Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Single nucleotide polymorphisms (SNPs) are growing in popularity as a genetic marker for investigating evolutionary processes. A panel of SNPs is often developed by comparing large quantities of DNA sequence data across multiple individuals to identify polymorphic sites. For non-model species, this is particularly difficult, as performing the necessary large-scale genomic sequencing often exceeds the resources available for the project. In this study, we trial the Bovine SNP50 BeadChip developed in cattle (Bos taurus) for identifying polymorphic SNPs in cervids Odocoileus hemionus (mule deer and black-tailed deer) and O. virginianus (white-tailed deer) in the Pacific Northwest. We found that 38.7% of loci could be genotyped, of which 5% (n = 1068) were polymorphic. Of these 1068 polymorphic SNPs, a mixture of putatively neutral loci (n = 878) and loci under selection (n = 190) were identified with the FST-outlier method. A range of population genetic analyses were implemented using these SNPs and a panel of 10 microsatellite loci. The three types of deer could readily be distinguished with both the SNP and microsatellite datasets. This study demonstrates that commercially developed SNP chips are a viable means of SNP discovery for non-model organisms, even when used between very distantly related species (the Bovidae and Cervidae families diverged some 25.1−30.1 million years before present)

The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events

Test of lepton flavour universality in W-boson decays into electrons and τ-leptons using pp collisions at s \sqrt{s} = 13 TeV with the ATLAS detector

A measurement of the ratio of the branching fractions, Rτ/e = B(W → τν)/B(W → eν), is performed using a sample of W bosons originating from top-quark decays to final states containing τ-leptons or electrons. This measurement uses pp collisions at s =13TeV, collected by the ATLAS experiment at the Large Hadron Collider during Run 2, corresponding to an integrated luminosity of 140fb−1. The W → τντ (with τ → eνeντ) and W →eνe decays are distinguished using the differences in the impact parameter distributions and transverse momentum spectra of the electrons. The measured ratio of branching fractions Rτ/e = 0.975±0.012(stat.)±0.020(syst.), is consistent with the Standard Model assumption of lepton flavour universality in W-boson decays

Configuration, Performance, and Commissioning of the ATLAS b-jet Triggers for the 2022 and 2023 LHC data-taking periods

In 2022 and 2023, the Large Hadron Collider produced approximately two billion hadronic interactions each second from bunches of protons that collide at a rate of 40 MHz. The ATLAS trigger system is used to reduce this rate to a few kHz for recording. Selections based on hadronic jets, their energy, and event topology reduce the rate to O(10) kHz while maintaining high efficiencies for important signatures resulting in b-quarks, but to reach the desired recording rate of hundreds of Hz, additional real-time selections based on the identification of jets containing b-hadrons (b-jets) are employed to achieve low thresholds on the jet transverse momentum at the High-Level Trigger. The configuration, commissioning, and performance of the real-time ATLAS b-jet identification algorithms for the early LHC Run 3 collision data are presented. These recent developments provide substantial gains in signal efficiency for critical signatures; for the Standard Model production of Higgs boson pairs, a 50% improvement in selection efficiency is observed in final states with four b-quarks or two b-quarks and two hadronically decaying tau-leptons

Search for vector-like leptons coupling to first- and second-generation Standard Model leptons in pp collisions at s \sqrt{s} = 13 TeV with the ATLAS detector

A search for pair production of vector-like leptons coupling to first- and secondgeneration Standard Model leptons is presented. The search is based on a dataset of proton-proton collisions at root s = 13 TeV recorded with the ATLAS detector during Run 2 of the Large Hadron Collider, corresponding to an integrated luminosity of 140fb-1. Events are categorised depending on the flavour and multiplicity of leptons (electrons or muons), as well as on the scores of a deep neural network targeting particular signal topologies according to the decay modes of the vector-like leptons. In each of the signal regions, the scalar sum of the transverse momentum of the leptons and the missing transverse momentum is analysed. The main background processes are estimated using dedicated control regions in a simultaneous fit with the signal regions to data. No significant excess above the Standard Model background expectation is observed and limits are set at 95% confidence level on the production cross-sections of vector-like electrons and muons as a function of the vector-like lepton mass, separately for SU(2) doublet and singlet scenarios. The resulting mass lower limits are 1220GeV (1270GeV) and 320GeV (400GeV) for vector-like electrons (muons) in the doublet and singlet scenarios, respectively

