scholarly journals A DNA barcode library for the butterflies of North America

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11157
Author(s):  
Jacopo D’Ercole ◽  
Vlad Dincă ◽  
Paul A. Opler ◽  
Norbert Kondla ◽  
Christian Schmidt ◽  
...  
Keyword(s):  
North America ◽  
Minimum Distance ◽  
Sequence Variation ◽  
Evolutionary Dynamics ◽  
Nearest Neighbor ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Reference Library ◽  
Future Studies ◽  
Intraspecific Distance

Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group.

scholarly journals Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae)

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 671-684 ◽  
Author(s):  
Axel Hausmann ◽  
Scott E. Miller ◽  
Jeremy D. Holloway ◽  
Jeremy R. deWaard ◽  
David Pollock ◽  
...  
Keyword(s):  
18Th Century ◽  
Dna Barcode ◽  
Data Systems ◽  
Dna Barcodes ◽  
Reference Library ◽  
Type Specimens ◽  
Voucher Specimen ◽  
Tropical Regions ◽  
Taxonomic Assignments ◽  
Insect Family

It is essential that any DNA barcode reference library be based upon correctly identified specimens. The Barcode of Life Data Systems (BOLD) requires information such as images, geo-referencing, and details on the museum holding the voucher specimen for each barcode record to aid recognition of potential misidentifications. Nevertheless, there are misidentifications and incomplete identifications (e.g., to a genus or family) on BOLD, mainly for species from tropical regions. Unfortunately, experts are often unavailable to correct taxonomic assignments due to time constraints and the lack of specialists for many groups and regions. However, considerable progress could be made if barcode records were available for all type specimens. As a result of recent improvements in analytical protocols, it is now possible to recover barcode sequences from museum specimens that date to the start of taxonomic work in the 18th century. The present study discusses success in the recovery of DNA barcode sequences from 2805 type specimens of geometrid moths which represent 1965 species, corresponding to about 9% of the 23 000 described species in this family worldwide and including 1875 taxa represented by name-bearing types. Sequencing success was high (73% of specimens), even for specimens that were more than a century old. Several case studies are discussed to show the efficiency, reliability, and sustainability of this approach.

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 barcodes reveal 63 overlooked species of Canadian beetles (Insecta, Coleoptera)

ZooKeys ◽  
2019 ◽  
Vol 894 ◽  
pp. 53-150 ◽  
Author(s):  
Mikko Pentinsaari ◽  
Robert Anderson ◽  
Lech Borowiec ◽  
Patrice Bouchard ◽  
Adam Brunke ◽  
...  
Keyword(s):  
North America ◽  
Dna Barcoding ◽  
Morphological Analysis ◽  
Dna Barcode ◽  
Junior Synonym ◽  
Dna Barcodes ◽  
Adventive Species ◽  
Taxonomic Confusion ◽  
First Time ◽  
Nearctic Region

This study demonstrates the power of DNA barcoding to detect overlooked and newly arrived taxa. Sixty-three species of Coleoptera representing 25 families are studied based on DNA barcode data and morphological analysis of the barcoded specimens. Three of the species involve synonymies or previous taxonomic confusion in North America, while the first Canadian records are published for 60 species. Forty-two species are adventive in North America, and 40 of these adventive species originate from the Palaearctic region. Three genera are recorded from the Nearctic region for the first time: Coelostoma Brullé, 1835 (Hydrophilidae), Scydmoraphes Reitter, 1891 (Staphylinidae), and Lythraria Bedel, 1897 (Chrysomelidae). Two new synonymies are established: Mycetoporus triangulatus Campbell, 1991 (Staphylinidae) is a junior synonym of Mycetoporus reichei Pandellé, 1869, syn. nov. while Bledius philadelphicus Fall, 1919 (Staphylinidae) is a junior synonym of Bledius gallicus (Gravenhorst, 1806), syn. nov. The previously suggested move of Ctenicera tigrina (Fall, 1901) to the genus Pseudanostirus Dolin, 1964 (Elateridae) is formalized, resulting in Pseudanostirus tigrinus (Fall, 1901), comb. nov.

scholarly journals A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae)

ZooKeys ◽  
2018 ◽  
Vol 759 ◽  
pp. 57-80 ◽  
Author(s):  
Michael J. Raupach ◽  
Karsten Hannig ◽  
Jérôme Morinière ◽  
Lars Hendrich
Keyword(s):  
Dna Barcode ◽  
Ground Beetles ◽  
Dna Barcodes ◽  
Haplotype Sharing ◽  
Reference Library ◽  
Considerable Difficulty ◽  
Molecular Species Identification ◽  
Difficult Genus ◽  
Species Pairs ◽  
Extensive Reference

The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amaraalpina/Amaratorrida and Amaracommunis/Amaraconvexior/Amaramakolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.

scholarly journals Efficiency of ITS1-5.8S-ITS2 region in identifying Cordyceps species

2020 ◽  
Vol 16 (4) ◽  
pp. 705-712
Author(s):  
Le Thi Thu Hien ◽  
Ha Hong Hanh
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nearest Neighbor ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Pcr Amplification ◽  
Cordyceps Sinensis ◽  
Its2 Region ◽  
Dna Barcodes ◽  
Plastid Genomes

