scholarly journals Evaluating the Species Boundaries of Green Microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) Using Integrative Taxonomy and DNA Barcoding with Further Implications for the Species Identification in Environmental Samples

PLoS ONE ◽  
2015 ◽  
Vol 10 (6) ◽  
pp. e0127838 ◽  
Author(s):  
Tatyana Darienko ◽  
Lydia Gustavs ◽  
Anja Eggert ◽  
Wiebke Wolf ◽  
Thomas Pröschold
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Environmental Samples ◽  
Integrative Taxonomy ◽  
Species Boundaries ◽  
Green Microalgae

The current approaches to the study of algae: DNA barcoding and DNA taxonomy

2021 ◽  
pp. 124-130
Author(s):  
Anna D. Temraleeva ◽  
Elena S. Krivina ◽  
Yury S. Bukin
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequencing ◽  
Dna Barcoding ◽  
Species Identification ◽  
Green Algae ◽  
Molecular Genetic ◽  
Algal Species ◽  
Species Boundaries ◽  
Sequencing Technology ◽  
Dna Taxonomy

The understanding of the impossibility of distinguishing algal species based on morphological features came with the development of DNA sequencing technology, which today is a necessary tool for defining species boundaries and testing traditional species concepts. The paper discusses popular approaches to species identification (DNA barcoding) and the description of new and revision of known species (DNA taxonomy) using molecular genetic methods. The requirements and limitations in their work are given, as well as examples of phylogenetic analysis of green algae from the clade Moewusinia and Parachlorella, including the genus Micractinium.

scholarly journals The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

2016 ◽  
Vol 371 (1702) ◽  
pp. 20160025 ◽  
Author(s):  
Xin Zhou ◽  
Paul B. Frandsen ◽  
Ralph W. Holzenthal ◽  
Clare R. Beet ◽  
Kristi R. Bennett ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Integrative Taxonomy ◽  
Tree Of Life ◽  
Species Level ◽  
Species Boundaries ◽  
Dna Barcodes ◽  
Index Numbers ◽  
Reference Specimens

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’.

scholarly journals Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3120 ◽  
Author(s):  
Liliana Santos ◽  
Artur Alves ◽  
Rui Alves
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Open Problem ◽  
Phylogenetic Trees ◽  
Species Boundaries ◽  
Species Separation ◽  
Phytosanitary Measures ◽  
Optimal Set ◽  
Disease Understanding

BackgroundSpecies identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genusDiaporthe. AccurateDiaporthespecies separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem.MethodsHere we addressed that problem by identifying five loci that have been sequenced in 142Diaportheisolates representing 96 species:TEF1,TUB,CAL,HISand ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees.ResultsAs expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying theTEF1-TUB-CAL-HIS4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus.DiscussionOur results question the current use of the ITS locus for DNA barcoding in the genusDiaportheand suggest thatTEF1might be a better choice if one locus barcoding needs to be done.

scholarly journals Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe

2017 ◽  
Author(s):  
Liliana Santos ◽  
Artur Alves ◽  
Rui Alves
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Open Problem ◽  
Phylogenetic Trees ◽  
Species Boundaries ◽  
Species Separation ◽  
Phytosanitary Measures ◽  
Optimal Set ◽  
Disease Understanding

Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods. Here, we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results. As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS four loci tree as almost equivalent to the five loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion. Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.

scholarly journals Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe

2017 ◽  
Author(s):  
Liliana Santos ◽  
Artur Alves ◽  
Rui Alves
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Open Problem ◽  
Phylogenetic Trees ◽  
Species Boundaries ◽  
Species Separation ◽  
Phytosanitary Measures ◽  
Optimal Set ◽  
Disease Understanding

Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods. Here, we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results. As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS four loci tree as almost equivalent to the five loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion. Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.

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

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.

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