Assessing Population Structure and Genetic Diversity in US Suffolk Sheep to Define a Framework for Genomic Selection

Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the United States was evaluated in four ways: 1) using genetic relationships from pedigree data [(n = 64 310 animals recorded in the US National Sheep Improvement Program (NSIP)]; 2) using molecular data (n = 304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n = 109) and Irish (n = 55) Suffolk sheep to those in the United States using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n = 18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (Ne) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (HE) and observed (HO) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the US population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by FST. Using these measures of genetic diversity, a framework for establishing a genomic reference population in US Suffolk sheep engaged in NSIP was proposed

Genetic impact of external Targhee sires at the U.S. Sheep Experiment Station: a case study of introgression

Sheep breeders requested that the U.S. Sheep Experiment Station (USSES) to participate in national genetic evaluation through the National Sheep Improvement Program (NSIP). The reasons included the need for (1) a comparison of the productivity of industry and United States Department of Agriculture (USDA) lines, (2) transparency of USDA flocks, (3) genetic ties for NSIP by sampling of industry flocks, and (4) development of premium genetic lines for public release. In response, USSES began to incorporate external sires from NSIP participating flocks into the USSES Targhee flock. Our objective, based on a pedigree analysis, was to test if introgression of external genetics into the flock was achieved. The pedigree included 13,189 animals with mean maximum generations, mean complete generations, and mean equivalent complete generations of 4.2, 1.8, and 2.6, respectively. The mean generation interval was 3.1 yr. The reference population was defined as lambs born from 2021 to 2023 (n = 792). Two additional populations were defined as the current mature ewe flock (n = 123) and the current mature rams (n = 14). The Genetic Conservation Index averaged 7.7 for the full population and 25.7 for the reference population. Overall inbreeding was 0.003 for the full population and 0.006 for the reference population. The rate of inbreeding was 0.0003 per generation. Average relatedness was 0.015 for the full population and 0.018 for the reference population. The effective number of founders, effective number of ancestors, and founder genome equivalents contributing to the reference population were 60, 39, and 19.1, respectively. The ratio of the effective number of founders to the effective number of ancestors was 1.5, indicating the presence of genetic bottlenecks. Measures of effective population size ranged from 102 to 547. Of the 704 offspring produced by external sires, 17 ram lambs and 132 ewe lambs were retained for breeding. The USSES sires produced 299 offspring with 2 ram lambs and 51 ewe lambs retained. Incorporating external sires resulted in a cumulative percentage of genetic variance of 48.8, 49.1, and 44.2 of external genetics for the reference population, current mature ewe flock, and current mature rams, respectively. Stakeholder needs were addressed by introgression of external sires and participation in NSIP, but future selection practices need to be modified to maintain a minimum of 50% USSES core genetics in the flock

Search for the Standard Model Higgs Boson in Tau Final States

This is the publisher's version, also available electronically from http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.102.251801.We present a search for the standard model Higgs boson using hadronically decaying tau leptons, in 1  fb(−1) of data collected with the D0 detector at the Fermilab Tevatron pp-bar collider. We select two final states: τ± plus missing transverse energy and b jets, and τ(+)τ(−) plus jets. These final states are sensitive to a combination of associated W/Z boson plus Higgs boson, vector boson fusion, and gluon-gluon fusion production processes. The observed ratio of the combined limit on the Higgs production cross section at the 95% C.L. to the standard model expectation is 29 for a Higgs boson mass of 115 GeV

Evidence for an anomalous like-sign dimuon charge asymmetry

This is the publisher's version, also available electronically from http://journals.aps.org/prd/abstract/10.1103/PhysRevD.82.032001

Search for Dark Photons from Supersymmetric Hidden Valleys

This is the publisher's version, also available electronically from http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.103.081802.We search for a new light gauge boson, a dark photon, with the D0 experiment. In the model we consider, supersymmetric partners are pair produced and cascade to the lightest neutralinos that can decay into the hidden sector state plus either a photon or a dark photon. The dark photon decays through its mixing with a photon into fermion pairs. We therefore investigate a previously unexplored final state that contains a photon, two spatially close leptons, and large missing transverse energy. We do not observe any evidence for dark photons and set a limit on their production

Assessment of genetic diversity and population structure of U.S. Polypay sheep from breed origins to future genomic selection

