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"evolutionary adaptation"
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Epitranscriptomics as a Candidate Universal Modulator of Dormancy Transitions
Dormancy has been widely recognized as an evolutionarily conserved strategy that enables cells and organisms to endure environmental stress, resource scarcity, or developmental arrest. While transcriptional regulation has been extensively studied in this context, increasing attention is being directed toward post‐transcriptional mechanisms that allow rapid and energy‐efficient control of gene expression. Among these, epitranscriptomic modifications, chemical marks added to RNA, have emerged as dynamic and reversible regulators of mRNA fate. In this perspective, it is proposed that RNA modifications can play a central role in establishing and maintaining dormancy across diverse biological systems. Evidence from plant seeds, microbial persisters, stem cells, and dormant cancer cells suggests that specific RNA marks, such as N6‐methyladenosine (m6A), influence mRNA stability, translation, and localization in a context‐dependent manner. It is argued that these modifications serve as a molecular interface between environmental signals and cellular responses, fine‐tuning the transition between active and paused states. This article presents a unifying model, grounded in epitranscriptomics, in which RNA modifications modulate entry into, maintenance of, and exit from dormancy across taxa by tuning mRNA stability, translation, and localization—an underexplored regulatory layer in inactive states—and highlights key mechanistic insights, evolutionary parallels, and outstanding questions at the intersection of RNA regulation and cellular dormancy. Dormancy is presented as a conserved, reversible survival program in which epitranscriptomic RNA modifications are proposed to provide a rapid, energy‐efficient layer that establishes, maintains, and terminates the state by modulating mRNA stability, translation, and localization. Evidence spanning seeds, microbial persisters, stem cells, and dormant cancer cells is synthesized to advance a unifying model in which RNA marks are positioned as a sensor–effector interface linking environmental cues to dormancy decisions. Key mechanisms and evolutionary parallels are outlined, and outstanding questions are identified to guide future tests of this framework.
Journal Article
Diversification, adaptation, and community assembly of the American oaks (Quercus), a model clade for integrating ecology and evolution
Ecologists and evolutionary biologists are concerned with explaining the diversity and composition of the natural world and are aware of the inextricable linkages between ecological and evolutionary processes that maintain the Earth’s life support systems. Yet examination of these linkages remains challenging due to the contrasting nature of focal systems and research approaches. Model clades provide a critical means to integrate ecology and evolution, as illustrated by the oaks (genus Quercus), an important model clade, given their ecological dominance, remarkable diversity, and growing phylogenetic, genomic, and ecological data resources. Studies of the clade reveal that their history of sympatric parallel adaptive radiation continues to influence community assembly today, highlighting questions on the nature and extent of coexistence mechanisms. Flexible phenology and hydraulic traits, despite evolutionary stasis, may have enabled adaptation to a wide range of environments within and across species, contributing to their high abundance and diversity. The oaks offer fundamental insights at the intersection of ecology and evolution on the role of diversification in community assembly processes, on the importance of flexibility in key functional traits in adapting to new environments, on factors contributing to persistence of long-lived organisms, and on evolutionary legacies that influence ecosystem function.
Journal Article
The FRAME: an expanded framework for reporting adaptations and modifications to evidence-based interventions
Background
This paper describes the process and results of a refinement of a framework to characterize modifications to interventions. The original version did not fully capture several aspects of modification and adaptation that may be important to document and report. Additionally, the earlier framework did not include a way to differentiate cultural adaptation from adaptations made for other reasons. Reporting additional elements will allow for a more precise understanding of modifications, the process of modifying or adapting, and the relationship between different forms of modification and subsequent health and implementation outcomes.
Discussion
We employed a multifaceted approach to develop the updated FRAME involving coding documents identified through a literature review, rapid coding of qualitative interviews, and a refinement process informed by multiple stakeholders. The updated FRAME expands upon Stirman et al.’s original framework by adding components of modification to report: (1) when and how in the implementation process the modification was made, (2) whether the modification was planned/proactive (i.e., an adaptation) or unplanned/reactive, (3) who determined that the modification should be made, (4) what is modified, (5) at what level of delivery the modification is made, (6) type or nature of context or content-level modifications, (7) the extent to which the modification is fidelity-consistent, and (8) the reasons for the modification, including (a) the intent or goal of the modification (e.g., to reduce costs) and (b) contextual factors that influenced the decision. Methods of using the framework to assess modifications are outlined, along with their strengths and weaknesses, and considerations for research to validate these measurement strategies.
Conclusion
The updated FRAME includes consideration of when and how modifications occurred, whether it was planned or unplanned, relationship to fidelity, and reasons and goals for modification. This tool that can be used to support research on the timing, nature, goals and reasons for, and impact of modifications to evidence-based interventions.
Journal Article
The adaptive evolution of virulence: a review of theoretical predictions and empirical tests
Why is it that some parasites cause high levels of host damage (i.e. virulence) whereas others are relatively benign? There are now numerous reviews of virulence evolution in the literature but it is nevertheless still difficult to find a comprehensive treatment of the theory and data on the subject that is easily accessible to non-specialists. Here we attempt to do so by distilling the vast theoretical literature on the topic into a set of relatively few robust predictions. We then provide a comprehensive assessment of the available empirical literature that tests these predictions. Our results show that there have been some notable successes in integrating theory and data but also that theory and empiricism in this field do not ‘speak’ to each other very well. We offer a few suggestions for how the connection between the two might be improved.
