New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment

The megadiverse Neotropical fish fauna lacks a comprehensive and reliable DNA reference database, which hampers precise species identification and DNA based biodiversity assessment in the region. Here, we developed a mitochondrial 12S ribosomal DNA reference database for 67 fish species, representing 54 genera, 25 families, and six major Neotropical orders. We aimed to develop mini-barcode markers (i.e. amplicons with less than 200 bp) suitable for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes and to determine a threshold value for fish species delimitation using 12S. Evaluation of the target amplicons demonstrated that both full-length library (565 bp) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish species. For species delimitation, interspecific genetic distance threshold values of 0.4% and 0.55% were defined using full-length and mini-barcodes, respectively. A custom reference database and specific mini-barcode markers are important assets for ecoregion scale DNA based biodiversity assessments (such as environmental DNA) that can help with the complex task of conserving the megadiverse Neotropical ichthyofauna

Shark-dust: high-throughput DNA sequencing of processing residues unveils widespread trade in threatened sharks and rays

Illegal fishing, unregulated bycatch, and market demand for certain products (e.g. fins) are largely responsible for the rapid global decline of shark and ray populations. Controlling trade of endangered species remains difficult due to product variety, taxonomic ambiguity and trade complexity. The genetic tools traditionally used to identify traded species typically target individual tissue samples, are time-consuming and/or species-specific. Here, we performed high-throughput sequencing of trace DNA fragments retrieved from dust and scraps left behind by trade activities. We metabarcoded ‘shark-dust’ samples from seven processing plants in the world’s biggest shark landing site (Java, Indonesia), and identified 54 shark and ray taxa (representing half of all chondrichthyan orders), half of which could not be recovered from tissue samples collected in parallel from the same sites. Importantly, over 80% of shark-dust sequences were found to belong to CITES-listed species. We argue that this approach is likely to become a powerful and cost-effective monitoring tool wherever wildlife is traded

Primer biases in the molecular assessment of diet in multiple insectivorous mammals

Our understanding of trophic interactions of small insectivorous mammals has been drastically improved with the advent of DNA metabarcoding. The technique has continued to be optimised over the years, with primer choice repeatedly being a vital factor for dietary inferences. However, the majority of dietary studies examining the effect of primer choice often rely on in silico analyses or comparing between species that occupy an identical niche type. Here, we apply DNA metabarcoding to empirically compare the prey detection capabilities of two widely used primer sets when assessing the diets of a flying (lesser horseshoe bat; Rhinolophus hipposideros) and two ground-dwelling insectivores (greater white-toothed shrew; Crocidura russula and pygmy shrew; Sorex minutus). Although R. hipposideros primarily rely on two prey orders (Lepidoptera and Diptera), the unique taxa detected by each primer shows that a combination of primers may be the best approach to fully describe bat trophic ecology. However, random forest classifier analysis suggests that one highly degenerate primer set detected the majority of both shrews’ diet despite higher levels of host amplification. The wide range of prey consumed by ground-dwelling insectivores can therefore be accurately documented from using a single broad-range primer set, which can decrease cost and labour. The results presented here show that dietary inferences will differ depending on the primer or primer combination used for insectivores occupying different niches (i.e., hunting in the air or ground) and demonstrate the importance of performing empirical pilot studies for novel study systems

Search for chargino-neutralino production with mass splittings near the electroweak scale in three-lepton final states in √s=13 TeV pp collisions with the ATLAS detector

A search for supersymmetry through the pair production of electroweakinos with mass splittings near the electroweak scale and decaying via on-shell W and Z bosons is presented for a three-lepton final state. The analyzed proton-proton collision data taken at a center-of-mass energy of √s=13  TeV were collected between 2015 and 2018 by the ATLAS experiment at the Large Hadron Collider, corresponding to an integrated luminosity of 139  fb−1. A search, emulating the recursive jigsaw reconstruction technique with easily reproducible laboratory-frame variables, is performed. The two excesses observed in the 2015–2016 data recursive jigsaw analysis in the low-mass three-lepton phase space are reproduced. Results with the full data set are in agreement with the Standard Model expectations. They are interpreted to set exclusion limits at the 95% confidence level on simplified models of chargino-neutralino pair production for masses up to 345 GeV

Search for Higgs bosons produced via vector-boson fusion and decaying into bottom quark pairs in √s =13 TeV pp collisions with the ATLAS detector

