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The interaction among evolutionary forces in the pathogenic fungus Mycosphaerella graminicola.

The population genetic dynamic of a species is driven by interactions among mutation, migration, drift, mating system, and selection, but it is rare to have sufficient empirical data to estimate values for all of these forces and to allow comparison of the relative magnitudes of these evolutionary forces. We combined data from a mark-release-recapture experiment, extensive population surveys, and computer simulations to evaluate interactions among these evolutionary forces in the pathogenic fungus Mycosphaerella graminicola. The results from these studies showed that, on average, the immigration rate was 0.027, the fraction of outcrossing individuals was 0.035, and the selection coefficient associated with immigrants was 0.106 each generation. We also estimated that effective population sizes for this fungus were larger than 24,000 and the mutation rate for the RFLP markers used in surveys and field experiments was approximately 4 x 10(-5). Computer simulations based on these estimates indicate that, on average, the global population of M. graminicola has reached equilibrium. Population genetic parameters including number of alleles, gene diversity, and population subdivision estimated from the computer simulations were surprisingly close to empirical estimates. Simulations also revealed that random drift is the major evolutionary force decreasing genetic variation in this fungus, followed by natural selection. The major force adding to genetic variation was mutation, followed by gene flow and sexual recombination. Gene flow played the leading role in decreasing population subdivision while natural selection was the major factor increasing population subdivision.

Ascomycota↗

Dynamics of a quantitative character subject only to stabilising selection.

The implications of stabilising selection on a quantitative trait, in the absence of other evolutionary forces, are theoretically investigated in a randomly mating population. The dynamics of various statistics that describe the alleles contributing to the trait are determined and used to infer the behaviour of the trait. Dynamical solutions of the distribution of allelic effects and the distribution of the trait are found when all initial distributions of allelic effects are Gaussian and linkage disequilibria are neglected. Some results for the behaviour of the mean and the variance of genotypic effects of the population, when subject to a moving optimum, are derived. When the initial distributions of allelic effects are not Gaussian, but possess a small asymmetry, the mean and the variance of the allelic effects differ only slightly from the Gaussian results. By contrast, the third central moments of allelic effects, are, at all loci, strictly zero in the Gaussian case but are generally non-zero for non-symmetric initial distributions. To leading order in a quantitative measure of the asymmetry of the distribution, we determine the third central moment of allelic effects.

Alleles↗

Precision Engineering of Evolution-Resilient Rice against Bacterial Blight.

The persistent conflict between rice and Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight, exemplifies a dynamic genetic arms race in agriculture. The cyclical deployment and erosion of major resistance (R) genes highlight the high adaptive potential of Xoo and the need for strategies that are durable rather than absolute. This review synthesizes a paradigm shift from reactive, single R-gene deployment toward proactive engineering of evolution-resilient resistance. We explore the molecular-genetic basis of Xoo adaptability, including TAL effector diversification, non-TAL virulence functions, genome variation, and immune suppression mechanisms. In response, we propose a framework for durable disease management with three connected components: precision disarmament through editing of susceptibility-gene effector-binding elements and executor/decoy designs; smart induction through targeted delivery and immune priming; and ecological fortification through protective microbiomes. We also discuss the limits, trade-offs, and field-validation requirements of these approaches. Integrating frontier technologies with evolutionary genetics, predictive genomics, and pathogen population dynamics can help develop rice varieties and deployment systems that are more difficult for Xoo populations to overcome.

CRISPR↗

The effect of climatic forcing on population synchrony and genetic structuring of the Canadian lynx.

The abundance of Canadian lynx follows 10-year density fluctuations across the Canadian subcontinent. These cyclic fluctuations have earlier been shown to be geographically structured into three climatic regions: the Atlantic, Continental, and Pacific zones. Recent genetic evidence revealed an essentially similar spatial structuring. Introducing a new population model, the "climate forcing of ecological and evolutionary patterns" model, we link the observed ecological and evolutionary patterns. Specifically, we demonstrate that there is greater phase synchrony within climatic zones than between them and show that external climatic forcing may act as a synchronizer. We simulated genetic drift by using data on population dynamics generated by the climate forcing of ecological and evolutionary patterns model, and we demonstrate that the observed genetic structuring can be seen as an emerging property of the spatiotemporal ecological dynamics.

Animals↗

Integrating multiscale mathematical modeling and multidimensional data reveals the effects of epigenetic instability on acquired drug resistance in cancer.

