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The alternative oxidase (AOX), a common terminal oxidase in the electron transfer chain (ETC) of plants, plays a crucial role in stress resilience and plant growth and development. Oat (Avena sativa), an important crop with high nutritional value, has not been comprehensively studied regarding the AsAOX gene family. Therefore, this study explored the responses and potential functions of the AsAOX gene family to various abiotic stresses and their potential evolutionary pathways. Additionally, we conducted a genome-wide analysis to explore the evolutionary conservation and divergence of AOX gene families among three Avena species (Avena sativa, Avena insularis, Avena longiglumis) and four Poaceae species (Avena sativa, Oryza sativa, Triticum aestivum, and Brachypodium distachyon). We identified 12 AsAOX, 9 AiAOX, and 4 AlAOX gene family members. Phylogenetic, motif, domain, gene structure, and selective pressure analyses revealed that most AsAOXs, AiAOXs, and AlAOXs are evolutionarily conserved. We also identified 16 AsAOX segmental duplication pairs, suggesting that segmental duplication may have contributed to the expansion of the AsAOX gene family, potentially preserving these genes through subfunctionalization. Chromosome polyploidization, gene structural variations, and gene fragment recombination likely contributed to the evolution and expansion of the AsAOX gene family as well. Additionally, we hypothesize that AsAOX2 may have potential function in resisting wounding and heat stresses, while AsAOX4 could be specifically involved in mitigating wounding stress. AsAOX11 might contribute to resistance against chromium and waterlogging stresses. AsAOX8 may have potential fuction in mitigating ABA-mediated stress. AsAOX12 and AsAOX5 are most likely to have potential function in mitigating salt and drought stresses, respectively. This study elucidates the potential evolutionary pathways of the AsAOXs gene family, explores their responses and potential functions to various abiotic stresses, identifies potential candidate genes for future functional studies, and facilitates molecular breeding applications in A. sativa. [ABSTRACT FROM AUTHOR]

Background & objectives Genetic analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) strains circulating in India during 2020-2022 was carried out to understand the evolution of potentially expanding and divergent clades. Methods SARS-CoV-2 sequences (n=612) randomly selected from among the sequences of samples collected through a nationwide network of Virus Research Diagnostic Laboratories during 2020 (n=1532) and Indian sequences available in Global Initiative on Sharing All Influenza Data during March 2020-March 2022 (n=53077), were analyzed using the phylo-geo haplotype network approach with reference to the Wuhan prototype sequence. Results On haplotype analysis, 420 haplotypes were revealed from 643 segregating sites among the sequences. Haplotype sharing was noted among the strains from different geographical regions. Nevertheless, the genetic distance among the viral haplotypes from different clades could differentiate the strains into distinct haplo groups regarding variant emergence. Interpretation & conclusions The haplotype analysis revealed that the G and GR clades were co-evolved and an epicentrefor the evolution of the GH, GK and GRA clades. GH was more frequently identified in northern parts of India than in other parts, whereas GK was detected less in north India than in other parts. Thus, the network analysis facilitated a detailed illustration of the pathways of evolution and circulation of SARS-CoV-2 variants. [ABSTRACT FROM AUTHOR]

