scholarly journals Heaven and hell: Spotlights on some DNA barcodes for species identification and delimitation in ground beetles

2019 ◽  
Vol 2 ◽  
Author(s):  
Thorsten Assmann ◽  
Estève Boutaud ◽  
Jörn Buse ◽  
Claudia Drees ◽  
Ariel-Leib-Leonid Friedman ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Intraspecific Variability ◽  
Cost Effective ◽  
Nuclear Data ◽  
Ground Beetles ◽  
Western Alps ◽  
Barcoding Gap

In the face of the decline of many insects, there is an increasing demand for contemporary, fast and cost-effective approaches to monitor the development of populations and species. Numerous scientists favor molecular methods, especially those involving barcoding of the CO1 gene, as an alternative to classical, morphology-based species identification. Moreover, DNA barcoding is also discussed as a suitable method to support species delimitations in complexes of closely related taxa. We used the available sequences of ground beetles from North and Central Europe with additional ones we generated from Southern Europe and the Middle East to draw conclusion about the practicability of such approach for ground beetles. In general, while strong intraspecific differentiations within the CO1 fragment seem to characterize some wingless species (e.g. Graphipterus serrator, Siagona longula, Carabus problematicus, some Platycarabus species), others do not display much intraspecific variability (e.g. Graphipterus multiguttatus and G. sharonae within the “G. serrator clade”). These results certainly complicate the application of a metabarcoding approach without a larger database to delimitate these ground beetles. Furthermore, these results limit the applicability of the well-known barcoding gap, in ecological studies. With regards to taxonomic problems, mitochondrial and nuclear DNA sequences can provide support for taxonomic decisions. For example, the two taxa Carabus variolosus and nodulosus are characterized predominantely by K2P values lower than the barcoding gap. In view of the otherwise strong intraspecific differentiation within the genus Carabus, these two taxa should be regarded as subspecies. In contrast, DNA barcoding can also help to identify "good" species. Mitochondrial and nuclear data suggest, for example, that an Oreonebria taxon and a Platycarabus taxon from the South-western Alps represent "good species", although they were usually considered as synonyms or subspecies. In another case, two tiger beetle taxa, which until a few months ago were considered to belong to the same species, show such strong differentiation that only two species can be postulated (Calomera aulicoides and C. littoralis winkleri). In summary, we can state that DNA sequences and the barcoding gap can help to define species delimitations in ground beetles. However, several species, including widespread sister species, cannot be identified by DNA barcoding for various reasons (e.g. young species or horizontal gene flow). Consequently, until an automated, fast, and reliable method to identify species from samples emerges, ecological investigations have to rely on classical, morphology-based identifications.

DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Álvaro J. Benítez ◽  
Dina Ricardo-Caldera ◽  
María Atencia-Pineda ◽  
Jesús Ballesteros-Correa ◽  
Julio Chacón-Pacheco ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Genetic Distances ◽  
Northern Region ◽  
Coi Gene ◽  
Individual Species ◽  
Species Variation ◽  
Molossus Molossus ◽  
Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Gregory AC Singer ◽  
Donal A Hickey
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Primate Species ◽  
Dna Barcodes ◽  
Global Biodiversity ◽  
Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

scholarly journals COI-based barcoding of Chinese vipers (Reptilia: Squamata: Viperidae)

2015 ◽  
Vol 36 (4) ◽  
pp. 361-372 ◽  
Author(s):  
Qin Liu ◽  
Fei Zhu ◽  
Guanghui Zhong ◽  
Yunyu Wang ◽  
Min Fang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Intraspecific Variability ◽  
Gene Fragment ◽  
Reference Library ◽  
Threshold Method ◽  
Cytochrome Oxidase Subunit ◽  
Barcoding Gap ◽  
Putative Species ◽  
Interspecific Divergence ◽  
Identification Of Species

