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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. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. Structural basis for expanded substrate specificities of human long chain acyl-CoA dehydrogenase and related acyl-CoA dehydrogenases

    Narayanan, Beena ; Xia, Chuanwu ; McAndrew, Ryan ; ... - Scientific Reports
    Crystal structures of human long-chain acyl-CoA dehydrogenase (LCAD) and the catalytically inactive Glu291Gln mutant, have been determined. These structures suggest that LCAD harbors functions beyond its historically defined role in mitochondrial β-oxidation of long and medium-chain fatty acids. LCAD is a homotetramer containing one FAD per 43 kDa subunit with Glu291 as the catalytic base. The substrate binding cavity of LCAD reveals key differences which makes it specific for longer and branched chain substrates. The presence of Pro132 near the start of the E helix leads to helix unwinding that, together with adjacent smaller residues, permits binding of bulky substratesmore » such as 3α, 7α, l2α-trihydroxy-5β-cholestan-26-oyl-CoA. This structural element is also utilized by ACAD11, a eucaryotic ACAD of unknown function, as well as bacterial ACADs known to metabolize sterol substrates. Sequence comparison suggests that ACAD10, another ACAD of unknown function, may also share this substrate specificity. These results suggest that LCAD, ACAD10, ACAD11 constitute a distinct class of eucaryotic acyl CoA dehydrogenases.« less

  10. Evolution of homologous recombination rates across bacteria

    Torrance, Ellis L. ; Burton, Corey ; Diop, Awa ; ... - Proceedings of the National Academy of Sciences of the United States of America
    Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as “quasi-sexual.” However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies. It is unclear whether these variations reflect natural variations across populations or are due to differences in methodologies. Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate—as a trait—remains to be accurately described. Here, we developedmore » an approach based on Approximate Bayesian Computation that integrates multiple signals of recombination to estimate recombination rates. We inferred the rate of recombination of 162 bacterial species and one archaeon and tested the robustness of our approach. Our results confirm that recombination rates vary drastically across bacteria; however, we found that recombination rate—as a trait—is conserved in several lineages but evolves rapidly in others. Although some traits are thought to be associated with recombination rate (e.g., GC-content), we found no clear association between genomic or phenotypic traits and recombination rate. Overall, our results provide an overview of recombination rate, its evolution, and its impact on bacterial evolution.« less
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