A comparative whole genome analysis was performed on three newly sequenced Escherichia coli O157:H7 strains with different stx profiles, previously isolated from feedlot cattle [C1-010 (stx1− , stx2c +), C1-057 (stx−), and C1-067 (stx1 +, stx2a +)], as well as five foodborne outbreak strains and six stx -negative strains from NCBI. Phylogenomic analysis demonstrated that the stx2c -carrying C1-010 and stx -negative C1-057 strains were grouped with the six NCBI stx -negative E. coli O157:H7 strains in Cluster 1, whereas the stx2a -carrying C1-067 and five foodborne outbreak strains were clustered together in Cluster 2. Based on different clusters, we selected the three newly sequenced strains, one stx2a -carrying strain, and the six NCBI stx -negative strains and identify their prophages at the stx insertion sites. All stx -carrying prophages contained both the three Red recombination genes (exo , bet , gam) and their repressor cI. On the other hand, the majority of the stx -negative prophages carried only the three Red recombination genes, but their repressor cI was absent. In the absence of the repressor cI , the consistent expression of the Red recombination genes in prophages might result in more frequent gene exchanges, potentially increasing the probability of the acquisition of stx genes. We further investigated each of the 10 selected E. coli O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two stx2a -carrying strains and one in the single stx2c -carrying and seven stx -negative strains were found to be associated with an upstream insertion sequence 629 within a conserved region among these strains. The presence of more unique metabolic pathway genes in stx2a -carrying E. coli O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the stx2c -carrying and stx -negative E. coli O157:H7 strains, the fact that they were grouped into the same phylogenomic cluster and had the same unique metabolic pathway genes suggested that they may also share closely related evolutionary pathways. As a consequence, gene exchange between them is more likely to occur. Results from this study could potentially serve as a basis to help develop strategies to reduce the prevalence of pathogenic E. coli O157:H7 in livestock and downstream food production environments. [ABSTRACT FROM AUTHOR]

Understanding the transition from nonplanar to planar clusters is crucial for the controllable synthesis of transition metal dichalcogenide (TMDC) monolayers. Using PtSe 2 as a model, we investigate how the chemical environment influences the nucleation and growth stages of monolayer PtSe 2 through structure searching and first-principles calculations. We established a comprehensive database of platinum selenide clusters (Pt x Se y , x = 1-10), analyzing 2095 unique clusters and identifying 191 stable isomers and 63 structures with the lowest formation energy on the convex hull. Our findings reveal a chemical environment-dependent phase transition from 3D structures to the planar T-phase of Pt x Se y clusters, representing an evolutionary route for PtSe 2 growth. Clusters such as PtSe 6 , Pt 2 Se 9 , Pt 3 Se 10 , and Pt 7 Se 10 in Pt-rich environments, as well as Pt 2 Se 15 and Pt 10 Se 32 in Se-rich environments, have been found to exhibit high stability. Additionally, the impact of varying chemical potentials of Pt and Se on the stability of these clusters is explored. PtSe 4 and PtSe 6 are found to be highly stable under most experimentally achievable chemical potential conditions and may serve as dominant precursors during PtSe 2 growth. This work advances our understanding of the nucleation processes of PtSe 2 and other T-phase TMDC materials.

Many animals improve offspring survival through parental care. Research on coevolution between parents has provided key insight into the genesis and maintenance of biparental care. However, understanding family dynamics more broadly requires assessing potential male–female coevolutionary processes in the more widespread and common context of uniparental care. Here, we explore how pre‐zygotic maternal contributions, jelly coats and oviposition sites, influence offspring dependency and change with the evolution of male‐only care in glassfrogs. Egg care appears ubiquitous among glassfrogs, with repeated evolutionary transitions from brief female‐only to extended male‐only care. Glassfrogs also exhibit a diversity of sex‐specific parental traits involving maternal egg‐jelly contributions, oviposition‐site choice, and egg‐attendance behaviors. We hypothesize these form functionally interchangeable suites of traits that mediate embryos' susceptibility to environmental risk. First, using parent‐removal field experiments, egg‐hydration assays, and comparative analyses, we found no evidence that evolutionary transitions in caring sex or care duration alter the adaptive functions or overall benefits of care (across eight species). Rather, the jelly contributions and oviposition‐site use associated with brief care influence embryo susceptibility to the same risks that are reduced by prolonged care. Next, we examined the diversity and evolutionary history of pre‐ and post‐zygotic parental traits, applying phylogenetic comparative methods to literature records and our field observations of 40 species (71 total, ~ 47 % of the family). Because pre‐zygotic maternal contributions determine embryo requirements, the evolution of male care might enable and/or compensate for reduced maternal contributions. Supporting this hypothesis, we found that the repeated evolution of complex male care is always associated with reductions in egg‐jelly and changes in oviposition sites. This phylogenetic pattern suggests that clutch phenotype might provide a general mechanism for the coevolution of parental investment in species with uniparental care. If different combinations of egg phenotypes and post‐zygotic care are ecologically equivalent, their interchangeability could allow parental traits to coevolve between the sexes without compromising offspring survival. Male‐only care is widespread in oviparous metazoans, occurring among annelids, molluscs, arthropods, fishes, and amphibians. Investigations of egg and clutch phenotypes offer new prospects for broadening research on the coevolutionary dynamics of parental care. [ABSTRACT FROM AUTHOR]

