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1. A haplotype‐resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

   https://doi.org/10.1111/nph.20463  

   Larson, Drew_A; Staton, Margaret_E; Kapoor, Beant; Islam‐Faridi, Nurul; Zhebentyayeva, Tetyana; Fan, Shenghua; Stork, Jozsef; Thomas, Austin; Ahmed, Alaa_S; Stanton, Elizabeth_C; et al (February 2025, New Phytologist)

   Summary White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important.We report the first haplotype‐resolved chromosome‐scale genome assembly ofQ. albaand conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data.Despite strongly conserved chromosome synteny and genome size acrossQuercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found thatQ. albahas high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus.The white oak genome represents a major new resource for studying genome diversity and evolution inQuercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution inQuercus. 

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2. Quantum Q -Systems and Fermionic Sums—The Non-Simply Laced Case

   https://doi.org/10.1093/imrn/rnaa198  

   Simon Lin, Mingyan (August 2020, International Mathematics Research Notices)

   null (Ed.)

   Abstract In this paper, we seek to prove the equality of the $$q$$-graded fermionic sums conjectured by Hatayama et al. [ 14] in its full generality, by extending the results of Di Francesco and Kedem [ 9] to the non-simply laced case. To this end, we will derive explicit expressions for the quantum $$Q$$-system relations, which are quantum cluster mutations that correspond to the classical $$Q$$-system relations, and write the identity of the $$q$$-graded fermionic sums as a constant term identity. As an application, we will show that these quantum $$Q$$-system relations are consistent with the short exact sequence of the Feigin–Loktev fusion product of Kirillov–Reshetikhin modules obtained by Chari and Venkatesh [ 5]. 

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3. Will “Tall Oaks from Little Acorns Grow”? White Oak (Quercus alba) Biology in the Anthropocene

   https://doi.org/10.3390/f15020269  

   Abbott, Albert G.; Staton, Margaret E.; Lohtka, John M.; DeWald, Laura E.; Zhebentyayeva, Tetyana; Kapoor, Beant; Thomas, Austin M.; Larson, Drew A.; Hadziabdic, Denita; DeBolt, Seth; et al (February 2024, Forests)

   Quercus alba L., also known as white oak, eastern white oak, or American white oak, is a quintessential North American species within the white oak section (Quercus) of the genus Quercus, subgenus Quercus. This species plays a vital role as a keystone species in eastern North American forests and plays a significant role in local and regional economies. As a long-lived woody perennial covering an extensive natural range, Q. alba’s biology is shaped by a myriad of adaptations accumulated throughout its natural history. Populations of Q. alba are crucial repositories of genetic, genomic, and evolutionary insights, capturing the essence of successful historical adaptations and ongoing responses to contemporary environmental challenges in the Anthropocene. This intersection offers an exceptional opportunity to integrate genomic knowledge with the discovery of climate-relevant traits, advancing tree improvement, forest ecology, and forest management strategies. This review provides a comprehensive examination of the current understanding of Q. alba’s biology, considering past, present, and future research perspectives. It encompasses aspects such as distribution, phylogeny, population structure, key adaptive traits to cyclical environmental conditions (including water use, reproduction, propagation, and growth), as well as the species’ resilience to biotic and abiotic stressors. Additionally, this review highlights the state-of-the-art research resources available for the Quercus genus, including Q. alba, showcasing developments in genetics, genomics, biotechnology, and phenomics tools. This overview lays the groundwork for exploring and elucidating the principles of longevity in plants, positioning Q. alba as an emerging model tree species, ideally suited for investigating the biology of climate-relevant traits. 

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4. q -opers, QQ -systems, and Bethe Ansatz II: Generalized minors

   https://doi.org/10.1515/crelle-2022-0084  

   Koroteev, Peter; Zeitlin, Anton M. (January 2023, Journal für die reine und angewandte Mathematik (Crelles Journal))

   Abstract In this paper, we describe a certain kind of q -connections on a projective line, namely Z -twisted ( G , q ) {(G,q)} -opers with regular singularities using the language of generalized minors. In part one we explored the correspondence between these q -connections and 𝑄𝑄 \mathit{QQ} -systems/Bethe Ansatz equations. Here we associate to a Z -twisted ( G , q ) {(G,q)} -oper a class of meromorphic sections of a G -bundle, satisfying certain difference equations, which we refer to as ( G , q ) {(G,q)} -Wronskians. Among other things, we show that the 𝑄𝑄 \mathit{QQ} -systems and their extensions emerge as the relations between generalized minors, thereby putting the Bethe Ansatz equations in the framework of cluster mutations known in the theory of double Bruhat cells. 

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5. Mantle Q structure from S ,  SS ,  SSS and SSSS amplitude measurements

   https://doi.org/10.1093/gji/ggac217  

   Zhu, Min; Sun, Shuyang; Zhou, Ying; Wu, Qingju (June 2022, Geophysical Journal International)

   SUMMARY The seismic quality factor (Q) of the Earth’s mantle is of great importance for the understanding of the physical and chemical properties that control mantle anelasticity. The radial structure of the Earth’s Q is less well resolved compared to its wave speed structure, and large discrepancies exist among global 1-D Q models. In this study, we build a global data set of amplitude measurements of S, SS, SSS and SSSS waves using earthquakes that occurred between 2009 and 2017 with moment magnitudes ranging from 6.5 to 8.0. Synthetic seismograms for those events are computed in a 1-D reference model PREM, and amplitude ratios between observed and synthetic seismograms are calculated in the frequency domain by spectra division, with measurement windows determined based on visual inspection of seismograms. We simulate wave propagation in a global velocity model S40RTS based on SPECFEM3D and show that the average amplitude ratio as a function of epicentral distance is not sensitive to 3-D focusing and defocusing for the source–receiver configuration of the data set. This data set includes about 5500 S and SS measurements that are not affected by mantle transition zone triplications (multiple ray paths), and those measurements are applied in linear inversions to obtain a preliminary 1-D Q model QMSI. This model reveals a high Q region in the uppermost lower mantle. While model QMSI improves the overall datafit of the entire data set, it does not fully explain SS amplitudes at short epicentral distances or the amplitudes of the SSS and SSSS waves. Using forward modelling, we modify the 1-D model QMSI iteratively to reduce the overall amplitude misfit of the entire data set. The final Q model QMSF requires a stronger and thicker high Q region at depths between 600 and 900 km. This anelastic structure indicates possible viscosity layering in the mid mantle. 

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