scholarly journals DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity

ZooKeys ◽  
2020 ◽  
Vol 921 ◽  
pp. 141-157 ◽  
Author(s):  
Peter Huemer ◽  
Ole Karsholt ◽  
Leif Aarvik ◽  
Kai Berggren ◽  
Oleksiy Bidzilya ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Barcode ◽  
Species Level ◽  
Coi Gene ◽  
Species Discrimination ◽  
Nominal Species ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
First Time

For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.

scholarly journals DNA barcode library of megadiverse Austrian Noctuoidea (Lepidoptera) – a nearly perfect match of Linnean taxonomy

2019 ◽  
Vol 7 ◽  
Author(s):  
Peter Huemer ◽  
Christian Wieser ◽  
Wolfgang Stark ◽  
Paul Hebert ◽  
Benjamin Wiesmair
Keyword(s):  
Cytochrome C Oxidase ◽  
Perfect Match ◽  
Dna Barcode ◽  
Coi Gene ◽  
Diverse Group ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Identification Performance ◽  
Intraspecific Divergence

The aim of the study was to establish a nationwide barcode library for the most diverse group of Austrian Lepidoptera, the Noctuoidea, with 5 families (Erebidae, Euteliidae, Noctuidae, Nolidae, Notodontidae) and around 690 species. Altogether, 3431 DNA barcode sequences from COI gene (cytochrome c oxidase 1) belonging to 671 species were gathered, with 3223 sequences >500 bp. The intraspecific divergence with a mean of only 0.17% is low in most species whereas interspecific distances to the Nearest Neighbour are significantly higher with an average of 4.95%. Diagnostic DNA barcodes were obtained for 658 species. Only 13 species (1.9% of the Austrian Noctuoidea) cannot be reliably identified from their DNA barcode (Setina aurita/Setina irrorella, Conisania leineri/Conisania poelli, Photedes captiuncula/Photedes minima, Euxoa obelisca/Euxoa vitta/Euxoa tritici, Mesapamaea secalella/Mesapamea secalis, Amphipoea fucosa/Amphipoea lucens). A similarly high identification performance was achieved by the Barcode Index (BIN) system. 671 species of Austrian Noctuoidea, representing 3202 records with BINs, are assigned to a total of 678 BINs. The vast majority of 649 species is placed into a single BIN, with only 13 species recognised as BIN-sharing (including the barcode sharing species above). Twenty-one species were assigned to more than one BIN and have to be checked for cryptic diversity in the future.

scholarly journals DNA barcodes identify medically important tick species in Canada

Genome ◽  
2017 ◽  
Vol 60 (1) ◽  
pp. 74-84 ◽  
Author(s):  
Danielle A. Ondrejicka ◽  
Kevin C. Morey ◽  
Robert H. Hanner
Keyword(s):  
Dna Barcode ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Genetic Cluster ◽  
Potential Health ◽  
Intraspecific Divergence ◽  
Coi Sequences ◽  
I Gene ◽  
Barcode Gap

Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5′ region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species. The tree topology was further supported by a BIN analysis. COI sequences generated were found to have a mean maximum intraspecific divergence of 1.59% and a mean nearest neighbour divergence of 12.8%, indicating a significant “barcode gap”. This study also revealed possible cryptic diversity among specimens morphologically identified as Ixodes soricis and Ixodes texanus. A PCR-based test for Borrelia burgdorferi determined that 18.1% of Lyme-competent ticks in this study were positive. This study is also the first to record a B. burgdorferi-positive exoskeleton. In conclusion, DNA barcoding is a powerful tool that clinicians can use to determine the identification of tick specimens which can help them to suggest whether an attached tick is a potential health risk.

