Avoiding the Interrogation Trap—Sample Training, Part 1

2019 ◽  
Vol 42 (6) ◽  
pp. 6-7
Keyword(s):  
Trap Sample

scholarly journals Validation of COI metabarcoding primers for terrestrial arthropods

2019 ◽  
Author(s):  
Vasco Elbrecht ◽  
Thomas WA Braukmann ◽  
Natalia V Ivanova ◽  
Sean WJ Prosser ◽  
Mehrdad Hajibabaei ◽  
...  
Keyword(s):  
Taxonomic Resolution ◽  
Minor Effect ◽  
Malaise Trap ◽  
Mock Community ◽  
Sequencing Platform ◽  
Amplification Bias ◽  
Terrestrial Arthropods ◽  
Primer Sets ◽  
Taxonomic Groups ◽  
Trap Sample

Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. Thus this study tests the performance of 36 primer sets on a mock community containing 374 species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets where also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from the 21 amplicon pools of the mock community and Malaise trap sample were used to select four primer sets for metabarcoding evaluation at different annealing temperatures (40-60 Co) using the mock community. Temperature did only have a minor effect on taxa recovery that varied with the specific primer pair. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrated that certain primer sets can recover most taxa in a diverse species assemblage. Thus there is no need to employ several primer sets targeting the same amplicon. While we identified several suited primer sets for arthropod metabarcoding, the primer selection depends on the targeted taxonomic groups, as well as DNA quality, desired taxonomic resolution, and sequencing platform employed for analysis.

scholarly journals Validation of COI metabarcoding primers for terrestrial arthropods

2019 ◽  
Author(s):  
Vasco Elbrecht ◽  
Thomas WA Braukmann ◽  
Natalia V Ivanova ◽  
Sean WJ Prosser ◽  
Mehrdad Hajibabaei ◽  
...  
Keyword(s):  
Taxonomic Resolution ◽  
Minor Effect ◽  
Malaise Trap ◽  
Mock Community ◽  
Sequencing Platform ◽  
Amplification Bias ◽  
Terrestrial Arthropods ◽  
Primer Sets ◽  
Taxonomic Groups ◽  
Trap Sample

Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. Thus this study tests the performance of 36 primer sets on a mock community containing 374 species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets where also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from the 21 amplicon pools of the mock community and Malaise trap sample were used to select four primer sets for metabarcoding evaluation at different annealing temperatures (40-60 Co) using the mock community. Temperature did only have a minor effect on taxa recovery that varied with the specific primer pair. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrated that certain primer sets can recover most taxa in a diverse species assemblage. Thus there is no need to employ several primer sets targeting the same amplicon. While we identified several suited primer sets for arthropod metabarcoding, the primer selection depends on the targeted taxonomic groups, as well as DNA quality, desired taxonomic resolution, and sequencing platform employed for analysis.

The PPS 3 time-series sediment trap and the trap sample processing techniques used during the ECOMARGE experiment

1990 ◽  
Vol 10 (9-11) ◽  
pp. 943-958 ◽  
Author(s):  
Serge Heussner ◽  
Claude Ratti ◽  
Jacques Carbonne
Keyword(s):  
Time Series ◽  
Sediment Trap ◽  
Sample Processing ◽  
Processing Techniques ◽  
Trap Sample

scholarly journals Early diagenesis of organic matter in water of Lake Haruna. (I) Flux of organic matter to the bottom by determination of carbon and nitrogen of sediment trap sample, particulates and sediments.

1985 ◽  
Vol 46 (4) ◽  
pp. 297-302 ◽  
Author(s):  
Kazuko OGURA ◽  
Masahiro OCHIAI ◽  
Kimitaka KAWAMURA ◽  
Kazuo FUKUSHIMA ◽  
Makoto SHIOYA ◽  
...  
Keyword(s):  
Organic Matter ◽  
Sediment Trap ◽  
Early Diagenesis ◽  
Carbon And Nitrogen ◽  
Trap Sample

scholarly journals Validation of COI metabarcoding primers for terrestrial arthropods

2019 ◽  
Author(s):  
Vasco Elbrecht ◽  
Thomas WA Braukmann ◽  
Natalia V Ivanova ◽  
Sean WJ Prosser ◽  
Mehrdad Hajibabaei ◽  
...  
Keyword(s):  
Taxonomic Resolution ◽  
Minor Effect ◽  
Malaise Trap ◽  
Mock Community ◽  
Sequencing Platform ◽  
Amplification Bias ◽  
Terrestrial Arthropods ◽  
Primer Sets ◽  
Taxonomic Groups ◽  
Trap Sample

Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. Thus this study tests the performance of 36 primer sets on a mock community containing 374 species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets where also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from the 21 amplicon pools of the mock community and Malaise trap sample were used to select four primer sets for metabarcoding evaluation at different annealing temperatures (40-60 Co) using the mock community. Temperature did only have a minor effect on taxa recovery that varied with the specific primer pair. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrated that certain primer sets can recover most taxa in a diverse species assemblage. Thus there is no need to employ several primer sets targeting the same amplicon. While we identified several suited primer sets for arthropod metabarcoding, the primer selection depends on the targeted taxonomic groups, as well as DNA quality, desired taxonomic resolution, and sequencing platform employed for analysis.

