scholarly journals A New Primer Pair for Barcoding Bees (Hymenoptera, Anthophila) Without Amplifying the Homologous Wolbachia Gene

2021 ◽  
Author(s):  
Christoph Bleidorn ◽  
Katharina Henze
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Small Sample ◽  
Test Set ◽  
Important Method ◽  
Bacterial Endosymbionts ◽  
Small Test ◽  
Taxonomic Groups ◽  
Sample Set ◽  
Standard Primer

Abstract ObjectivesDNA barcoding became an important method for the identification and monitoring of bees. However, standard primer pairs used for barcoding often result in (co-) amplification of bacterial endosymbionts of the genus Wolbachia, which are widespread among bee species. Here we designed a new primer pair and compared it with the performance of the standard Folmer-primers for small sample set of bees representing the main taxonomic groups of bees.ResultsThe newly designed primer pair (BeeCox1F1/BeeCox1R2) clearly outperformed the standard barcoding primer (LCO1490/HCO2198). By generating barcodes for a small test set of bees we found that the new primer pair produced in all cases clear sequences for unambiguous species identification using BOLD. In contrast, the standard barcoding primers often resulted in the amplification of the homologous Wolbachia gene, which either resulted in a mixed chromatogram signal or identification of the bacterial endosymbiont instead of the host.

scholarly journals A new primer pair for barcoding of bees (Hymenoptera: Anthophila) without amplifying the orthologous coxA gene of Wolbachia bacteria

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Christoph Bleidorn ◽  
Katharina Henze
Keyword(s):  
Dna Barcoding ◽  
Small Sample ◽  
High Similarity ◽  
High Quality ◽  
Test Set ◽  
Bacterial Endosymbionts ◽  
Small Test ◽  
Taxonomic Groups ◽  
Sample Set ◽  
Standard Primer

Abstract Objectives DNA barcoding became an effective method for the identification and monitoring of bees. However, standard primer pairs used for barcoding often result in (co-) amplification of bacterial endosymbionts of the genus Wolbachia, which are widespread among bee species. Here we designed a new primer pair and compared it with the performance of the standard Folmer-primers for a small sample set of bees representing the main taxonomic groups of bees. Results The newly designed primer pair (BeeCox1F1/BeeCox1R2) outperformed the standard barcoding primer (LCO1490/HCO2198). By generating barcodes for a small test set of bees we found that the new primer pair produced high-quality sequences in all cases for unambiguous species identification using BOLD. Conversely, the standard barcoding primers often co-amplified the homologous Wolbachia gene and resulted in mixed chromatogram signals. These sequences showed high similarity with the bacterial endosymbiont instead of the host.

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

scholarly journals Updated Kriging-Assisted Shape Optimization of a Gravity Dam

Water ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 87
Author(s):  
Yongqiang Wang ◽  
Ye Liu ◽  
Xiaoyi Ma
Keyword(s):  
Surrogate Model ◽  
Computational Cost ◽  
Region Of Interest ◽  
Optimization Procedure ◽  
Optimal Shape ◽  
Small Sample ◽  
Gravity Dam ◽  
Kriging Surrogate Model ◽  
Gravity Dams ◽  
Sample Set

The numerical simulation of the optimal design of gravity dams is computationally expensive. Therefore, a new optimization procedure is presented in this study to reduce the computational cost for determining the optimal shape of a gravity dam. Optimization was performed using a combination of the genetic algorithm (GA) and an updated Kriging surrogate model (UKSM). First, a Kriging surrogate model (KSM) was constructed with a small sample set. Second, the minimizing the predictor strategy was used to add samples in the region of interest to update the KSM in each updating cycle until the optimization process converged. Third, an existing gravity dam was used to demonstrate the effectiveness of the GA–UKSM. The solution obtained with the GA–UKSM was compared with that obtained using the GA–KSM. The results revealed that the GA–UKSM required only 7.53% of the total number of numerical simulations required by the GA–KSM to achieve similar optimization results. Thus, the GA–UKSM can significantly improve the computational efficiency. The method adopted in this study can be used as a reference for the optimization of the design of gravity dams.

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.

Stepwise Response Surface Method and its Application in Reliability Analysis of Ship Hull Structure

2002 ◽  
Vol 124 (4) ◽  
pp. 226-230 ◽  
Author(s):  
Lei Yu ◽  
Purnendu K. Das ◽  
Yunlong Zheng
Keyword(s):  
Response Surface ◽  
Goodness Of Fit ◽  
Weighting Factor ◽  
Small Sample ◽  
Surface Approach ◽  
Hull Structure ◽  
One Step ◽  
Actual Contribution ◽  
Sample Set ◽  
Robust Response

A stepwise response surface approach is proposed in this paper. The response surface is determined by modified stepwise regression, so that the square and cross terms can be absorbed into the model automatically according to their actual contribution, which is calculated by repeated variance analysis. Besides, by applying a weighting factor to the statistical value of contribution and changing the thresholds of introduction and rejection, the entry of each term can be controlled in a fairly flexible manner. None other criteria than those in the traditional statistics are needed to check the goodness of fit. Considering the relatively small sample set at the beginning, the algorithm starts with a linear response surface. As the adaptive iteration proceeds, the bar to quadratic terms is lifted gradually to allow ordered entry. Since the sampling points in one step of iteration are recycled in the succeeding ones, a simple experimental design is enough to fit a robust response surface. A double bottom hull system is analyzed with randomized Young’s modulus, load distribution, and geometric properties. The sensitivity analysis is also performed with respect to the random variables and the parameters in their distributions.

scholarly journals Herbalogical studies of Ranae oviductus (Hamayou) and its species identification using DNA barcoding method

2019 ◽  
Vol 49 (8) ◽  
pp. 1032-1040
Author(s):  
LiQiu ZHANG ◽  
JingYuan SONG ◽  
CaiXiang XIE ◽  
JinXin LIU ◽  
Li XIANG ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification
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