Measurements of WH and ZH production with Higgs boson decays into bottom quarks and direct constraints on the charm Yukawa coupling in 13 TeV pp collisions with the ATLAS detector

A study of the Higgs boson decaying into bottom quarks (H → b ̄ b) and charm quarks (H → c ̄ c) is performed, in the associated production channel of the Higgs boson with a W or Z boson, using 140fb−1 of proton-proton collision data at √s = 13TeV collected by the ATLAS detector. The individual production of WH and ZH with H → b ̄ b is established with observed (expected) significances of 5.3 (5.5) and 4.9 (5.6) standard deviations, respectively. Differential cross-section measurements of the gauge boson transverse momentum within the simplified template cross-section framework are performed in a total of 13 kinematical f iducial regions. The search for the H → c ̄ c decay yields an observed (expected) upper limit at 95% confidence level of 11.5 (10.6) times the Standard Model prediction. The results are also used to set constraints on the charm coupling modifier, resulting in |κc| < 4.2 at 95% confidence level. Combining the H → b ̄ b and H → c ̄ c measurements constrains the absolute value of the ratio of Higgs-charm and Higgs-bottom coupling modifiers (|κc/κb|) to be less than 3.6 at 95% confidence level

Search for supersymmetry using vector boson fusion signatures and missing transverse momentum in pp collisions at √s = 13 TeV with the ATLAS detector

This paper presents a search for supersymmetric particles in models with highly compressed mass spectra, in events consistent with being produced through vector boson fusion. The search uses 140 fb−1 of proton-proton collision data at √s = 13 TeV collected by the ATLAS experiment at the Large Hadron Collider. Events containing at least two jets with a large gap in pseudorapidity, large missing transverse momentum, and no reconstructed leptons are selected. A boosted decision tree is used to separate events consistent with the production of supersymmetric particles from those due to Standard Model backgrounds. The data are found to be consistent with Standard Model predictions. The results are interpreted using simplified models of R-parity-conserving supersymmetry in which the lightest supersymmetric partner is a bino-like neutralino with a mass similar to that of the lightest chargino and second-to-lightest neutralino, both of which are wino-like. Lower limits at 95% confidence level on the masses of next-to-lightest supersymmetric partners in this simplified model are established between 117 and 120 GeV when the lightest supersymmetric partners are within 1 GeV in mass

Measurement of double-differential charged-current Drell-Yan cross-sections at high transverse masses in pp collisions at √s = 13 TeV with the ATLAS detector

This paper presents a first measurement of the cross-section for the charged-current Drell-Yan process $pp\rightarrow W^{\pm} \rightarrow \ell^{\pm} \nu$ above the resonance region, where $\ell$ is an electron or muon. The measurement is performed for transverse masses, $m_{\text{T}}^{\text{W}}$, between 200 GeV and 5000 GeV, using a sample of 140 fb$^{-1}$ of $pp$ collision data at a centre-of-mass energy of $\sqrt{s}$ = 13 TeV collected by the ATLAS detector at the LHC during 2015-2018. The data are presented single differentially in transverse mass and double differentially in transverse mass and absolute lepton pseudorapidity. A test of lepton flavour universality shows no significant deviations from the Standard Model. The electron and muon channel measurements are combined to achieve a total experimental precision of 3% at low $m_{\text{T}}^{\text{W}}$. The single- and double differential $W$-boson charge asymmetries are evaluated from the measurements. A comparison to next-to-next-to-leading-order perturbative QCD predictions using several recent parton distribution functions and including next-to-leading-order electroweak effects indicates the potential of the data to constrain parton distribution functions. The data are also used to constrain four fermion operators in the Standard Model Effective Field Theory formalism, in particular the lepton-quark operator Wilson coefficient $c_{\ell q}^{(3)}.