Biological identifications through DNA barcodes: the case of the Crustacea

2007 ◽  
Vol 64 (2) ◽  
pp. 272-295 ◽  
Author(s):  
Filipe O Costa ◽  
Jeremy R deWaard ◽  
James Boutillier ◽  
Sujeevan Ratnasingham ◽  
Robert T Dooh ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Sequence Divergence ◽  
Species Level ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Cytochrome C Oxidase I ◽  
Sequence Profile ◽  
Amino Acid Data ◽  
Nucleotide Sequence Divergence ◽  
Diverse Groups

The ability of a 650 base pair section of the mitochondrial cytochrome c oxidase I (COI) gene to provide species-level identifications has been demonstrated for large taxonomic assemblages of animals such as insects, birds, and fishes, but not for the subphylum Crustacea, one of the most diverse groups of arthropods. In this study, we test the ability of COI to provide identifications in this group, examining two disparate levels in the taxonomic hierarchy — orders and species. The first phase of our study involved the development of a sequence profile for 23 dominant crustacean orders, based upon the analysis of 150 species, each belonging to a different family. The COI amino acid data placed these taxa into cohesive assemblages whose membership coincided with currently accepted boundaries at the order, superorder, and subclass levels. Species-level resolution was subsequently examined in an assemblage of Decapoda and in representatives of the genera Daphnia (Cladocera) and Gammarus (Amphipoda). These studies revealed that levels of nucleotide sequence divergence were from 19 to 48 times greater between congeneric species than between individuals of a species. We conclude that sequence variation in the COI barcode region will be very effective for discriminating species of Crustacea.

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.

scholarly journals Technical Limitations Associated With Molecular Barcoding of Arthropod Bloodmeals Taken From North American Deer Species

2020 ◽  
Vol 57 (6) ◽  
pp. 2002-2006
Author(s):  
Erin M Borland ◽  
Daniel A Hartman ◽  
Matthew W Hopken ◽  
Antoinette J Piaggio ◽  
Rebekah C Kading
Keyword(s):  
Mitochondrial Gene ◽  
Blood Feeding ◽  
Species Level ◽  
Coi Gene ◽  
Cytochrome C Oxidase I ◽  
Molecular Barcoding ◽  
Deer Species ◽  
Multiple Loci ◽  
D Loop ◽  
Level Identification

Abstract Accurate species-level identification of the source of arthropod bloodmeals is important for deciphering blood feeding patterns of field-collected specimens. Cytochrome c oxidase I (COI) mitochondrial gene sequencing has been used for this purpose; however, species resolution can be difficult to obtain from certain vertebrate genera, including Odocoileus. Sanger sequencing of mitochondrial genes was employed to identify the bloodmeal source of wild-caught mosquitoes trapped in Greeley, Colorado. Initial sequencing of the COI gene of mitochondrial DNA in bloodmeals was inadequate for species-level resolution of bloodmeals from deer in the genus Odocoileus, with current databases returning low fidelity matches to multiple genera. The use of the hypervariable D loop of the control region provided species-level identification of white-tailed deer (Order: Artiodactyla, Family: Cervidae, Odocoileus virginianus); however, taxonomic identification was successful only to genus for mule (O. hemionus hemionus) and black-tailed deer (O. hemionus columbianus). We advocate the use of multiple loci for bloodmeal analysis and the buildout of available databases to include multiple mitochondrial reference genes for reliable host species identification.

Morphological and molecular evidence for a new species of longnose skate (Rajiformes: Rajidae: Dipturus) from Argentinean waters based on DNA barcoding

Zootaxa ◽  
2008 ◽  
Vol 1921 (1) ◽  
pp. 35-46 ◽  
Author(s):  
JUAN MARTIN DÍAZ DE ASTARLOA ◽  
EZEQUIEL MABRAGAÑA ◽  
ROBERT HANNER ◽  
DANIEL E. FIGUEROA
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Color Pattern ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Southwestern Atlantic ◽  
Cytochrome C Oxidase I ◽  
Molecular Approaches ◽  
A New Species

A new species of Dipturus is described from ten specimens collected off Patagonia, Argentina. Morphological and molecular approaches were used to compare among specimens of recognized Dipturus species. By comparing morphometric, meristic and mitochondrial cytochrome c oxidase I (COI) sequence data, specimens referred to as longnose skate and originally regarded as D. chilensis were shown to be a discrete species as distinguished from both the Yellownose skate, D. chilensis and the Roughskin skate, D. trachyderma. Dipturus argentinensis n. sp. can be distinguished from all other southwestern Atlantic longnose skate species by its color pattern, lack of squamation on both upper and lower surfaces of the disc, and a long, thin tail that is approximately half the total length. The new species has one median row of 10 to 24 small caudal thorns, one or two interdorsal thorns and 35 to 40, and 34 to 43 tooth rows on upper and lower jaws, respectively. The 648 base pair COI mitochondrial DNA “barcodes” derived from specimens of D. argentinensis are identical to each other and exhibit greater than 3% sequence divergence from all other Dipturus species similarly characterized to date. Taken together, these independent morphological and molecular observations serve to corroborate one another and thus provide strong evidence for the recognition of D. argentinensis as a new species.