Green light to an integrative view of Microscolex phosphoreus (Dugès, 1837) (Annelida: Clitellata: Acanthodrilidae)

Zootaxa ◽  
2018 ◽  
Vol 4496 (1) ◽  
pp. 175 ◽  
Author(s):  
EMILIA ROTA ◽  
SVANTE MARTINSSON ◽  
CHRISTER ERSÉUS ◽  
VALENTIN N. PETUSHKOV ◽  
NATALJA S. RODIONOVA ◽  
...  
Keyword(s):  
New Species ◽  
Dna Barcode ◽  
Green Light ◽  
Genetic Evidence ◽  
Coi Gene ◽  
Correct Identification ◽  
Cryptic Diversity ◽  
Separate Species ◽  
Integrative View ◽  
First Time

The small synanthropic and peregrine earthworm Microscolex phosphoreus (Dugès, 1837) is reported for the first time from Siberia. Morphological and DNA barcode (COI) analyses of this and widely separate samples worldwide demonstrate that, as currently identified, M. phosphoreus is a heterogeneous taxon, with divergent lineages occurring often in the same locality and hardly providing geographically structured genetic signals. The combined morphological and genetic evidence suggests that at least four of the found clades should be reclassified as separate species, both morphologically and genetically distinct from each other. However, as the specimen number was limited and only the COI gene was studied for the genetic work, we hesitate in formally describing new species. There would also be the problem of assigning the available names to specific lineages. Our findings encourage careful external and anatomical examination and using reliable characters such as the interchaetal distances and spermathecal morphology for correct identification and for deeper evaluation of cryptic diversity in this interesting bioluminescent worm. 

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 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 new species of Litarachna Walter, 1925 (Acari: Hydrachnidia: Pontarachnidae) from Corozal Bay (Belize), described based upon morphology and DNA barcodes

Acarologia ◽  
2021 ◽  
Vol 61 (3) ◽  
pp. 602-613
Author(s):  
Lucia Montes-Ortiz ◽  
Tom Goldschmidt ◽  
Lourdes Vásquez-Yeomans ◽  
Manuel Elías-Gutiérrez
Keyword(s):  
Dna Barcode ◽  
Morphological Description ◽  
Estuarine System ◽  
Dna Barcodes ◽  
Sem Images ◽  
The Family ◽  
Coi Sequences ◽  
First Time ◽  
A New Species ◽  
Electronic Microscope

A new planktonic species of the marine water mites of the family Pontarachnidae Koenike, 1910 is described from Corozal Bay, an estuarine system in Belize. The morphological description includes Scanning Electronic Microscope (SEM) images and is augmented by an analysis of DNA cytochrome c oxidase I (COI) sequences, the DNA barcode, used for the first time for a species description in this group.

scholarly journals Differentiation of Cyanthillium cinereum, a smoking cessation herb, from its adulterant Emilia sonchifolia using macroscopic and microscopic examination, HPTLC profiles and DNA barcodes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Kannika Thongkhao ◽  
Veerachai Pongkittiphan ◽  
Thatree Phadungcharoen ◽  
Chayapol Tungphatthong ◽  
Santhosh Kumar J. Urumarudappa ◽  
...  
Keyword(s):  
Quality Control ◽  
Smoking Cessation ◽  
Microscopic Examination ◽  
Dna Barcode ◽  
Species Level ◽  
Raw Material ◽  
Phytochemical Analysis ◽  
Dna Barcodes ◽  
Leaf Base

Abstract Cyanthillium cinereum (L.) H.Rob. is one of the most popular herbal smoking cessation aids currently used in Thailand, and its adulteration with Emilia sonchifolia (L.) DC. is often found in the herbal market. Therefore, the quality of the raw material must be considered. This work aimed to integrate macro- and microscopic, chemical and genetic authentication strategies to differentiate C. cinereum raw material from its adulterant. Different morphological features between C. cinereum and E. sonchifolia were simply recognized at the leaf base. For microscopic characteristics, trichome and pappus features were different between the two plants. HPTLC profiles showed a distinct band that could be used to unambiguously differentiate C. cinereum from E. sonchifolia. Four triterpenoid compounds, β-amyrin, taraxasterol, lupeol, and betulin, were identified from the distinct HPTLC band of C. cinereum. The use of core DNA barcode regions; rbcL, matK, ITS and psbA-trnH provided species-level resolution to differentiate the two plants. Taken together, the integration of macroscopic and microscopic characterization, phytochemical analysis by HPTLC and DNA barcoding distinguished C. cinereum from E. sonchifolia. The signatures of C. cinereum obtained here can help manufacturers to increase the quality control of C. cinereum raw material in commercialized smoking cessation products.