Biological and dynamic mechanisms by which Drug-tolerant persister (DTP) cells contribute to the development of acquired drug resistance have not been fully elucidated. Here, by integrating multidimensional data from drug-treated PC9 cells, we developed a novel multiscale mathematical model from an evolutionary perspective that encompasses epigenetic and cellular population dynamics. By coupling stochastic simulation with quantitative analysis, we identified epigenetic instability as the most prominent kinetic feature related to the emergence of DTP cell subpopulations and the effectiveness of intermittent treatment. Moreover, we revealed the optimal schedule for intermittent treatment, including the optimal area for therapeutic time and drug holidays. By leveraging single-cell RNA-seq data characterizing the drug tolerance of lung cancer, we validated the predictions made by our model and further revealed previously unrecognized biological features of DTP cells, such as cell autophagy and migration, as well as new biomarker genes of therapeutic tolerance. Our work not only provides a paradigm for the integration of multiscale mathematical models with newly emerging genomics data but also improves our understanding of the crucial roles of DTP cells and offers guidance for developing new intermittent treatment strategies against acquired drug resistance in cancer.

Drug Resistance, Neoplasm↗

Comparative genomics of the monophasic variant of Salmonella Typhimurium: analysis of Colombian genomes and their relationship with international lineages.

The monophasic variant of Salmonella enterica serovar Typhimurium (STVM) represents a growing threat to global public health owing to its wide dissemination, capacity to adapt to multiple hosts, and antimicrobial resistance. In this study, 98 STVM isolates recovered in Colombia (57 from humans and 41 from pig farms and abattoirs) were genomically characterized between 2015 and 2022 and compared with 102 representative genomes of international lineages by whole-genome sequencing (WGS) and phylogenomic analysis. Phylogenomic analysis revealed the existence of two well-defined endemic lineages in Colombia (Clusters 1 and 2), arising from independent introduction events and subsequent local stabilization. Both lineages comprise isolates of human and swine origin without clear phylogenetic separation by host species, suggesting active zoonotic cocirculation and closely integrated interspecies transmission dynamics. Marked differences were observed in the accessory genome, including the differential presence of prophages (e.g., Gifsy-2, Fels-2, SW9), virulence plasmids, and resistance profiles. The Colombian lineages exhibited a high frequency of the pSTV plasmid (85%, n = 84/98) and a substantial burden of resistance determinants to quinolones (such as qnrB19, 74.5%; gyrA S83F mutation, 19.4%), phenicols (floR), tetracyclines (tetA, tetB), β-lactams (blaTEM-1B), and heavy metals. In contrast, the Colombian genomes clustered with the European ST34 lineage lacked pSTV but retained resistance and heavy metal operons. These findings demonstrate that international and endemic lineages coexist in Colombia with independent evolutionary trajectories, underscoring the need to strengthen genomic surveillance under the "One Health" approach to anticipate emerging threats and develop integrated control strategies.IMPORTANCEThe monophasic variant of Salmonella Typhimurium (STVM) has emerged as a predominant serovar in both humans and swine internationally. In Colombia, a fundamental question driving this study was whether local isolates belonged to international lineages or represented endemic strains. This study provides the first comprehensive genomic characterization demonstrating that two Colombian endemic lineages circulate simultaneously between humans and pigs without phylogenetic separation by host species, confirming active zoonotic transmission. The results demonstrate the coexistence of both lineages, each with distinctive repertoires of mobile genetic elements and specific antimicrobial resistance profiles. Understanding these transmission dynamics and evolutionary patterns is crucial for public health, as it demonstrates how zoonotic pathogens can establish locally adapted lineages with distinct resistance patterns. The genomic evidence of sustained interspecies circulation highlights the critical need for integrated surveillance strategies under the "One Health" framework. This will enable anticipating emerging threats, tracing transmission routes, and developing targeted interventions in food production systems.

One Health↗

The effect of phenotypic plasticity on evolution in multipeaked fitness landscapes.

When facing the challenge of developing an individual that best fits its environment, nature demonstrates an interesting combination of two fundamentally different adaptive mechanisms: genetic evolution and phenotypic plasticity. Following numerous computational models, it has become the accepted wisdom that lifetime acclimation (e.g. via learning) smooths the fitness landscape and consequently accelerates evolution. However, analytical studies, focusing on the effect of phenotypic plasticity on evolution in simple unimodal landscapes, have often found that learning hinders the evolutionary process rather than accelerating it. Here, we provide a general framework for studying the effect of plasticity on evolution in multipeaked landscapes and introduce a rigorous mathematical analysis of these dynamics. We show that the convergence rate of the evolutionary process in a given arbitrary one-dimensional fitness landscape is dominated by the largest descent (drawdown) in the landscape and provide numerical evidence to support an analogous dominance also in multidimensional landscapes. We consider several schemes of phenotypic plasticity and examine their effect on the landscape drawdown, identifying the conditions under which phenotypic plasticity is advantageous. The lack of such a drawdown in unimodal landscapes vs. its dominance in multipeaked landscapes accounts for the seemingly contradictory findings of previous studies.