Cordyceps genus is a well-known traditional medicine worldwide. It contains abundant physiological active compounds that were demonstrated to perform benefit in reducing progression of cancer as well as protecting human health. Accurately classifying species in this genus is essential in order to prevent commercial counterfeit medicines. Nowadays, a taxonomic classification of species based on DNA sequences can overcome the existed limitation in identifying by using only morphological characteristics of this genus. DNA barcodes are standard short genomic regions that are universally present in target lineages and has sufficient sequence variation to discriminate species in the genus. A variety of loci has been suggested as DNA barcodes for plants, including genes and non-coding regions in the nuclear and plastid genomes such as psbA-trnH, matK, rbcL, and ITS. Thus, the objective of this study was to identify selected species of Cordyceps genus using DNA barcodes. Seven strains of Cordyceps were collected. Total DNA extraction and purification, PCR amplification and DNA sequencing were performed with standard chemicals and kits. The candidate ITS1-5.8S-ITS2 region was amplified and sequenced. Data were analyzed using Bioedit 7.2.6 and MEGA 7 softwares. Analysis of seven obtained DNA barcode sequences of collected samples revealed that the ITS1-5.8S-ITS2 region provided high species discriminating power for Cordyceps genus. Accordingly, phylogenetic trees based on this DNA barcode exhibited six samples had closed relationship to Cordyceps militaris, while another specimen was the nearest neighbor to Cordyceps sinensis with average similarities at 99.82% and 99.81%, respectively. Our results support the identification of valuable medicinal plant species within Cordyceps genus.

scholarly journals OLICH: A reference library of DNA barcodes for Nordic lichens

2019 ◽  
Vol 7 ◽  
Author(s):  
Gunnhild Marthinsen ◽  
Siri Rui ◽  
Einar Timdal
Keyword(s):  
Species Identification ◽  
Dna Barcode ◽  
Its Sequences ◽  
New Combination ◽  
Dna Barcodes ◽  
Reference Library ◽  
Additional Species ◽  
First Time ◽  
Barcode Gap

DNA barcodes are increasingly being used for species identification amongst the lichenised fungi. This paper presents a dataset aiming to provide an authoritative DNA barcode sequence library for a wide array of Nordic lichens. We present 1324 DNA barcode sequences (nrITS) for 507 species in 175 genera and 25 orders. Thirty-eight species are new to GenBank and, for 25 additional species, ITS sequences are here presented for the first time. The dataset covers 20–21% of the Nordic lichenised species. Barcode gap analyses are given and discussed for the three genera Cladonia, Ramalina and Umbilicaria. The new combination Bryobilimbia fissuriseda (Poelt) Timdal, Marthinsen & Rui is proposed for Mycobilimbia fissuriseda and Nordic material of the species, currently referred to as Pseudocyphellaria crocata and Psoroma tenue ssp. boreale, are shown to belong in Pseudocyphellaria citrina and Psoroma cinnamomeum, respectively.

scholarly journals DNA barcoding of marine fish species from Rongcheng Bay, China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5013 ◽  
Author(s):  
Lijuan Wang ◽  
Zhihao Wu ◽  
Mengxia Liu ◽  
Wei Liu ◽  
Wenxi Zhao ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Dna Barcode ◽  
Gc Content ◽  
Genetic Distances ◽  
Dna Barcodes ◽  
Reference Library ◽  
Fish Species Identification ◽  
Northern Yellow Sea ◽  
Coastal Bay

Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.

scholarly journals DNA barcode reference library construction and genetic diversity and structure analysis of Amomum villosum Lour. (Zingiberaceae) populations in Guangdong Province

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12325
Author(s):  
Lu Gong ◽  
Danchun Zhang ◽  
Xiaoxia Ding ◽  
Juan Huang ◽  
Wan Guan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Dna Barcode ◽  
Group Method ◽  
Germplasm Resources ◽  
Dna Barcodes ◽  
Reference Library ◽  
Genetic Diversity And Structure ◽  
Amomum Villosum

Background Amomum villosum Lour. is the plant that produces the famous traditional Chinese medicine Amomi Fructus. Frequent habitat destruction seriously threatens A. villosum germplasm resources. Genetic diversity is very important to the optimization of germplasm resources and population protection, but the range of inherited traits within A. villosum is unclear. In this study, we analyzed the genetic diversity and genetic structures of A. villosum populations in Guangdong and constructed a local reference DNA barcode library as a resource for conservation efforts. Methods DNA barcoding and Inter-Simple Sequence Repeat (ISSR) markers were used to investigate the population genetics of A. villosum. Five universal DNA barcodes were amplified and used in the construction of a DNA barcode reference library. Parameters including percentage of polymorphic sites (PPB), number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity index (H), and Shannon’s polymorphism information index (I) were calculated for the assessment of genetic diversity. Genetic structure was revealed by measuring Nei’s gene differentiation coefficient (Gst), total population genetic diversity (Ht), intra-group genetic diversity (Hs), and gene flow (Nm). Analysis of molecular variance (AMOVA), Mantel tests, unweighted pair-group method with arithmetic mean (UPGMA) dendrogram, and principal co-ordinates (PCoA) analysis were used to elucidate the genetic differentiation and relationship among populations. Results A total of 531 sequences were obtained from the five DNA barcodes with no variable sites from any of the barcode sequences. A total of 66 ISSR bands were generated from A. villosum populations using the selected six ISSR primers; 56 bands, 84.85% for all the seven A. villosum populations were polymorphic. The A. villosum populations showed high genetic diversity (H = 0.3281, I = 0.4895), whereas the gene flow was weak (Nm = 0.6143). Gst (0.4487) and AMOVA analysis indicated that there is obvious genetic differentiation amongA. villosum populations and more genetic variations existed within each population. The genetic relationship of each population was relatively close as the genetic distances were between 0.0844 and 0.3347.

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.

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