Journal Article
Molecular mechanisms of adaptive evolution revealed by global selection for glyphosate resistance
The human-directed, global selection for glyphosate resistance in weeds has revealed a fascinating diversity of evolved resistance mechanisms, including herbicide sequestration in the vacuole, a rapid cell death response, nucleotide polymorphisms in the herbicide target (5-enolpyruvylshikimate-3-phosphate synthase, EPSPS) and increased gene copy number of EPSPS. For this latter mechanism, two distinct molecular genetic mechanisms have been observed, a tandem duplication mechanism and a large extrachromosomal circular DNA (eccDNA) that is tethered to the chromosomes and passed to gametes at meiosis. These divergent mechanisms have a range of consequences for the spread, fitness, and inheritance of resistance traits, and, particularly in the case of the eccDNA, demonstrate how evolved herbicide resistance can generate new insights into plant adaptation to contemporary environmental stress.
Journal Article
Lagging adaptation to warming climate in Arabidopsis thaliana
If climate change outpaces the rate of adaptive evolution within a site, populations previously well adapted to local conditions may decline or disappear, and banked seeds from those populations will be unsuitable for restoring them. However, if such adaptational lag has occurred, immigrants from historically warmer climates will outperform natives and may provide genetic potential for evolutionary rescue. We tested for lagging adaptation to warming climate using banked seeds of the annual weed Arabidopsis thaliana in common garden experiments in four sites across the species’ native European range: Valencia, Spain; Norwich, United Kingdom; Halle, Germany; and Oulu, Finland. Genotypes originating from geographic regions near the planting site had high relative fitness in each site, direct evidence for broad-scale geographic adaptation in this model species. However, genotypes originating in sites historically warmer than the planting site had higher average relative fitness than local genotypes in every site, especially at the northern range limit in Finland. This result suggests that local adaptive optima have shifted rapidly with recent warming across the species’ native range. Climatic optima also differed among seasonal germination cohorts within the Norwich site, suggesting that populations occurring where summer germination is common may have greater evolutionary potential to persist under future warming. If adaptational lag has occurred over just a few decades in banked seeds of an annual species, it may be an important consideration for managing longer-lived species, as well as for attempts to conserve threatened populations through ex situ preservation.
Journal Article
Rapid adaptive evolution in novel environments acts as an architect of population range expansion
Colonization and expansion into novel landscapes determine the distribution and abundance of species in our rapidly changing ecosystems worldwide. Colonization events are crucibles for rapid evolution, but it is not known whether evolutionary changes arise mainly after successful colonization has occurred, or if evolution plays an immediate role, governing the growth and expansion speed of colonizing populations. There is evidence that spatial evolutionary processes can speed range expansion within a few generations because dispersal tendencies may evolve upwards at range edges. Additionally, rapid adaptation to a novel environment can increase population growth rates, which also promotes spread. However, the role of adaptive evolution and the relative contributions of spatial evolution and adaptation to expansion are unclear. Using a model system, red flour beetles (Tribolium castaneum), we either allowed or constrained evolution of populations colonizing a novel environment and measured population growth and spread. At the end of the experiment we assessed the fitness and dispersal tendency of individuals originating either from the core or edge of evolving populations or from nonevolving populations in a common garden. Within six generations, evolving populations grew three times larger and spread 46% faster than populations in which evolution was constrained. Increased size and expansion speed were strongly driven by adaptation, whereas spatial evolutionary processes acting on edge subpopulations contributed less. This experimental evidence demonstrates that rapid evolution drives both population growth and expansion speed and is thus crucial to consider for managing biological invasions and successfully introducing or reintroducing species for management and conservation.
Journal Article
Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral
Can genetic adaptation in reef-building corals keep pace with the current rate of sea surface warming? Here we combine population genomics, biophysical modeling, and evolutionary simulations to predict future adaptation of the common coral Acropora millepora on the Great Barrier Reef (GBR). Genomics-derived migration rates were high (0.1-1% of immigrants per generation across half the latitudinal range of the GBR) and closely matched the biophysical model of larval dispersal. Both genetic and biophysical models indicated the prevalence of southward migration along the GBR that would facilitate the spread of heat-tolerant alleles to higher latitudes as the climate warms. We developed an individual-based metapopulation model of polygenic adaptation and parameterized it with population sizes and migration rates derived from the genomic analysis. We find that high migration rates do not disrupt local thermal adaptation, and that the resulting standing genetic variation should be sufficient to fuel rapid region-wide adaptation of A. millepora populations to gradual warming over the next 20-50 coral generations (100-250 years). Further adaptation based on novel mutations might also be possible, but this depends on the currently unknown genetic parameters underlying coral thermal tolerance and the rate of warming realized. Despite this capacity for adaptation, our model predicts that coral populations would become increasingly sensitive to random thermal fluctuations such as ENSO cycles or heat waves, which corresponds well with the recent increase in frequency of catastrophic coral bleaching events.
Journal Article
Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales)
• Investigating the interaction between environmental heterogeneity and local adaptation is critical for understanding the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood.
• We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as the genetic basis of local adaptation using RAD-seq and plastome data.
• We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome–environment association analyses identified 16 putatively adaptive loci related mainly to biotic and abiotic stress resistance.
• Our genome-wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing future conservation efforts.
Journal Article