DNA barcoding seeks to assemble a standardized reference library for rapid and unambiguous identification of species, and can be used to screen for potentially cryptic species. The 5′ region of cytochrome oxidase subunit I (COI), which is a mitochondrial DNA (mtDNA) gene fragment, has been proposed as a universal marker for this purpose among animals. However, DNA barcoding of reptiles is still supported only by few datasets compared with other groups. We investigated the utilization of COI to discriminate 34 putative species of vipers, representing almost 92% of the recorded species in China. Based on a total of 241 sequences, our results indicated that the average degree of intraspecific variability (0.0198) tends to be one-sixth the average of interspecific divergence (0.0931), but no barcoding gap was detected between them. The threshold method, BLOG analyses and tree-based methods all can identify species with a high success rate. These results consistently suggested the usefulness and reliability of the DNA barcoding approach in Chinese vipers.

scholarly journals Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization ofEphesiella,EphesiopsisandSphaerodorum

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5783 ◽  
Author(s):  
María Capa ◽  
Torkild Bakken ◽  
Karin Meißner ◽  
Arne Nygren
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Intraspecific Variability ◽  
Morphological Data ◽  
Nominal Species ◽  
Type Specimens ◽  
Diagnostic Features ◽  
28S Rdna Sequence

BackgroundLong-bodied sphaerodorids (Annelida, Sphaerodoridae) is the common name for members of the three closely and morphologically homogenous currently accepted genera of benthic marine bristle worms:Ephesiella,EphesiopsisandSphaerodorum. Members of this group share the presence of two dorsal and longitudinal rows of macrotubercles with terminal papillae, and two longitudinal rows of microtubercles, features that are unique among sphaerodorids. Genera are distinguished by the chaetae morphology. Members ofEphesiellaare characterised by having compound chaetae (except, sometimes, simple chaetae in the first chaetigers),Sphaerodorumbear only simple chaetae, andEphesiopsishave both compound and simple chaetae in all parapodia.MethodsMitochondrial (partial COI and 16S rDNA) and nuclear (partial 18S rDNA and 28S rDNA) sequence data of long-bodied sphaerodorids with compound and simple chaetae, and an outgroup of additional seven sphaerodorid species were analysed separately and in combination using Bayesian inference (BA), and Maximum Likelihood (ML) methods. Long-bodied sphaerodorids from around the world (including type specimens) were examined under a range of optical equipment in order to evaluate putative generic and specific diagnostic features, in addition to intraspecific variability.ResultsPhylogenetic analyses of mitochondrial and nuclear DNA sequences of specimens identified asEphesiellaandSphaerodorum,based on chaeta morphology, were performed.SphaerodorumandEphesiellawere recovered as paraphyletic and nested within each other. Revision of current nominal species diagnostic features are performed and discussed.DiscussionResults contradict current generic definitions. Recovery of paraphyletic compound and simple chaetae clades urge the synonymization of these two genera of long-bodied sphaerodorids. Morphological data also suggest the synonymization ofEphesiopsis.

scholarly journals A Molecular Phylogeny of Kingfishers (Alcedinidae) With Insights Into Early Biogeographic History

The Auk ◽  
2006 ◽  
Vol 123 (2) ◽  
pp. 487-499 ◽  
Author(s):  
Robert G. Moyle
Keyword(s):  
Dna Sequences ◽  
Pacific Islands ◽  
Nuclear Dna ◽  
Nuclear Data ◽  
Australian Region ◽  
Biogeographic History ◽  
Species Analysis ◽  
The Family ◽  
Dispersal Events ◽  
Natural Groups

