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  1. Abstract— The genus Solidago represents a taxonomically challenging group due to its sheer number of species, putative hybridization, polyploidy, and shallow genetic divergence among species. Here we use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri , a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri. A multivariate analysis of both discrete and continuous morphological data revealed no clear distinction between S. ulmifolia var. palmeri and Solidago ulmifolia var. ulmifolia . Solidago ulmifolia var. palmeri ’s status was also assessed with a phylogenomic and SNP clustering analysis of data generated with the “Angiosperms353” probe kit. Neither analysis supported Solidago ulmifolia var. palmeri as a distinct taxon, and we suggest that this name should be discarded. The status of Solidago delicatula (formerly known as Solidago ulmifolia var. microphylla ) was also assessed. Both morphological and phylogenetic analyses supported the species status of S. delicatula and we suggest maintaining this species at its current rank. These results highlight the utility of the Angiosperms353 probe kit, both with herbarium tissue and at lower taxonomic levels. Indeed, this is the first study to utilize this kit to identify genetic groups within a species. 
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  2. Abstract Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals 1 . These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample. 
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    Free, publicly-accessible full text available May 11, 2024
  3. Abstract The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications 1,2 . Although the resolution of these regions in the first complete assembly of a human genome—the Telomere-to-Telomere Consortium’s CHM13 assembly (T2T-CHM13)—provided a model of their homology 3 , it remained unclear whether these patterns were ancestral or maintained by ongoing recombination exchange. Here we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologous sequences. Utilizing an all-to-all comparison of the human pangenome from the Human Pangenome Reference Consortium 4 (HPRC), we find that contigs from all of the SAACs form a community. A variation graph 5 constructed from centromere-spanning acrocentric contigs indicates the presence of regions in which most contigs appear nearly identical between heterologous acrocentric chromosomes in T2T-CHM13. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the pseudo-homologous regions than in the corresponding short and long arms, indicating higher rates of recombination 6,7 . The pseudo-homologous regions include sequences that have previously been shown to lie at the breakpoint of Robertsonian translocations 8 , and their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14 and 21. The ubiquity of signals of recombination between heterologous acrocentric chromosomes seen in the HPRC draft pangenome suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed from cytogenetic studies 50 years ago 9 . 
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    Free, publicly-accessible full text available May 11, 2024
  4. Free, publicly-accessible full text available August 1, 2024
  5. Free, publicly-accessible full text available July 1, 2024
  6. A<sc>bstract</sc>

    Measurements of Higgs boson production cross-sections are carried out in the diphoton decay channel using 139 fb1ofppcollision data at$$ \sqrt{s} $$s= 13 TeV collected by the ATLAS experiment at the LHC. The analysis is based on the definition of 101 distinct signal regions using machine-learning techniques. The inclusive Higgs boson signal strength in the diphoton channel is measured to be$$ {1.04}_{-0.09}^{+0.10} $$1.040.09+0.10. Cross-sections for gluon-gluon fusion, vector-boson fusion, associated production with aWorZboson, and top associated production processes are reported. An upper limit of 10 times the Standard Model prediction is set for the associated production process of a Higgs boson with a single top quark, which has a unique sensitivity to the sign of the top quark Yukawa coupling. Higgs boson production is further characterized through measurements of Simplified Template Cross-Sections (STXS). In total, cross-sections of 28 STXS regions are measured. The measured STXS cross-sections are compatible with their Standard Model predictions, with ap-value of 93%. The measurements are also used to set constraints on Higgs boson coupling strengths, as well as on new interactions beyond the Standard Model in an effective field theory approach. No significant deviations from the Standard Model predictions are observed in these measurements, which provide significant sensitivity improvements compared to the previous ATLAS results.

     
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    Free, publicly-accessible full text available July 1, 2024
  7. A bstract A search for Higgs boson pair production in events with two b -jets and two τ -leptons is presented, using a proton–proton collision dataset with an integrated luminosity of 139 fb − 1 collected at $$ \sqrt{s} $$ s = 13 TeV by the ATLAS experiment at the LHC. Higgs boson pairs produced non-resonantly or in the decay of a narrow scalar resonance in the mass range from 251 to 1600 GeV are targeted. Events in which at least one τ -lepton decays hadronically are considered, and multivariate discriminants are used to reject the backgrounds. No significant excess of events above the expected background is observed in the non-resonant search. The largest excess in the resonant search is observed at a resonance mass of 1 TeV, with a local (global) significance of 3 . 1 σ (2 . 0 σ ). Observed (expected) 95% confidence-level upper limits are set on the non-resonant Higgs boson pair-production cross-section at 4.7 (3.9) times the Standard Model prediction, assuming Standard Model kinematics, and on the resonant Higgs boson pair-production cross-section at between 21 and 900 fb (12 and 840 fb), depending on the mass of the narrow scalar resonance. 
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    Free, publicly-accessible full text available July 1, 2024