A search for the bb ¯ decay of the Standard Model Higgs boson produced through vector-boson fusion is presented. Three mutually exclusive channels are considered: two all-hadronic channels and a photon-associated channel. Results are reported from the analysis of up to 30.6 fb −1 of pp data at s √ =13 TeV collected with the ATLAS detector at the LHC. The measured signal strength relative to the Standard Model prediction from the combined analysis is 2.5 +1.4 −1.3 for inclusive Higgs boson production and 3.0 +1.7 −1.6 for vector-boson fusion production only

Measurement of jet fragmentation in Pb+Pb and pp collisions at √s NN =5.02 TeV with the ATLAS detector

This paper presents a measurement of jet fragmentation functions in 0.49 nb −1 of Pb+Pb collisions and 25 pb −1 of pp collisions at √ sNN =5.02 TeV collected in 2015 with the ATLAS detector at the LHC. These measurements provide insight into the jet quenching process in the quark-gluon plasma created in the aftermath of ultra-relativistic collisions between two nuclei. The modifications to the jet fragmentation functions are quantified by dividing the measurements in Pb+Pb collisions by baseline measurements in pp collisions. This ratio is studied as a function of the transverse momentum of the jet, the jet rapidity, and the centrality of the collision. In both collision systems, the jet fragmentation functions are measured for jets with transverse momentum between 126 GeV and 398 GeV and with an absolute value of jet rapidity less than 2.1. An enhancement of particles carrying a small fraction of the jet momentum is observed, which increases with centrality and with increasing jet transverse momentum. Yields of particles carrying a very large fraction of the jet momentum are also observed to be enhanced. Between these two enhancements of the fragmentation functions a suppression of particles carrying an intermediate fraction of the jet momentum is observed in Pb+Pb collisions. A small dependence of the modifications on jet rapidity is observed

Search for vector-boson resonances decaying to a top quark and bottom quark in the lepton plus jets final state in pp collisions at √s=13TeV with the ATLAS detector

A search for new charged massive gauge bosons, W_, is performed with the ATLAS detector at the LHC. Data were collected in proton–proton collisions at a center-of-mass energy of √s=13TeVand correspond to an integrated luminosity of 36.1fb−1. This analysis searches for W_bosons in the W_→t¯bdecay channel in final states with an electron or muon plus jets. The search covers resonance masses between 0.5 and 5.0TeVand considers right-handed W_bosons. No significant deviation from the Standard Model (SM) expectation is observed and upper limits are set on the W_→t¯bcross section times branching ratio and the W_boson effective couplings as a function of the W_boson mass. For right-handed W_bosons with coupling to the SM particles equal to the SM weak coupling constant, masses below 3.15TeVare excluded at the 95% confidence level. This search is also combined with a previously published ATLAS result for W_→t¯bin the fully hadronic final state. Using the combined searches, right-handed W_bosons with masses below 3.25TeVare excluded at the 95% confidence level

Search for long-lived particles produced in pp collisions at √s=13 TeV that decay into displaced hadronic jets in the ATLAS muon spectrometer

A search for the decay of neutral, weakly interacting, long-lived particles using data collected by the ATLAS detector at the LHC is presented. The analysis in this paper uses 36.1 fb−1 of proton-proton collision data at √s=13 TeV recorded in 2015–2016. The search employs techniques for reconstructing vertices of long-lived particles decaying into jets in the muon spectrometer exploiting a two-vertex strategy and a novel technique that requires only one vertex in association with additional activity in the detector that improves the sensitivity for longer lifetimes. The observed numbers of events are consistent with the expected background and limits for several benchmark signals are determined

Search for light resonances decaying to boosted quark pairs and produced in association with a photon or a jet in proton–proton collisions at √s=13 TeV with the ATLAS detector

This Letter presents a search for new light resonances decaying to pairs of quarks and produced in association with a high-pT photon or jet. The dataset consists of proton–proton collisions with an integrated luminosity of 36.1 fb−1at a centre-of-mass energy of √s=13TeV recorded by the ATLAS detector at the Large Hadron Collider. Resonance candidates are identified as massive large-radius jets with substructure consistent with a particle decaying into a quark pair. The mass spectrum of the candidates is examined for local excesses above background. No evidence of a new resonance is observed in the data, which are used to exclude the production of a lepto-phobic axial-vector Z boson