scholarly journals High-Level Diversity of Dinoflagellates in the Natural Environment, Revealed by Assessment of Mitochondrial cox1 and cob Genes for Dinoflagellate DNA Barcoding

2008 ◽  
Vol 75 (5) ◽  
pp. 1279-1290 ◽  
Author(s):  
Senjie Lin ◽  
Huan Zhang ◽  
Yubo Hou ◽  
Yunyun Zhuang ◽  
Lilibeth Miranda
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Natural Environment ◽  
Diagnostic Technique ◽  
Long Island Sound ◽  
Distance Threshold ◽  
Mirror Lake ◽  
Primer Sets ◽  
The One ◽  
High Level

ABSTRACT DNA barcoding is a diagnostic technique for species identification using a short, standardized DNA. An effective DNA barcoding marker would be very helpful for unraveling the poorly understood species diversity of dinoflagellates in the natural environment. In this study, the potential utility for DNA barcoding of mitochondrial cytochrome c oxidase 1 (cox1) and cytochrome b (cob) was assessed. Among several primer sets examined, the one amplifying a 385-bp cob fragment was most effective for dinoflagellates. This short cob fragment is easy to sequence and yet possess reasonable taxon resolution. While the lack of a uniform gap between interspecific and intraspecific distances poses difficulties in establishing a phylum-wide species-discriminating distance threshold, the variability of cob allows recognition of species within particular lineages. The potential of this cob fragment as a dinoflagellate species marker was further tested by applying it to an analysis of the dinoflagellate assemblages in Long Island Sound (LIS) and Mirror Lake in Connecticut. In LIS, a highly diverse assemblage of dinoflagellates was detected. Some taxa can be identified to the species and some to the genus level, including a taxon distinctly related to the bipolar species Polarella glacialis, and the large number of others cannot be clearly identified, due to the inadequate database. In Mirror Lake, a Ceratium species and an unresolved taxon were detected, exhibiting a temporal transition from one to the other. We demonstrate that this 385-bp cob fragment is promising for lineage-wise dinoflagellate species identification, given an adequate database.

scholarly journals Species Identification by Bayesian Fingerprinting: A Powerful Alternative to DNA Barcoding

2016 ◽  
Author(s):  
Ziheng Yang ◽  
Bruce Rannala
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Model Comparison ◽  
Sequence Data ◽  
Single Species ◽  
Species Variation ◽  
Distance Threshold ◽  
Coalescent Model ◽  
Multispecies Coalescent ◽  
Bayesian Model Comparison

A number of methods have been developed to use genetic sequence data to identify and delineate species. Some methods are based on heuristics, such as DNA barcoding which is based on a sequence-distance threshold, while others use Bayesian model comparison under the multispecies coalescent model. Here we use mathematical analysis and computer simulation to demonstrate large differences in statistical performance of species identification between DNA barcoding and Bayesian inference under the multispecies coalescent model as implemented in the bpp program. We show that a fixed genetic-distance threshold as used in DNA barcoding is problematic for delimiting species, even if the threshold is "optimized", because different species have different population sizes and different divergence times, and therefore display different amounts of intra-species versus inter-species variation. In contrast, bpp can reliably delimit species in such situations with only one locus and rarely supports a wrong assignment with high posterior probability. While under-sampling or rare specimens may pose problems for heuristic methods, bpp can delimit species with high power when multi-locus data are used, even if the species is represented by a single specimen. Finally we demonstrate that bpp may be powerful for delimiting cryptic species using specimens that are misidentified as a single species in the barcoding library.

scholarly journals Towards writing the encyclopaedia of life: an introduction to DNA barcoding

2005 ◽  
Vol 360 (1462) ◽  
pp. 1805-1811 ◽  
Author(s):  
Vincent Savolainen ◽  
Robyn S Cowan ◽  
Alfried P Vogler ◽  
George K Roderick ◽  
Richard Lane
Keyword(s):  
Natural History ◽  
Dna Barcoding ◽  
Species Identification ◽  
Life Stage ◽  
Diagnostic Technique ◽  
Scientific Conference ◽  
Natural History Museums ◽  
History Museum ◽  
History Museums ◽  
Biodiversity Inventories

An international consortium of major natural history museums, herbaria and other organizations has launched an ambitious project, the ‘Barcode of Life Initiative’, to promote a process enabling the rapid and inexpensive identification of the estimated 10 million species on Earth. DNA barcoding is a diagnostic technique in which short DNA sequence(s) can be used for species identification. The first international scientific conference on Barcoding of Life was held at the Natural History Museum in London in February 2005, and here we review the scientific challenges discussed during this conference and in previous publications. Although still controversial, the scientific benefits of DNA barcoding include: (i) enabling species identification, including any life stage or fragment, (ii) facilitating species discoveries based on cluster analyses of gene sequences (e.g. cox1 = CO1 , in animals), (iii) promoting development of handheld DNA sequencing technology that can be applied in the field for biodiversity inventories and (iv) providing insight into the diversity of life.

