Author(s):  
Carlos Pedraza-Lara ◽  
Marco A Garduño-Sánchez ◽  
Isabel Téllez-García ◽  
Stephany Rodríguez-González ◽  
Eduardo Nuple-Juárez ◽  
...  
Keyword(s):  
Species Richness ◽  
Dna Barcoding ◽  
Species Delimitation ◽  
Nature Reserve ◽  
New Records ◽  
Dna Barcode ◽  
Coi Gene ◽  
Baseline Knowledge ◽  
Identification Of Species ◽  
Diverse Groups

Abstract Identification of species involved in cadaveric decomposition, such as scavenger Diptera, is a fundamental step for the use of entomological evidence in court. Identification based on morphology is widely used in forensic cases; however, taxonomic knowledge of scavenger fauna is poor for many groups and for many countries, particularly Neotropical ones. A number of studies have documented the utility of a DNA barcoding strategy to assist in the identification of poorly known and diverse groups, particularly in cases involving immature states or fragmented organisms. To provide baseline knowledge of the diversity of scavenger Diptera in the Valley of Mexico, we generated a DNA barcode collection comprised of sequences of the cytochrome c oxidase subunit 1 (COI) gene for all families sampled at a nature reserve located in this region. We collected and identified specimens on the basis of morphology and a species delimitation analysis. Our analyses of 339 individuals delineated 42 species distributed across nine families of Diptera. The richest families were Calliphoridae (9 species), Sarcophagidae (7 species), and Phoridae (6 species). We found many of the species previously recorded for the Valley of Mexico, plus 18 new records for the region. Our study highlights the utility of DNA barcoding as a first-step strategy to assess species richness of poorly studied scavenger fly taxa.

scholarly journals Molecular identification of two gobi fishes of Bangladesh using cytochrome oxidase subunit I (CoI) gene sequences

2017 ◽  
Vol 44 (2) ◽  
pp. 175-184
Author(s):  
Mehnus Tabassum ◽  
Hawa Jahan ◽  
Gulshan Ara Latifa
Keyword(s):  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Coi Gene ◽  
Cytochrome Oxidase Subunit ◽  
Molecular Systematic ◽  
Cytochrome Oxidase Subunit I ◽  
Multiple Sequence ◽  
Oxidase Subunit

DNA barcoding has been proposed as a means of quick species identification using a short standardized segment of DNA. Two species (Eleotris fusca and Glossogobius giuris) from the family Gobiidae and Eleotridae were selected for DNA barcoding using samples collected from different regions of Bangladesh. Cytochrome Oxidase Subunit I (COI) gene was sequenced from two different gobi fishes and compared with two previously published similar sequences from the genera Eleotris and Glossogobius. Multiple sequence alignment and the molecular systematic study were performed. The DNA barcode technique identified the two species. The study provides a good example of how DNA barcoding can build upon its primary mission of species identification and use available data to integrate genetic variation investigated at the local scale into a global framework.Bangladesh J. Zool. 44(2): 175-184, 2016

scholarly journals DNA barcoding of Zygaenidae (Lepidoptera): results and perspectives

2019 ◽  
Vol 42 (2) ◽  
pp. 137-150
Author(s):  
Konstantin A. Efetov ◽  
Anna V. Kirsanova ◽  
Zoya S. Lazareva ◽  
Ekaterina V. Parshkova ◽  
Gerhard M. Tarmann ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Coi Gene ◽  
Dna Barcodes ◽  
The Family ◽  
The World ◽  
Biological Characters

The present study provides a DNA barcode library for the world Zygaenidae (Lepidoptera). This study reports 1031 sequence data of the COI gene DNA barcodes for more than 240 species in four of the five subfamilies of the family Zygaenidae. This is about 20% of the world Zygaenidae species. Our results demonstrate the specificity of the COI gene sequences at the species level in most of the studied Zygaenidae and agree with already established taxonomic opinions. The study confirms the effectiveness of DNA barcoding as a tool for determination of most Zygaenidae species. However, some of the results are contradictory. Some cases of shared barcodes have been found, as well as cases of deep intraspecific sequence divergence in species that are well separated by morphological and biological characters. These cases are discussed in detail. Overall, when combined with morphological and biochemical data, as well as biological and ecological observations, DNA barcoding results can be a useful support for taxonomic decisions.

Use of DNA barcode in the identification of fish species from Ribeira de Iguape Basin and coastal rivers from São Paulo State (Brazil)

DNA Barcodes ◽  
2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Jefferson Monteiro Henriques ◽  
Guilherme José Costa Silva ◽  
Fernando Yuldi Ashikaga ◽  
Robert Hanner ◽  
Fausto Foresti ◽  
...  
Keyword(s):  
Species Identification ◽  
Species Concept ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Morphological Identification ◽  
Operational Taxonomic Units ◽  
Paulo State ◽  
Species Complexes ◽  
Definition Of

AbstractSpecies identification is a difficult task, ranging from the definition of the species concept itself to the definition of the threshold for speciation. DNA Barcode technology uses a fragment of the Cytochrome Oxidase I (COI) gene as a molecular tool that many studies have already validated as a tool for species identification. DNA barcode sequences for COI were generated and analyzed from 805 specimens. The General Mixed Yule Coalescent (GMYC) analysis recognized 99 independent evolution units, and the Barcode Index Numbers (BIN) approach pointed to the existence of 104 BINs (interpreted as distinct species). By cross-tabulating the results of all approaches, we identified 109 Molecular Operational Taxonomic Units (MOTU) by at least one methodology. In most cases (89 MOTUs), the genetic approaches are in agreement with morphological identification, and the discrepant results of MOTUs are in the complex groups, which have many morphological similarities but may represent species complexes.

scholarly journals DNA barcoding of Deltocephalus Burmeister leafhoppers (Cicadellidae, Deltocephalinae, Deltocephalini) in China

ZooKeys ◽  
2019 ◽  
Vol 867 ◽  
pp. 55-71 ◽  
Author(s):  
Hong Zhang ◽  
Yalin Zhang ◽  
Yani Duan
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Distinct Species ◽  
Genetic Distances ◽  
Coi Gene ◽  
Mitochondrial Coi ◽  
Chinese Populations ◽  
The Status ◽  
Morphological Variants

We investigated the feasibility of using the DNA barcode region in identifying Deltocephalus from China. Sequences of the barcode region of the mitochondrial COI gene were obtained for 98 specimens (Deltocephalusvulgaris – 88, Deltocephaluspulicaris – 5, Deltocephalusuncinatus – 5). The average genetic distances among morphological and geographical groups of D.vulgaris ranged from 0.9% to 6.3% and among the three species of Deltocephalus ranged from 16.4% to 21.9% without overlap, which effectively reveals the existence of a “DNA barcoding gap”. It is important to assess the status of these morphological variants and explore the genetic variation among Chinese populations of D.vulgaris because the status of this species has led to taxonomic confusion because specimens representing two distinct morphological variants based on the form of the aedeagus are often encountered at a single locality. Forty-five haplotypes (D.vulgaris – 36, D.pulicaris – 5, D.uncinatus – 4) were defined to perform the phylogenetic analyses; they revealed no distinct lineages corresponding either to the two morphotypes of D.vulgaris or to geographical populations. Thus, there is no evidence that these variants represent genetically distinct species.

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