scholarly journals Validation of COI metabarcoding primers for terrestrial arthropods

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7745 ◽  
Author(s):  
Vasco Elbrecht ◽  
Thomas W.A. Braukmann ◽  
Natalia V. Ivanova ◽  
Sean W.J. Prosser ◽  
Mehrdad Hajibabaei ◽  
...  
Keyword(s):  
Degraded Dna ◽  
Taxonomic Resolution ◽  
Effect Of Temperature ◽  
Gut Contents ◽  
Minor Effect ◽  
Malaise Trap ◽  
Mock Community ◽  
Terrestrial Arthropods ◽  
Primer Sets ◽  
Trap Sample

Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests the performance of 36 primer sets on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets were also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from both mock community and Malaise trap sample metabarcoding were used to select four primer sets for additional evaluation at different annealing temperatures (40–60 °C) using the mock community. The effect of temperature varied by primer pair but overall it only had a minor effect on taxon recovery. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrates that certain primer sets can recover most taxa in a diverse species assemblage. Thus, based our experimental set up, there is no need to employ several primer sets targeting the same gene region. We identify several suitable primer sets for arthropod metabarcoding, and specifically recommend BF3 + BR2, as it is not affected by primer slippage and provides maximal taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter fragment and is therefore ideal when targeting degraded DNA (e.g., from gut contents).

Latitudinal and seasonal changes of nocturnal illumination with a hypothesis about their effect on catches of insects in light-traps

1984 ◽  
Vol 74 (2) ◽  
pp. 279-298 ◽  
Author(s):  
John Bowden
Keyword(s):  
Seasonal Changes ◽  
Light Trap ◽  
Light Sources ◽  
Summer Solstice ◽  
Light Traps ◽  
Time And Space ◽  
Trap Catches ◽  
Trap Sample ◽  
Over Time

AbstractAn account is given of changes in nocturnal illumination at the spring and autumn equinoxes and summer and winter solstices at latitudes between 50 and 60°N. A Relative Trap Index (RTI) was devised to describe changes in light-trap effectiveness and used to adjust catches of Noctuidae and Geometridae for change in trap effectiveness caused by seasonal and latitudinal change in nocturnal illumination at latitudes between 50 and 58°N. When so adjusted, catches were frequently larger in northern than in southern latitudes, not smaller as unadjusted catches show. It is clear that unless light-trap catches are adjusted to allow for changes of illumination, comparisons over time and space, particularly those which involve assumptions about sample constancy, are suspect. Because of the large differences in RTI that may exist between northern and southern traps, particularly in summer and between the summer solstice and other times, it may be necessary to use different light sources at different times of year to maintain a consistent trap sample.

Four new genera of Schizopteridae (Hemiptera: Heteroptera) from the Afrotropical and Neotropical regions

Zootaxa ◽  
2020 ◽  
Vol 4768 (1) ◽  
pp. 95-111 ◽  
Author(s):  
CHRISTIANE WEIRAUCH ◽  
ALEXANDER KNYSHOV ◽  
ROCHELLE HOEY-CHAMBERLAIN
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Wing Venation ◽  
New Genera ◽  
Undescribed Species ◽  
Electron Microscopic ◽  
Male And Female ◽  
Scanning Electron Microscopic ◽  
Trap Sample ◽  
Scanning Electron

Despite a recent surge of taxonomic work on the dipsocoromorphan family Schizopteridae, new genus-level taxa remain to be documented and described. The curation of Malaise and Yellow Pan Trap sample residues from Central and South America and Cameroon resulted in the discovery of five undescribed species that based on combined molecular and morphological phylogenetic analyses represent four phylogenetically isolated lineages within non-hypselosomatine Schizopteridae. To accommodate these new species, we here describe the four new genera Caucanannus gen. n. (Colombia, Ecuador, and Brazil) with Caucanannus perplexus sp. n. and Caucanannus novissimis sp. n.; Kamakonocoris gen. n. (Cameroon) with Kamakonocoris carinata sp. n.; Perittonannus gen. n. (Costa Rica) with Perittonannus antiquus sp. n.; and Rimanannus gen. n. (Cameroon) with Rimanannus camerunensis sp. n. The four genera are characterized by distinctive wing venation and male and female genitalic features. We provide habitus photographs and document morphological details using digital macrophotography as well as light compound microscopic and scanning electron microscopic images. Maps and measurements are also included. 

Avoiding the Interrogation Trap—Sample Training, Part 2

2019 ◽  
Vol 42 (7) ◽  
pp. 6-7
Keyword(s):  
Trap Sample
Sign in / Sign up

Export Citation Format

Share Document