Identifying spiders through DNA barcodes

2005 ◽  
Vol 83 (3) ◽  
pp. 481-491 ◽  
Author(s):  
Rowan D.H Barrett ◽  
Paul D.N Hebert
Keyword(s):  
Mating Systems ◽  
Mitochondrial Gene ◽  
Model Systems ◽  
Dna Barcodes ◽  
Cytochrome C Oxidase I ◽  
Accurate Identification ◽  
Spider Species ◽  
Taxonomic Impediment ◽  
Gene Coding ◽  
Identification Tool

With almost 40 000 species, the spiders provide important model systems for studies of sociality, mating systems, and sexual dimorphism. However, work on this group is regularly constrained by difficulties in species identification. DNA-based identification systems represent a promising approach to resolve this taxonomic impediment, but their efficacy has only been tested in a few groups. In this study, we demonstrate that sequence diversity in a standard segment of the mitochondrial gene coding for cytochrome c oxidase I (COI) is highly effective in discriminating spider species. A COI profile containing 168 spider species and 35 other arachnid species correctly assigned 100% of subsequently analyzed specimens to the appropriate species. In addition, we found no overlap between mean nucleotide divergences at the intra- and inter-specific levels. Our results establish the potential of COI as a rapid and accurate identification tool for biodiversity surveys of spiders.

Comment on "Identifying spiders through DNA barcodes"

2005 ◽  
Vol 83 (3) ◽  
pp. 498-504 ◽  
Author(s):  
Lorenzo Prendini
Keyword(s):  
Mitochondrial Gene ◽  
Cost Effective ◽  
Identification System ◽  
Morphological Identification ◽  
Life Stages ◽  
Dna Barcodes ◽  
Cytochrome C Oxidase I ◽  
Taxonomic Impediment ◽  
Gene Coding ◽  
Global Identification

R.D.H. Barrett and P.D.N Hebert have demonstrated that it is possible to identify members of a mostly local spider fauna using a short fragment of the mitochondrial gene coding for cytochrome c oxidase I. There are instances where DNA-based identification may be very useful, e.g., in identifying juvenile life stages of groups in which adults are required for morphological identification, or matching morphologically different sexes or life stages when those associations are unknown. DNA-based identification may be the easiest and most cost-effective way, or even the only feasible way, to address some of these questions. However, these are also the least challenging problems in taxonomy, and their solution is unlikely to relieve the "taxonomic impediment". Furthermore, to promote the utility of DNA barcoding as a global identification system, these authors must demonstrate that their approach works for distinguishing all the members of a speciose clade, wherever in the world they occur. Much of diversity occurs allopatrically and neither the study by R.D.H. Barrett and P.D.N. Hebert, nor any other presented to date, even begins to address the feasibility of DNA-based identification at this level of detail.

Pl@ntwood: A Computer-Assisted Identification Tool for 110 species of amazon trees based on wood Anatomical Features

IAWA Journal ◽  
2011 ◽  
Vol 32 (2) ◽  
pp. 221-232 ◽  
Author(s):  
Carolina Sarmiento ◽  
Pierre Détienne ◽  
Christine Heinz ◽  
Jean-François Molino ◽  
Pierre Grard ◽  
...  
Keyword(s):  
Tree Species ◽  
Tropical Species ◽  
Computer Assisted ◽  
Accurate Identification ◽  
Anatomical Features ◽  
System A ◽  
Microscopic Features ◽  
On Line ◽  
User Friendly ◽  
Identification Tool

Sustainable management and conservation of tropical trees and forests require accurate identification of tree species. Reliable, user-friendly identification tools based on macroscopic morphological features have already been developed for various tree floras. Wood anatomical features provide also a considerable amount of information that can be used for timber traceability, certification and trade control. Yet, this information is still poorly used, and only a handful of experts are able to use it for plant species identification. Here, we present an interactive, user-friendly tool based on vector graphics, illustrating 99 states of 27 wood characters from 110 Amazonian tree species belonging to 34 families. Pl@ntWood is a graphical identification tool based on the IDAO system, a multimedia approach to plant identification. Wood anatomical characters were selected from the IAWA list of microscopic features for hardwood identification, which will enable us to easily extend this work to a larger number of species. A stand-alone application has been developed and an on-line version will be delivered in the near future. Besides allowing non-specialists to identify plants in a user-friendly interface, this system can be used with different purposes such as teaching, conservation, management, and selftraining in the wood anatomy of tropical species.

Species delimitation in the leaf beetle genus Macroplea (Coleoptera, Chrysomelidae) based on mitochondrial DNA, and phylogeographic considerations

2006 ◽  
Vol 37 (4) ◽  
pp. 467-479 ◽  
Author(s):  
Gregor Kölsch ◽  
Bo Vest Pedersen ◽  
Olof Biström
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Species Delimitation ◽  
Mitochondrial Gene ◽  
Leaf Beetle ◽  
Genetic Distances ◽  
Amino Acid Substitutions ◽  
Species Status ◽  
Leaf Beetles ◽  
Gene Coding

AbstractThe genus Macroplea Samouelle, 1819 is a group of highly specialized aquatic leaf beetles occurring in the Palaearctic. Since the members of this genus are morphologically very similar, we addressed the question of species identification and delimitation by analysing the second half of the mitochondrial gene coding for the cytochrome oxidase I (COI) subunit. Species limits are inferred from the multimodal frequency distribution of genetic distances between specimens: low genetic distances within a species are clearly set apart from distances between species. The species status of the hitherto controversial species M. japana (Jacoby, 1885) is confirmed. The pattern of nucleotide and amino acid substitutions is discussed in the light of functional domains of the COI molecule. Although the data are preliminary, the results provide new data on the distribution of the species. Together with the phylogenetic analysis they allow for a discussion of the phylogeography of the genus.