Anthropogenic changes in the biosphere, driven mainly by human cultural habits and technological advances, are altering the direction of evolution on Earth, with ongoing and permanent changes modifying uncountable interactions between organisms, the environment, and humankind itself. While numerous species may go extinct, others will be favored due to strong human influences. The Bio-Evolutionary Anthropocene hypothesizes that directly or indirectly human-driven organisms, including alien species, hybrids, and genetically modified organisms, will have major roles in the evolution of life on Earth, shifting the evolutionary pathways of all organisms through novel biological interactions in all habitats. We anticipate that, in future scenarios, novel organisms will be continuously created, and contemporary native organisms with no obvious economic use will decline—while anthropogenic-favored and novel organisms will spread. The Bio-Evolutionary Anthropocene hypothesis therefore predicts that humankind and novel organisms will interact within a strong evolutionary bias that will lead to unexpected, and probably irreversible, outcomes for the evolution of life on our planet. [ABSTRACT FROM AUTHOR]

To date a considerable amount of data on sympatric diversification of the laсustrine fish has been accumulated and many important advances made. However, the evolutionary mechanisms of the process still remain unclear. The paper discusses fish polymorphism in the water bodies of different latitudes, but the major focus is the question of sympatry in the charrs of the genus Salvelinus across the northern lakes. Numerous cases of diversification were comparatively analyzed, which provides evidence for the existence of several main pathways of evolutionary process. The pathways are controlled by environmental factors, which determine the structure of the lake ecosystems in the northern latitudes. [ABSTRACT FROM AUTHOR]

The rate of change in selective pressures is one of the main factors that determines the likelihood that populations can adapt to stress conditions. Generally, the reduction in the population size that accompanies abrupt environmental changes makes it difficult to generate and select adaptive mutations. However, in systems with high genetic diversity, as happens in RNA viruses, mutations with beneficial effects under new conditions can already be present in the population, facilitating adaptation. In this work, we have propagated an RNA bacteriophage (Qβ) at temperatures higher than the optimum, following different patterns of change. We have determined the fitness values and the consensus sequences of all lineages throughout the evolutionary process in order to establish correspondences between fitness variations and adaptive pathways. Our results show that populations subjected to a sudden temperature change gain fitness and fix mutations faster than those subjected to gradual changes, differing also in the particular selected mutations. The life-history of populations prior to the environmental change has great importance in the dynamics of adaptation. The conclusion is that in the bacteriophage Qβ, the standing genetic diversity together with the rate of temperature change determine both the rapidity of adaptation and the followed evolutionary pathways.