Knowledge of past and present genetic diversity within a breed is critical for the design and optimization of breeding programs as well as the development of strategies for the conservation of genetic resources. The Polypay sheep breed was developed at the U.S. Sheep Experiment Station (USSES) in 1968 with the goal of improving productivity in Western U.S. range flocks. It has since flourished in the more intensively managed production systems throughout the U.S. The genetic diversity of the breed has yet to be documented. Therefore, the primary objective of this study was to perform a comprehensive evaluation of the genetic diversity and population structure of U.S. Polypay sheep using both pedigree- and genomic-based methods. Pedigree data from 193 Polypay flocks participating in the National Sheep Improvement Program (NSIP) were combined with pedigree records from USSES (n = 162,997), tracing back to the breed’s origin. A subset of these pedigreed sheep from 32 flocks born from 2011 to 2023 were genotyped with the GGP Ovine 50K BeadChip containing 51,867 single nucleotide polymorphisms (SNPs). Four subgroups were used for the pedigree-based analyses: 1) the current generation of animals born in 2020–2022 (n = 20,701), 2) the current generation with a minimum of four generations of known ancestors (n = 12,685), 3) only genotyped animals (n = 1,856), and 4) the sires of the current generation (n = 509). Pedigree-based inbreeding for the full population was 2.2%, with a rate of inbreeding of 0.22% per generation. Pedigree-based inbreeding, Wright’s inbreeding, and genomic inbreeding based on runs of homozygosity were 2.9%, 1.3%, and 5.1%, respectively, for the genotyped population. The effective population size ranged from 41 to 249 for the pedigree-based methods and 118 for the genomic-based estimate. Expected and observed heterozygosity levels were 0.409 and 0.403, respectively. Population substructure was evident based on the fixation index (FST), principal component analysis, and model-based population structure. These analyses provided evidence of differentiation from the foundation flock (USSES). Overall, the Polypay breed exhibited substantial genetic diversity and the presence of a population substructure that provides a basis for the implementation of genomic selection in the breed

Search for charged Higgs bosons in decays of top quarks

This is the publisher's version, also available electronically from http://journals.aps.org/prd/abstract/10.1103/PhysRevD.80.051107.We present a search for charged Higgs bosons in decays of top quarks, in the mass range 800.24 for m(H±)=80  GeV and B(t→H(+b))>0.19 for mH±=155  GeV at the 95% C.L

Measurement of the top quark mass in final states with two leptons

This is the publisher's version, also available electronically from http://journals.aps.org/prd/abstract/10.1103/PhysRevD.80.092006.We present measurements of the top quark mass (mt) in tt-bar candidate events with two final state leptons using 1  fb(−1) of data collected by the D0 experiment. Our data sample is selected by requiring two fully identified leptons or by relaxing one lepton requirement to an isolated track if at least one jet is tagged as a b jet. The top quark mass is extracted after reconstructing the event kinematics under the tt-bar hypothesis using two methods. In the first method, we integrate over expected neutrino rapidity distributions, and in the second we calculate a weight for the possible top quark masses based on the observed particle momenta and the known parton distribution functions. We analyze 83 candidate events in the data and obtain mt=176.2±4.8(stat)±2.1(sys)  GeV and mt=173.2±4.9(stat)±2.0(sys)  GeV for the two methods, respectively. Accounting for correlations between the two methods, we combine the measurements to obtain mt=174.7±4.4(stat)±2.0(sys)  GeV

Direct Measurement of the W Boson Width

This is the publisher's version, also available electronically from http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.103.231802.We present a direct measurement of the width of the W boson using the shape of the transverse mass distribution of W→eν candidate events. Data from approximately 1  fb(−1) of integrated luminosity recorded at s√=1.96  TeV by the D0 detector at the Fermilab Tevatron pp-bar collider are analyzed. We use the same methods and data sample that were used for our recently published W boson mass measurement, except for the modeling of the recoil, which is done with a new method based on a recoil library. Our result, 2.028±0.072  GeV, is in agreement with the predictions of the standard model

Search for New Fermions (“Quirks”) at the Fermilab Tevatron Collider

This is the publisher's version, also available electronically from http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.105.211803.We report results of a search for particles with anomalously high ionization in events with a high transverse energy jet and large missing transverse energy in 2.4  fb(−1) of integrated luminosity collected by the D0 experiment at the Fermilab Tevatron pp-bar collider. Production of such particles (quirks) is expected in scenarios with extra QCD-like SU(N) sectors, and this study is the first dedicated search for such signatures. We find no evidence of a signal and set a lower mass limit of 107, 119, and 133 GeV for the mass of a charged quirk with strong dynamics scale Λ in the range from 10 keV to 1 MeV and N=2, 3, and 5, respectively