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.

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 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.

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.

Differentiation and Interrelations of Two Representatives of Laudakia stellio Complex (Reptilia: Agamidae) in Israel

2011 ◽  
Vol 4 (2) ◽  
pp. 102-114 ◽  
Author(s):  
Evgenyi N. Panov ◽  
Larissa Yu. Zykova
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Habitat Preference ◽  
Additional Data ◽  
Near East ◽  
Field Studies ◽  
Subspecies Level ◽  
Limited Gene Flow ◽  
Study Sites ◽  
And Behavior

Field studies were conducted in Central Negev within the breeding range of Laudakia stellio brachydactyla and in NE Israel (Qyriat Shemona) in the range of an unnamed form (tentatively “Near-East Rock Agama”), during March – May 1996. Additional data have been collected in Jerusalem at a distance of ca. 110 km from the first and about 170 km from the second study sites. A total of 63 individuals were caught and examined. The animals were marked and their subsequent movements were followed. Social and signal behavior of both forms were described and compared. Lizards from Negev and Qyriat Shemona differ from each other sharply in external morphology, habitat preference, population structure, and behavior. The differences obviously exceed the subspecies level. At the same time, the lizards from Jerusalem tend to be intermediate morphologically between those from both above-named localities, which permits admitting the existence of a limited gene flow between lizard populations of Negev and northern Israel. The lizards from NE Israel apparently do not belong to the nominate subspecies of L. stellio and should be regarded as one more subspecies within the species.

DNA barcoding of Antarctic marine zooplankton for species identification and recognition

2014 ◽  
Vol 24 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Fangping CHENG ◽  
Minxiao WANG ◽  
Song SUN ◽  
Chaolun LI ◽  
Yongshan ZHANG
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Marine Zooplankton ◽  
Antarctic Marine

Population fragmentation causes inadequate gene flow and increases extinction risk

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Gene Flow ◽  
Extinction Risk ◽  
Random Mating ◽  
Large Population ◽  
Isolated Population ◽  
Population Fragmentation ◽  
Single Population ◽  
Total Size ◽  
Limited Gene Flow

Most species now have fragmented distributions, often with adverse genetic consequences. The genetic impacts of population fragmentation depend critically upon gene flow among fragments and their effective sizes. Fragmentation with cessation of gene flow is highly harmful in the long term, leading to greater inbreeding, increased loss of genetic diversity, decreased likelihood of evolutionary adaptation and elevated extinction risk, when compared to a single population of the same total size. The consequences of fragmentation with limited gene flow typically lie between those for a large population with random mating and isolated population fragments with no gene flow.

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