Comparative efficacy of four candidate DNA barcode regions for identification of Vicia species

2015 ◽  
Vol 15 (4) ◽  
pp. 286-295 ◽  
Author(s):  
Sebastin Raveendar ◽  
Jung-Ro Lee ◽  
Donghwan Shim ◽  
Gi-An Lee ◽  
Young-Ah Jeon ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Resolving Power ◽  
Conservation Strategies ◽  
Species Discrimination ◽  
Dna Barcodes ◽  
Additional Tool ◽  
Germplasm Collections ◽  
Classification Tool ◽  
Individual Locus

AbstractThe genus Vicia L., one of the earliest domesticated plant genera, is a member of the legume tribe Fabeae of the subfamily Papilionoideae (Fabaceae). The taxonomic history of this genus is extensive and controversial, which has hindered the development of taxonomic procedures and made it difficult to identify and share these economically important crop resources. Species identification through DNA barcoding is a valuable taxonomic classification tool. In this study, four DNA barcodes (ITS2, matK, rbcL and psbA-trnH) were evaluated on 110 samples that represented 34 taxonomically best-known species in the Vicia genus. Topologies of the phylogenetic trees based on an individual locus were similar. Individual locus-based analyses could not discriminate closely related Vicia species. We proposed a concatenated data approach to increase the resolving power of ITS2. The DNA barcodes matK, psbA-trnH and rbcL were used as an additional tool for phylogenetic analysis. Among the four barcodes, three-barcode combinations that included psbA-trnH with any two of the other barcodes (ITS2, matK or rbcL) provided the best discrimination among Vicia species. Species discrimination was assessed with bootstrap values and considered successful only when all the conspecific individuals formed a single clade. Through sequencing of these barcodes from additional Vicia accessions, 17 of the 34 known Vicia species could be identified with varying levels of confidence. From our analyses, the combined barcoding markers are useful in the early diagnosis of targeted Vicia species and can provide essential baseline data for conservation strategies, as well as guidance in assembling germplasm collections.

Two new feather mites (Acari: Analgoidea) isolated from the grey-headed woodpecker, Picus canus (Piciformes: Picidae) in Korea

2019 ◽  
Vol 24 (11) ◽  
pp. 2167-2183
Author(s):  
Yeong-deok Han ◽  
Sergey V. Mironov ◽  
Gi-sik Min
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Dna Barcodes ◽  
Feather Mites ◽  
Oxidase Subunit ◽  
Two New Species ◽  
First Time

Two new species of feather mites from the superfamily Analgoidea are described from the grey-headed woodpecker, Picus canus, in Korea: Neopteronyssus koreanus sp. nov. (Pteronyssidae) and Proterothrix picinus sp. nov. (Proctophyllodidae: Pterodectinae). Feather mites of the genera Neopteronyssus Mironov, 2002 and Proterothrix Gaud, 1968 are described for the first time in Korea. Morphological descriptions of both new species are complemented with partial sequences of their mitochondrial cytochrome c oxidase subunit I (COI) gene as DNA barcodes.

New records and their associated DNA barcodes of the butterfly family Hesperiidae in Tibet, China

Zootaxa ◽  
2019 ◽  
Vol 4674 (4) ◽  
pp. 426-438
Author(s):  
CHENGLONG CAO ◽  
SIYAO HUANG ◽  
YONGQIANG XU ◽  
HAOMIN WU ◽  
TIANPENG CHEN ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Morphological Study ◽  
New Records ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Species Cluster ◽  
The Family ◽  
Interspecific Genetic Distance ◽  
Coi Sequences ◽  
First Time

The specimens of the family Hesperiidae collected from Tibet during 2016–2018 are identified using morphology. COI sequences of 76 individuals are newly obtained. The result of our morphological study is congruent with COI gene analyses. Maximum likehood (ML) and Bayesina inferences (BI) analyses reveal that individuals identified morphologically as the same species cluster cohesively. The minimum interspecific genetic distance is 1.7% between Halpe aucma and H. filda, and the genetic distance between conspecific individuals ranged from 0 to 0.2% for the genus Halpe. A total of 51 species are recognized, and six of them, Celaenorrhinus consanguineus Leech, 1891, Barca bicolor (Oberthür, 1896), Aeromachus propinquus Alphéraky, 1897, Pedesta bivitta (Oberthür, 1886), Baoris penicillata chapmani Evans, 1937, and Ochlodes brahma Moore, 1878, are reported from Tibet for the first time, and the last species is new to China. 

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