Abstract The phylogeny of kingfishers was reconstructed by comparing mitochondrial and nuclear DNA sequences representing 38 ingroup species. Analysis of the combined data and the nuclear data alone recovered the Alcedininae as the basal lineage in the family. This basal arrangement, and support for many relationships within the three subfamilies, allows discussion of biogeographic issues. The Australian region and Pacific islands display the highest diversity of kingfishers, but this diversity is not a reflection of a long history in the region. Rather, high diversity and endemism in the Australian region is inferred to result from relatively recent radiations from southern Asia. The most parsimonious explanation for the origin of New World taxa is two dispersal events from the Old World. Within the large Halcyon radiation, the phylogeny is well resolved and allows evaluation of generic assignments. The phylogeny supports splitting Todiramphus from Halcyon. Todiramphus and Syma are sister taxa, as are Halcyon and Pelargopsis. Thus, merging or retaining those genera is a more subjective decision. Although not fully resolved, relationships within the alcedinines indicate that Ceyx and Alcedo, as currently delimited, are not natural groups. Phylogénie Moléculaire des Alcedinidae avec un Aperçu de l'Histoire Biogéographique Ancienne

scholarly journals Multilocus DNA barcoding – Species Identification with Multilocus Data

2017 ◽  
Author(s):  
Junning Liu ◽  
Jiamei Jiang ◽  
Shuli Song ◽  
Luke Tornabene ◽  
Ryan Chabarria ◽  
...  
Keyword(s):  
Gene Flow ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Siniperca Chuatsi ◽  
Coi Barcoding ◽  
Long Time ◽  
Limited Gene Flow ◽  
Mitochondrial Locus ◽  
Applied Fields

AbstractSpecies identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of barcoding is not always effective when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus barcoding framework that is based on gene capture and “next-generation” sequencing and provide both empirical and simulation tests of its efficacy. We examine genetic distinctness in two pairs of fishes that are sister-species: Siniperca chuatsi vs. S. kneri and Sicydium altum vs. S. adelum, where the COI barcoding approach failed species identification in both cases. Results revealed that distinctness between S. chuatsi and S. kneri increased as more independent loci were added. By contrast S. altum and S. adelum could not be distinguished even with all loci. Analyses of population structure and gene flow suggested that the two species of Siniperca diverged from each other a long time ago but have unidirectional gene flow, whereas the two species of Sicydium are not separated from each other and have high bidirectional gene flow. Simulations demonstrate that under limited gene flow (< 0.00001 per gene per generation) and enough separation time (> 100000 generation), we can correctly identify species using more than 90 loci. Finally, we selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA barcoding.

scholarly journals Finding a suitable DNA barcode for Mesoamerican orchids

Lankesteriana ◽  
2015 ◽  
Vol 7 (1-2) ◽  
Author(s):  
Guillaume Gigot ◽  
Jonathan Van Alphen-Stahl ◽  
Diego Bogarín ◽  
Jorge Warner ◽  
Mark Chase ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Molecular Technique ◽  
Biodiversity Inventories

Recently, DNA barcoding has emerged as an effec- tive tool for species identification. This has the poten- tial for many useful applications in conservation, such as biodiversity inventories, forensics and trade sur- veillance. It is being developed as an inexpensive and rapid molecular technique using short and standard- ized DNA sequences for species identification.  

scholarly journals DNA Barcoding, species delineation and taxonomy: a historical perspective

DNA Barcodes ◽  
2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Nicolas Hubert ◽  
Robert Hanner
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Molecular Taxonomy ◽  
Species Delineation ◽  
New Paradigm ◽  
Species Discovery ◽  
Traditional Taxonomy ◽  
Speed Up ◽  
Mature Field

AbstractDNA barcoding is a system designed to provide species identification by using standardized gene regions as internal species tag. Foreseen since its earlier development as a solution to speed up the pace of species discovery, DNA barcoding has established as a mature field of biodiversity sciences filing the conceptual gap between traditional taxonomy and different fields of molecular systematics. Initially proposed as a tool for species identification, DNA barcoding has also been applied in taxonomy routines for automated species delineation. Species identification and species delineation, however, should be considered as distinct activities relying on different theoretical and methodological backgrounds. The aim of the present review is to provide an overview of the use of DNA sequences in taxonomy, since the earliest development of molecular taxonomy until the development of DNA barcoding. We further present the differences between procedures of species identification and species delineation and highlight how DNA barcoding proposed a new paradigm that helps promote more sustainable practices in taxonomy.

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