Adaptation, Biological↗

The evolution of the calpain family as reflected in paralogous chromosome regions.

Calpains, the Ca(2+)-dependent intracellular proteinases, are involved in the regulation of distinct cellular pathways including signal transduction and processing, cytoskeleton dynamics, and muscle homeostasis. To investigate the evolutionary origin of diverse calpain subfamilies, a phylogenetic study was carried out. The topology of the calpain phylogenetic tree has shown that some of the gene duplications occurred before the divergence of the protostome and deuterostome lineages. Other gene doublings, leading to vertebrate-specific calpain forms, took place during early chordate evolution and coincided with genome duplications as disclosed by the localization of calpain genes to paralogous chromosome regions in the human genome. On the basis of the phylogenetic tree, the time of gene duplications, and the localization of calpain genes, we propose a model of tandem and chromosome duplications for the evolution of vertebrate-specific calpain forms. The data presented here are consistent with scenarios proposed for the evolution of other multigene families.

Amino Acid Sequence↗

Escape and survival: transposon adaptations in the face of insect host silencing.

Transposable elements (TEs) are mobile genetic sequences that have long resided within host genomes. Over this shared history, a continuous process of co-evolution has forged a diverse array of dynamic TE-host interactions. In an evolutionary arms race, hosts must silence TEs to protect genome integrity from deleterious mutations by TE insertions, while TEs must evade this silencing to survive. TE adaptations to host genomes have recently gained prominence, following many discoveries in eukaryotic genomes. Here, I discuss TE strategies to evade host silencing and ensure their long-term persistence within host genomes, focusing on insects as the primary model system. Furthermore, by describing host silencing, I postulate potential evasive mechanisms that may drive TE adaptation within host genomes.

Journal Article↗

Equilibrium selection in evolutionary games with random matching of players.

We discuss stochastic dynamics of populations of individuals playing games. Our models possess two evolutionarily stable strategies: an efficient one, where a population is in a state with the maximal payoff (fitness) and a risk-dominant one, where players are averse to risks. We assume that individuals play with randomly chosen opponents (they do not play against average strategies as in the standard replicator dynamics). We show that the long-run behavior of a population depends on its size and the mutation level.

Animals↗

What can we learn about ecology and evolution from the fossil record?

The increased application of abundance data embedded within a more detailed and precise environmental context is enabling paleontologists to explore more rigorously the dynamics and underlying processes of ecological and evolutionary change in deep time. Several recent findings are of special theoretical interest. Community membership is commonly more stable and persistent than expected by chance, even in the face of the extreme environmental changes of the Ice Ages, and major evolutionary novelties commonly lie dormant for tens of millions of years before the ecological explosions of the clades that possess them. As we discuss here, questions such as these cannot be adequately addressed without the use of the fossil record.

Animals↗

Integration of ethnobotany and phytochemistry. dream or reality?

The major challenge of this paper comprises an attempt to compare the wealth of folk-information based on "traditional knowledge" with the efficacy of a chemo-biological background based on scientific knowledge. Surprisingly, correlations between plant uses (as food and medicine) and evolutionary status according to morphology (as assigned by Sporne indices) and metabolism (as assigned by diversity of phytochemicals) obey strikingly uniform systematic and evolutionary trends. The resulting patterns suggest a dynamic chemical mechanism for the bioactivity in plants regulated by the antagonistic gallate/caffeate pair. This finding is an important step toward the construction of a coherent chemo-biological language by a dynamic holistic quantitative methodology, one of the most potent prospects for understanding the functioning of nature.

Biological Evolution↗

The challenge of emerging and re-emerging infectious diseases.

Infectious diseases have for centuries ranked with wars and famine as major challenges to human progress and survival. They remain among the leading causes of death and disability worldwide. Against a constant background of established infections, epidemics of new and old infectious diseases periodically emerge, greatly magnifying the global burden of infections. Studies of these emerging infections reveal the evolutionary properties of pathogenic microorganisms and the dynamic relationships between microorganisms, their hosts and the environment.

Animals↗

Sexual selection affects local extinction and turnover in bird communities.

