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  1. Does adaption require a complex symphony or just “three chords and the truth?”

    Udekwu, Klas I. ; Marx, Christopher J. - PLoS Biology (Online)
    How predictable are the collateral effects of adaptation? This primer covers a new study of evolved yeast strains published in PLOS Biology suggests that growth across environments is fairly predictable because the selected mutations only affected a few latent fitness-impacting phenotypes.

  2. Moment-based adaptive time integration for thermal radiation transport

    Southworth, Ben Scott ; Walton, Steven Taylor ; Roberts, Steven B. ; ... - Journal of Computational Physics
    Here, in this paper we develop a framework for moment-based adaptive time integration of deterministic multifrequency thermal radiation transpot (TRT). We generalize our recent semi-implicit-explicit (IMEX) integration framework for gray TRT to multifrequency TRT, and also introduce a semi-implicit variation that facilitates higher-order integration of TRT, where each stage is implicit in all components except opacities. To appeal to the broad literature on adaptivity with Runge–Kutta methods, we derive new embedded methods for four asymptotic preserving IMEX Runge–Kutta schemes we have found to be robust in our previous work on TRT and radiation hydrodynamics. We then use a moment-based high-order-low-ordermore » representation of the transport equations. Due to the high dimensionality, memory is always a concern in simulating TRT. We form error estimates and adaptivity in time purely based on temperature and radiation energy, for a trivial overhead in computational cost and memory usage compared with the base second order integrators. We then test the adaptivity in time on the tophat and Larsen problem, demonstrating the ability of the adaptive algorithm to naturally vary the timestep across 4–5 orders of magnitude, ranging from the dynamical timescales of the streaming regime to the thick diffusion limit.« less

  3. An efficient second-order adaptive procedure for inserting CAD geometries into hexahedral meshes using volume fractions

    Granzow, Brian Neal ; Bond, Stephen David ; Powell, Michael Joseph ; ... - Engineering with Computers
    Here, this paper is concerned with inserting three-dimensional computer-aided design (CAD) geometries into meshes composed of hexahedral elements using a volume fraction representation. An adaptive procedure for doing so is presented. The procedure consists of two steps. The first step performs spatial acceleration using a k-d tree. The second step involves subdividing individual hexahedra in an adaptive mesh refinement (AMR)-like fashion and approximating the CAD geometry linearly (as a plane) at the finest subdivision. The procedure requires only two geometric queries from a CAD kernel: determining whether or not a queried spatial coordinate is inside or outside the CAD geometrymore » and determining the closest point on the CAD geometry’s surface from a given spatial coordinate. We prove that the procedure is second-order accurate for sufficiently smooth geometries and sufficiently refined background meshes. We demonstrate the expected order of accuracy is achieved with several verification tests and illustrate the procedure’s effectiveness for several exemplar CAD geometries.« less

  4. To immunity and beyond: the central role of jasmonate signalling in beneficial root–microbe–environment interactions

    Marqués‐Gálvez, José Eduardo ; Weston, David J. ; Veneault‐Fourrey, Claire - New Phytologist
    Jasmonates (JAs) have traditionally been studied for their defensive roles against wounding and detrimental organisms, but they are also crucial hormones for plant–microbe beneficial interactions. Here, we review the most recent advances in this overlooked field. We cover the evolutionary divergences of JA biosynthesis and signalling across various plant lineages and present the molecular mechanisms of action through which beneficial microbes interact with the host JA signalling pathway as well as environmental integration. Special emphasis is given to the cutting‐edge tools to study the spatial compartmentalization and cell and tissue specialization of JA signalling. This review underscores the role ofmore » the JA signalling pathway, with the MYELOCYTOMATOSIS2 transcription factor as a potential integrator of biotic and environmental cues, and highlights its significance in mutualistic interactions.« less

  5. Cross-kingdom comparative genomics reveal the metabolic potential of fungi for lignin turnover in deadwood

    Kijpornyongpan, Teeratas ; Kuatsjah, Eugene ; Komp, Evan ; ... - Nature Ecology and Evolution
    Deadwood is a major carbon source in forests, and yet the fate of this carbon remains a gap in our understanding of global carbon cycling. Lignin, the most recalcitrant biopolymer in wood, is mainly decayed through extracellular enzymatic and chemical processes initiated by white-rot fungi. However, the intracellular conversion of lignin decay products has been overlooked in the fungal kingdom. Here we integrate comparative genomic and phylogenetic analyses to understand the distribution and evolution of enzymes responsible for modifying lignin-related aromatic compounds-such as decarboxylases, hydroxylases, dioxygenases and other downstream ring-cleavage enzymes-that funnel carbon to central metabolism across the bacterial andmore » the fungal kingdoms. We demonstrate that specific fungal lineages conserve these enzyme families, and that the abilities to enzymatically depolymerize lignin and catabolize lignin-related aromatic compounds are not necessarily coupled. Our analyses also reveal an expanded substrate specificity of aromatic ring-cleavage enzymes during fungal evolution, as well as a clade of extracellular enzymes among them, broadening the spatial range of these biochemical capabilities. Together, our results highlight a large diversity of fungal enzymes and hosts that warrant further investigation for inclusion into carbon cycling models and biotechnological applications for the conversion of aromatic compounds.« less

