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  1. Abstract

    Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral,Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two CaribbeanAcroporaspecies as well as their dominant dinoflagellate symbiont,Symbiodinium ‘fitti’.SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybridsmore »between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the generaBreviolum, Cladocopium, andDurusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called theStandardTools forAcroporidGenotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific.

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  2. Free, publicly-accessible full text available August 1, 2023
  3. Free, publicly-accessible full text available November 1, 2022
  4. null (Ed.)
  5. Free, publicly-accessible full text available April 1, 2023
  6. Abstract The two-detector design of the NOvA neutrino oscillation experiment, in which two functionally identical detectors are exposed to an intense neutrino beam, aids in canceling leading order effects of cross-section uncertainties. However, limited knowledge of neutrino interaction cross sections still gives rise to some of the largest systematic uncertainties in current oscillation measurements. We show contemporary models of neutrino interactions to be discrepant with data from NOvA, consistent with discrepancies seen in other experiments. Adjustments to neutrino interaction models in GENIE are presented, creating an effective model that improves agreement with our data. We also describe systematic uncertainties onmore »these models, including uncertainties on multi-nucleon interactions from a newly developed procedure using NOvA near detector data.« less