Predicting extinction risks has become a central goal for conservation and evolutionary biologists interested in population and community dynamics. Several factors have been put forward to explain risks of extinction, including ecological and life history characteristics of individuals. For instance, factors that affect the balance between natality and mortality can have profound effects on population persistence. Sexual selection has been identified as one such factor. Populations under strong sexual selection experience a number of costs ranging from increased predation and parasitism to enhanced sensitivity to environmental and demographic stochasticity. These findings have led to the prediction that local extinction rates should be higher for speciespopulations with intense sexual selection. We tested this prediction by analyzing the dynamics of natural bird communities at a continental scale over a period of 21 years (1975-1996), using relevant statistical tools. In agreement with the theoretical prediction, we found that sexual selection increased risks of local extinction (dichromatic birds had on average a 23% higher local extinction rate than monochromatic species). However, despite higher local extinction probabilities, the number of dichromatic species did not decrease over the period considered in this study. This pattern was caused by higher local turnover rates of dichromatic species, resulting in relatively stable communities for both groups of species. Our results suggest that these communities function as metacommunities, with frequent local extinctions followed by colonization. Anthropogenic factors impeding dispersal might therefore have a significant impact on the global persistence of sexually selected species.

Animals↗

Social dynamics and the quantifying of social forces.

SOCIAL AND INDUSTRIAL EVOLUTIONARY PROCESSES ARE CONSIDERED TO BE A SEQUENCE OF REPLACEMENTS OR SUBSTITUTIONS: new ideas for old, new labor patterns for old, new technologies for old. The logistic equation has often been used to describe population growth processes and replacement processes. It sometimes suffers from contradicting observational data. It is shown here that the deviations are often associated with unusual intermittent events-wars, strikes, economic panics, etc.-and that in many cases a few years after the event it can be abstracted as an instantaneous delta function impulse. After the event, the evolutionary process continues along its normal course. A formula is derived to use the observational data to determine the strength of the impulse modeling an event.

Journal Article↗

Thermodynamics constrains the evolution of insect population growth rates: "warmer is better".

Diverse biochemical and physiological adaptations enable different species of ectotherms to survive and reproduce in very different temperature regimes, but whether these adaptations fully compensate for the thermodynamically depressing effects of low temperature on rates of biological processes is debated. If such adaptations are fully compensatory, then temperature-dependent processes (e.g., digestion rate, population growth rate) of cold-adapted species will match those of warm-adapted species when each is measured at its own optimal temperature. Here we show that cold-adapted insect species have much lower maximum rates of population growth than do warm-adapted species, even when we control for phylogenetic relatedness. This pattern also holds when we use a structural-equation model to analyze alternative hypotheses that might otherwise explain this correlation. Thus, although physiological adaptations enable some insects to survive and reproduce at low temperatures, these adaptations do not overcome the "tyranny" of thermodynamics, at least for rates of population increase. Indeed, the sensitivity of population growth rates of insects to temperature is even greater than predicted by a recent thermodynamic model. Our findings suggest that adaptation to temperature inevitably alters the population dynamics of insects. This result has broad evolutionary and ecological consequences.

Adaptation, Physiological↗

Repetitive conundrums of centromere structure and function.

In the last few years, a paradox has emerged regarding the relationship of centromere structure and its function. Most centromeric DNAs analyzed to date are composed of a remarkably complex array of repeat structures. In contrast, recent analyses of neocentromeric DNA reveal that repetitive DNA is not a prerequisite for centromere activity. The ubiquity of repetitive sequences among diverse species at sites of primary constriction argues that there is a strong evolutionary link between centromere structure and function. Dynamic mutational processes resulting in amplification, deletion and transposition of repetitive sequences appear to occur frequently in such regions, resulting in considerable interspecific diversity in structure and sequence. One possible solution to this conundrum may be that the rapid accumulation of repetitive sequences within centromeric and pericentromeric DNA is a consequence of functionally active centromeres. Emerging repetitive structures at centromeric sites may be an important byproduct of a functional centromere which ensures that site as an evolutionarily favored position in subsequent meiotic and mitotic lineages. The recent identification of large gene duplications in the vicinity of centromeres may be another example of the enhanced mutational lability of such regions of the genome.

Centromere↗

Sex linkage of minisatellite bands in bobcats (Felis rufus).

Minisatellite DNA profiles using the multilocus human probe 33.6 are presented for 27 captive bobcats (Felis rufus) of documented geographic and genetic origins. The results show that 30% of the finger-printing bands present in males are sex linked. The effect of sex on band sharing was attributed to the presence of male-specific hemizygotic bands belonging to a minisatellite cluster located in the nonrecombinant region of the Y chromosome. A combination of mechanisms might drive the dynamics of minisatellite loci and allow different evolutionary rates depending on the recombinational capability of the chromosomal locations involved. We discuss the utility of sex-linked fingerprinting bands as genetic markers for the study and management of bobcats.

Animals↗