scholarly journals PCR-based detection of cow’s milk in goat and sheep cheeses marketed in the Czech Republic

2011 ◽  
Vol 24 (No. 3) ◽  
pp. 127-132 ◽  
Author(s):  
E. Mašková ◽  
I. Paulíčková
Keyword(s):  
Mitochondrial Gene ◽  
Retail Trade ◽  
Animal Origin ◽  
The Czech Republic ◽  
Goat Cheese ◽  
Gene Coding ◽  
Reverse Primer ◽  
Pcr Method ◽  
Italian Origin ◽  
Species Specific

A method based on the polymerase chain reaction (PCR) principle was validated for detecting cow’s milk in goat and sheep cheeses. DNA was isolated from the cheeses using the isolation kit Invisorb Spin Food I by Invitek Co., designed for the samples of animal origin. The PCR method applied utilizes the sequence of the mitochondrial gene coding cytochrome b which is specific for mammals. It uses the common forward primer and the reverse primer species-specific. After electrophoresis, cow DNA was characterised by the fragment of the size of 274 bp, goat DNA by the fragment of 157 bp, and sheep DNA by the fragment of 331 bp. The detection limit of the PCR method described (1%) was determined with model samples made from pure goat cheese with a defined addition of cheese made from cow’s milk. The method validated was applied in the analysis of 17 goat cheeses and 7 sheep cheeses obtained from retail trade. Products of Czech, Slovak, French, Dutch, and Italian origin were examined. The presence of undeclared cow’s milk was detected in three kinds of goat cheese and in one of sheep cheese.  

scholarly journals Using DNA barcodes to assess identity and diversity of Dendropsophus minutus: Failure?

Zootaxa ◽  
2008 ◽  
Vol 1691 (1) ◽  
pp. 67 ◽  
Author(s):  
M. ALEX SMITH
Keyword(s):  
Cytochrome C ◽  
Small Group ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Gene Region ◽  
Dna Barcodes ◽  
Taxonomic Groups

The 5' end (Folmer or Barcode region) of cytochrome c oxidase 1 (CO1) has been proposed as the gene region of choice for a standardized animal DNA barcode (Hebert et al. 2003). Concerns have been raised regarding the decision to utilize this particular mitochondrial gene region as a barcode. Nevertheless, widely divergent taxonomic groups have reported success using CO1 for both species identification and discovery. The utility of CO1 for barcoding amphibians was raised early on (Vences, et al. 2005) and concerns for this group were reported widely (Waugh 2007)—although some considered that the reporting of the concerns outstripped the data that had been analyzed at that point (Smith et al. 2008). Indeed, our analysis of CO1 for a small group of Holarctic amphibians was neither more difficult to generate nor to analyze than for other groups where we have utilized the technique.

DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae)

2006 ◽  
Vol 36 (2) ◽  
pp. 337-350 ◽  
Author(s):  
Shelley L Ball ◽  
Karen F Armstrong
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Insect Pest ◽  
Reference Sequence ◽  
Identification System ◽  
Pest Species ◽  
Dna Barcodes ◽  
Data Set

Reliable and rapid identification of exotic pest species is critical to biosecurity. However, identification of morphologically indistinct specimens, such as immature life stages, that are frequently intercepted at borders is often impossible. Several DNA-based methods have been used for species identification; however, a more universal and anticipatory identification system is needed. Consequently, we tested the ability of DNA "barcodes" to identify species of tussock moths (Lymantriidae), a family containing several important pest species. We sequenced a 617 base pair fragment of the mitochondrial gene cytochrome c oxidase 1 for 20 lymantriid species. We used these, together with other Noctuoidea species sequences from GenBank and the Barcoding of Life Database to create a "profile" or reference sequence data set. We then tested the ability of this profile to provide correct species identifications for 93 additional lymantriid specimens from a data set of mock unknowns. Of the unknowns, 100% were correctly identified by the cytochrome c oxidase 1 profile. Mean interspecific sequence (Kimura 2-parameter) divergence was an order of magnitude greater (14%) than mean intraspecific divergence (<1%). Four species showed deeper genetic divergences among populations. We conclude that DNA barcodes provide a highly accurate means of identifying lymantriid species and show considerable promise as a universal approach to DNA-based identification of pest insects.

scholarly journals Nature of an inserted sequence in the mitochondrial gene coding for the 15S ribosomal RNA of yeast

1982 ◽  
Vol 10 (5) ◽  
pp. 1625-1633 ◽  
Author(s):  
Frédéric Sor ◽  
Hiroshi Fukuhara
Keyword(s):  
Ribosomal Rna ◽  
Mitochondrial Gene ◽  
Gene Coding

scholarly journals What DNA barcodes reveal: microhabitat preference, hunting strategy and dispersal ability drive genetic variation across Iberian spider species

2021 ◽  
Author(s):  
Marc Domènech ◽  
Jagoba Malumbres‐Olarte ◽  
Alba Enguídanos ◽  
Cesc Múrria ◽  
Miquel A. Arnedo
Keyword(s):  
Genetic Variation ◽  
Dispersal Ability ◽  
Dna Barcodes ◽  
Spider Species ◽  
Microhabitat Preference ◽  
Hunting Strategy

scholarly journals Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yun Song ◽  
Yongjiang Zhang ◽  
Jin Xu ◽  
Weimin Li ◽  
MingFu Li
Keyword(s):  
Chloroplast Genome ◽  
Size Structure ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Intergenic Spacer ◽  
Dna Barcodes ◽  
Ecological Value ◽  
Accurate Identification ◽  
Chloroplast Genomes ◽  
Phylogenetic Implications

AbstractThe pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.

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.

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