  6. The hierarchical growth of bright central galaxies and intracluster light as traced by the magnitude gap

    Golden-Marx, Jesse B ; Zhang, Y ; Ogando, R L C ; ... - Monthly Notices of the Royal Astronomical Society
    Using a sample of 2800 galaxy clusters identified in the Dark Energy Survey across the redshift range 0.20 < z < 0.60, we characterize the hierarchical assembly of bright central galaxies (BCGs) and the surrounding intracluster light (ICL). To quantify hierarchical formation we use the stellar mass–halo mass (SMHM) relation, comparing the halo mass, estimated via the mass–richness relation, to the stellar mass within the BCG + ICL system. Moreover, we incorporate the magnitude gap (M14), the difference in brightness between the BCG (measured within 30 kpc) and fourth brightest cluster member galaxy within 0.5 $$R_{200,c}$$, as a third parametermore » in this linear relation. The inclusion of M14, which traces BCG hierarchical growth, increases the slope and decreases the intrinsic scatter, highlighting that it is a latent variable within the BCG + ICL SMHM relation. Moreover, the correlation with M14 decreases at large radii. However, the stellar light within the BCG + ICL transition region (30 –80 kpc) most strongly correlates with halo mass and has a statistically significant correlation with M14. Since the transition region and M14 are independent measurements, the transition region may grow due to the BCG’s hierarchical formation. Additionally, as M14 and ICL result from hierarchical growth, we use a stacked sample and find that clusters with large M14 values are characterized by larger ICL and BCG + ICL fractions, which illustrates that the merger processes that build the BCG stellar mass also grow the ICL. Furthermore, this may suggest that M14 combined with the ICL fraction can identify dynamically relaxed clusters.« less

  7. Direct prediction of saturated neoclassical tearing modes in slab using an equilibrium approach

    Balkovic, E. ; Loizu, J. ; Graves, J. P. ; ... - Plasma Physics and Controlled Fusion
    We demonstrate for the first time that the nonlinear saturation of neoclassical tearing modes (NTMs) can be found directly using a variational principle based on Taylor relaxation, without needing to simulate the intermediate, resistivity-dependent dynamics. As in previous investigations of classical tearing mode saturation (Loizu et al 2020 Phys. Plasmas 27 070701; Loizu and Bonfiglio 2023 J. Plasma Phys. 89 905890507), we make use of Stepped Pressure Equilibrium Code (SPEC) (Hudson et al 2012 Phys. Plasmas 19 112502), an equilibrium solver based on the variational principle of the multi-region relaxed magnetohydrodynamics (MHDs), featuring stepped pressure profiles and arbitrary magnetic topology.more » We work in slab geometry and employ a simple bootstrap current model Jbs = C$$\boldsymbol{\nabla}$$p to study the bootstrap-driven tearing modes, scanning over the asymptotic matching parameter Δ' and bootstrap current strength. Saturated island widths produced by SPEC agree well with the predictions of an initial value resistive MHDs code (Huang and Bhattacharjee 2016 Astrophys. J. 818 20) while being orders of magnitude faster to calculate. Additionally, we observe good agreement with a simple analytical modified Rutherford equation, without requiring any fitting coefficients. The match is obtained for both linearly unstable classical tearing modes in the presence of bootstrap current, and NTMs, which are linearly stable but nonlinear-unstable due to the effects of the bootstrap current.« less

  8. ZW sex chromosome structure in Amborella trichopoda

    Carey, Sarah B. ; Aközbek, Laramie ; Lovell, John T. ; ... - Nature Plants (Online)
    Sex chromosomes have evolved hundreds of times across the flowering plant tree of life; their recent origins in some members of this clade can shed light on the early consequences of suppressed recombination, a crucial step in sex chromosome evolution. Amborella trichopoda, the sole species of a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly contiguous assemblies of the Z and W chromosomes. We identify a ~3-megabase sex-determination region (SDR) captured in two strata that includes a ~300-kilobase inversion thatmore » is enriched with repetitive sequences and contains a homologue of the Arabidopsis METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) genes, which are known to be involved in fertility. However, the remainder of the SDR does not show patterns typically found in non-recombining SDRs, such as repeat accumulation and gene loss. These findings are consistent with the hypothesis that dioecy is derived in Amborella and the sex chromosome pair has not significantly degenerated.« less

  9. Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study

    Kim, Seungwon ; Kigozi, Godfrey ; Martin, Michael A. ; ... - Virus Evolution
    There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994–2018) and four hyperendemic Lake Victoria fishing communities (2011–2018) under continuous surveillance. HIV subtype was assignedmore » using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.« less

  10. Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes

    Goff, Jennifer L. ; Lui, Lauren M. ; Nielsen, Torben N. ; ... - ISME Communications
    Abstract Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to bemore » MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.« less
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