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

Relations between carbon removal rates, biofilm size and density of a novel anaerobic reactor: the inverse turbulent bed

2000 ◽  
Vol 41 (4-5) ◽  
pp. 253-260 ◽  
Author(s):  
P. Buffière ◽  
R. Moletta
Keyword(s):  
Removal Rate ◽  
Removal Rates ◽  
Carbon Removal ◽  
Biofilm Growth ◽  
Loading Rates ◽  
Biomass Activity ◽  
High Turbulence ◽  
The One ◽  
High Level ◽  
Very High

An anaerobic inverse turbulent bed, in which the biogas only ensures fluidisation of floating carrier particles, was investigated for carbon removal kinetics and for biofilm growth and detachment. The range of operation of the reactor was kept within 5 and 30 kgCOD· m−3· d−1, with Hydraulic Retention Times between 0.28 and 1 day. The carbon removal efficiency remained between 70 and 85%. Biofilm size were rather low (between 5 and 30 μm) while biofilm density reached very high values (over 80 kgVS· m−3). The biofilm size and density varied with increasing carbon removal rates with opposite trends; as biofilm size increases, its density decreases. On the one hand, biomass activity within the reactor was kept at a high level, (between 0.23 and 0.75 kgTOC· kgVS· d−1, i.e. between 0.6 and 1.85 kgCOD·kgVS · d−1).This result indicates that high turbulence and shear may favour growth of thin, dense and active biofilms. It is thus an interesting tool for biomass control. On the other hand, volatile solid detachment increases quasi linearly with carbon removal rate and the total amount of solid in the reactor levels off at high OLR. This means that detachment could be a limit of the process at higher organic loading rates.

scholarly journals Testing Todd: family types and development

2021 ◽  
pp. 1-18
Author(s):  
Jerg Gutmann ◽  
Stefan Voigt
Keyword(s):  
Rule Of Law ◽  
Civil Society Organizations ◽  
The Rule Of Law ◽  
State Fragility ◽  
Family Types ◽  
Low Levels ◽  
Parsimonious Model ◽  
The One ◽  
High Level

Abstract Many years ago, Emmanuel Todd came up with a classification of family types and argued that the historically prevalent family types in a society have important consequences for its economic, political, and social development. Here, we evaluate Todd's most important predictions empirically. Relying on a parsimonious model with exogenous covariates, we find mixed results. On the one hand, authoritarian family types are, in stark contrast to Todd's predictions, associated with increased levels of the rule of law and innovation. On the other hand, and in line with Todd's expectations, communitarian family types are linked to racism, low levels of the rule of law, and late industrialization. Countries in which endogamy is frequently practiced also display an expectedly high level of state fragility and weak civil society organizations.

scholarly journals The S66 Non-Covalent Interactions Benchmark Reconsidered Using Explicitly Correlated Methods Near the Basis Set Limit

2018 ◽  
Vol 71 (4) ◽  
pp. 238 ◽  
Author(s):  
Manoj K. Kesharwani ◽  
Amir Karton ◽  
Nitai Sylvetsky ◽  
Jan M. L. Martin
Keyword(s):  
Computational Cost ◽  
The Other ◽  
Basis Set ◽  
Basis Sets ◽  
Explicitly Correlated ◽  
Non Covalent Interactions ◽  
Explicitly Correlated Methods ◽  
The One ◽  
High Level ◽  
Covalent Interactions

The S66 benchmark for non-covalent interactions has been re-evaluated using explicitly correlated methods with basis sets near the one-particle basis set limit. It is found that post-MP2 ‘high-level corrections’ are treated adequately well using a combination of CCSD(F12*) with (aug-)cc-pVTZ-F12 basis sets on the one hand, and (T) extrapolated from conventional CCSD(T)/heavy-aug-cc-pV{D,T}Z on the other hand. Implications for earlier benchmarks on the larger S66×8 problem set in particular, and for accurate calculations on non-covalent interactions in general, are discussed. At a slight cost in accuracy, (T) can be considerably accelerated by using sano-V{D,T}Z+ basis sets, whereas half-counterpoise CCSD(F12*)(T)/cc-pVDZ-F12 offers the best compromise between accuracy and computational cost.

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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