We have established a translation-coupled RNA replication system within a cell-like compartment, and conducted an experimental evolution of the RNA molecules in the system. Then, we obtained a time series of occurrence frequencies of 91 individual genotypes through random sampling and next-generation sequencing. The time series showed a complex clonal interference and a polymorphic population called the “quasispecies”. By fitting a deterministic kinetic model of evolvable simple self-replicators to the time series, we estimated the fitness value and “putative appearance time point” for each of the 91 major genotypes identified, where the putative appearance time point is defined as a certain time point at which a certain mutant genotype is supposed to appear in the deterministic kinetic model. As a result, the kinetic model was well fitted and additionally we confirmed that the estimated fitness values for 11 genotypes were considerably close to the experimentally measured ones ( Ichihashi et al., 2015 ). In this sequel paper, with the theoretical basis of the deterministic kinetic model, we present the details of inference of the fitness values and putative appearance time points for the 91 genotypes. It may be possible to apply this methodology to other self-replicating molecules, viruses and bacteria. [ABSTRACT FROM AUTHOR]

In the context of carbon-neutral, countries are urging a social-wide transition to decarbonization. However, the efficiency of this transition has not been as expected due to the game of benefits among relevant players. Here, we develop a quadrilateral evolutionary game model that highlights the complex interactions at a multi-player level, including producers, regulators, third-party certifiers, and consumers, in order to analyze evolutionary pathways and stable strategies. Our results suggest that: (1) there are significant correlations among the quadrilateral game players, and the benign interactions among them will effectively drive the social-wide low-carbon transition; (2) if consumers have higher low-carbon preferences, producers will be attracted to actively choose the low-carbon transition strategy, which may form a stable portfolio strategy; (3) proper interventions, such as reducing transition costs, increasing reputation loss, and raising consumers' whistle-blowing abilities, can help promote the systematic evolution to the low-carbon state; and (4) rent-seeking behavior between producers and third-party certifiers should be strongly monitored by regulators, and higher penalties can prevent their duty dereliction. These findings provide significant implications for policy-makers to make better-informed decisions about the social-wide low-carbon transition in the context of carbon-neutral. • The evolutionary game model on low-carbon transition is constructed. • Consumers' low-carbon preference is the priority factor of transition willingness. • Strong regulation can urge producers to transit into low-carbon production. • Higher penalties to avoid collusion, higher validity of low-carbon certificates. • Whistle-blowing behavior actively affects the evolutionary system. [ABSTRACT FROM AUTHOR]

Experimentalist forms of governance have burgeoned across policy areas and institutional contexts in recent years. Recognizing that experimentalist forms of governance can evolve along a plethora of distinct pathways, this paper inquires how the evolutionary nature of experimentalism can be explored in greater depth. Linking the framework of experimentalist governance to that of Evolutionary Governance Theory (EGT), the paper identifies three driving mechanisms of contingency in experimentalism: governance being (1) self-referential, (2) rooted in observation, and (3) steered by dependencies. The paper then refers to recent efforts in the realm of energy transition governance in the Netherlands to illustrate how these contingency mechanisms can help to interrogate the variegated evolutionary pathways that experimentalist governance may have in practice. Building on this Dutch empirical context, the paper puts forward evolutionary path- and context-mapping as a fruitful tool for identifying and disentangling the myriad of pathways along which experimentalism may manifest itself. [ABSTRACT FROM AUTHOR]

Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.

The rate of change in selective pressures is one of the main factors that determines the likelihood that populations can adapt to stress conditions. Generally, the reduction in the population size that accompanies abrupt environmental changes makes it difficult to generate and select adaptive mutations. However, in systems with high genetic diversity, as happens in RNA viruses, mutations with beneficial effects under new conditions can already be present in the population, facilitating adaptation. In this work, we have propagated an RNA bacteriophage (Qβ) at temperatures higher than the optimum, following different patterns of change. We have determined the fitness values and the consensus sequences of all lineages throughout the evolutionary process in order to establish correspondences between fitness variations and adaptive pathways. Our results show that populations subjected to a sudden temperature change gain fitness and fix mutations faster than those subjected to gradual changes, differing also in the particular selected mutations. The life-history of populations prior to the environmental change has great importance in the dynamics of adaptation. The conclusion is that in the bacteriophage Qβ, the standing genetic diversity together with the rate of temperature change determine both the rapidity of adaptation and the followed evolutionary pathways. [ABSTRACT FROM AUTHOR]