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.

Notes on the molecular taxonomy of the Proclossiana eunomia complex (Lepidoptera, Nymphalidae: Argynnini): analysis of DNA barcodes

2018 ◽  
Vol 8 (1) ◽  
pp. 222-232 ◽  
Author(s):  
R. V. Yakovlev ◽  
N. A. Shapoval ◽  
G. N. Kuftina ◽  
A. V. Kulak ◽  
S. V. Kovalev
Keyword(s):  
Body Size ◽  
Molecular Taxonomy ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Coi Gene ◽  
Wing Pattern ◽  
Molecular Approach ◽  
Dna Barcodes ◽  
Morphological Differences ◽  
Proclossiana Eunomia

The Proclossiana eunomia (Esper, 1799) complex is currently composed of the several subspecies distributed throughout Palaearсtic region and North America. Despite the fact that some of the taxa have differences in wing pattern and body size, previous assumptions on taxonomy not supported by molecular data. Therefore, the identity of certain populations of this complex has remained unclear and the taxonomic status of several recently described taxa is debated. Here, we provide insights into systematics of some Palaearctic members of this group using molecular approach, based on the analysis of the barcoding fragment of the COI gene taking into account known morphological differences.

Sequence variation and evolution of nuclear DNA in man and the primates

1981 ◽  
Vol 292 (1057) ◽  
pp. 133-142 ◽  
Keyword(s):  
Dna Sequence ◽  
Sequence Variation ◽  
Nuclear Dna ◽  
Sequence Divergence ◽  
Gene Arrangement ◽  
Human Populations ◽  
Genetic Changes ◽  
Detailed Structural Analysis ◽  
Dna Sequence Variation ◽  
History Of

Recent advances in nucleic acid technology have facilitated the detection and detailed structural analysis of a wide variety of genes in higher organisms, including those in man. This in turn has opened the way to an examination of the evolution of structural genes and their surrounding and intervening sequences. In a study of the evolution of haemoglobin genes and neighbouring sequences in man and the primates, we have investigated gene arrangement and DNA sequence divergence both within and between species ranging from Old World monkeys to man. This analysis is beginning to reveal the evolutionary constraints that have acted on this region of the genome during primate evolution. Furthermore, DNA sequence variation, both within and between species, provides, in principle, a novel and powerful method for determining inter-specific phylogenetic distances and also for analysing the structure of present-day human populations. Application of this new branch of molecular biology to other areas of the human genome should prove important in unravelling the history of genetic changes that have occurred during the evolution of man.

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 Occurrence and molecular identification of an invasive rice strain of fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) from Sindh, Pakistan, using mitochondrial cytochrome c oxidase I gene sequences

2021 ◽  
Author(s):  
Sumaira Yousaf ◽  
Abdul Rehman ◽  
Mariyam Masood ◽  
Kazam Ali ◽  
Nazia Suleman
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Spodoptera Frugiperda ◽  
Fall Armyworm ◽  
Coi Gene ◽  
Invasive Pest ◽  
Mitochondrial Cytochrome ◽  
Cytochrome C Oxidase I ◽  
Gene Sequences ◽  
Rice Strain

AbstractThe fall armyworm (FAW), an invasive pest of maize, is an emerging threat in Southern Asia after America and Europe. Recently, this notorious pest has also been found in different areas of Pakistan. To assess its presence in Pakistan, a survey was carried out in the provinces of Punjab, Sindh, and Khyber Pakhtunkhwa during May–October 2019. We observed the highest incidence of FAW in Sindh with maximum impact in districts Tando-Allahyar and Hyderabad. These samples were identified as Spodoptera frugiperda on the morphological and taxonomical bases. However, morphological identification of this pest is very difficult at early larval instars. Here, we use the mitochondrial cytochrome c oxidase I (COI) gene region for the precise identification of larva of this invasive pest at species level. Two different regions of COI gene (COI-5′ and COI-3′) were used as molecular markers for the identification of this species. DNA sequence similarity searches of the obtained COI gene sequences (NCBI GenBank Accession Nos. MW241537, MW241538, MW349515, MW349516, MW349493 and MW349494) revealed that genetically it is more than 99% identical to S. frugiperda. The phylogenetic analysis indicated it as the rice-strain (R-strain). Both 3′- and 5′-fragment tree topologies showed that the collected samples of the FAW species belong to the R-strain. To the best of our knowledge, this is the first report providing molecular evidence for the existence of R-strain of S. frugiperda that was found feeding on maize crop in Sindh, Pakistan, using COI gene sequences as a marker.

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