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At least 721 records · Page 40Linked to original sources
PubMed2001

Reaction norms with bifurcations shaped by evolution.

Two versions of a model for the evolution of seasonal polyphenism investigate the evolution of reaction norm bifurcation and branching. The first version is without a specific submodel for morphological development and the second has an explicit developmental map. Version 1 is evolutionarily relatively unconstrained: (i) reaction norms are specified by matrices containing the probabilities of occurrence of environment-phenotype combinations, (ii) all conceivable reaction norm matrices are reachable through a sequence of mutations, and (iii) small as well as large mutational effects occur. This version is used to find the evolutionarily stable strategy favoured by the population ecology that is characterized by stabilizing viability selection with a cyclically fluctuating selection optimum. When the strength of selection is large and when the lag between initiation of development and selection on mature phenotype is not a multiple of half the period of the environmental cycle, a branching reaction norm evolves. In the second model version, branching reaction norms occur for certain parameter combinations of the developmental submodel, but the evolution of this pattern is often constrained. The evolutionary trajectory becomes trapped in a local selective optimum for the parameters of the developmental system. Substantial developmental noise evolves, but mutations that produce a selectively advantageous branching pattern do not occur from there.

Animals↗
PubMed1985

Quantitative models of hybrid dysgenesis: rapid evolution under transposition, extrachromosomal inheritance, and fertility selection.

A model of the P-M system of hybrid dysgenesis is presented which incorporates single-site transposition of P factors in M cytotype, determination of offspring cytotype by both maternal cytotype and maternal or offspring nuclear genotype, and strong fertility selection in dysgenic individuals. The conditions required for the initial invasion of P factors into a pure M population, information concerning stable polymorphisms, and results of numerical iterations depicting the dynamic, nonequilibrium behavior of the system are summarized. While conditions for initial increase are independent of the rate of cytotype switching, the rate of evolution is accelerated by increased production of dysgenic individuals. If the transposition rate is sufficiently high to overcome the fertility barrier opposing P factors introduced into M populations, then convergence to high frequencies of the P factor occurs very rapidly. Under intense fertility depression, the phase of rapid increase may be preceded by an extended period of gradual increase at low frequencies.

Animals↗
PubMed2006

Drosophila flies in "Evolution Canyon" as a model for incipient sympatric speciation.

The genetic basis of population divergence leading to adaptive radiation and speciation is a major unresolved problem of evolutionary biology. Molecular elucidation of "speciation genes" advanced recently, yet it remains without clear identification of the gene complexes participating in reproductive isolation between natural populations, particularly, in sympatry. Genetic divergence was discovered between Drosophila melanogaster populations inhabiting ecologically contrasting, opposite slopes in "Evolution Canyon" (EC), Mt. Carmel, Israel. Interslope migration of flies is easy and verified. Nevertheless, significant interslope D. melanogaster population divergence was established at EC involving habitat choice, mate choice, thermal and drought tolerances, adaptive genes, and mobile elements. Parallel patterns of stress tolerance, habitat choice, and mate choice were demonstrated in Drosophila simulans at EC, although on a smaller scale. However, some tests for interslope genetic differentiation in Drosophila, derived from the opposite EC slopes, gave somewhat controversial results. Here we present new empirical data on interslope genetic divergence of Drosophila at EC, and summarize previous supporting and controversial results. We suggest that Drosophila populations at EC represent a rare example, demonstrating how selection overrides migration, and propose an ad hoc ecological model of incipient sympatric divergence.

Adaptation, Biological↗
PubMed2005

Virulence evolution in emerging infectious diseases.

Models of virulence evolution generally consider the outcome of competition between resident and mutant parasite strains at or near endemic equilibrium. Less studied is what happens during the initial phases of invasion and adaptation. Understanding initial adaptive dynamics is particularly important in the context of emerging diseases in wildlife and humans, for which rapid and accurate intervention may be of the essence. To address the question of virulence evolution in emerging diseases, we employ a simple stochastic modeling framework. As is intuitive, the pathogen strains most likely to emerge are those with the highest net reproductive rates (R0). We find, however, that stochastic events shape the properties of emerging pathogens in sometimes unexpected ways. First, the mean virulence of emerging pathogens is expected to be larger in dense host populations and/or when transmission is high, due to less restrictive conditions for the spread of the pathogen. Second, a positive correlation between average virulence and transmissibility emerges due to a combination of drift and selection. We conclude that at least in the initial phases of adaptation, special assumptions about constraints need not be invoked to explain some virulence-transmission correlations and that virulence management practices should consider how residual variation in transmission and virulence can be selected to reduce the prevalence and/or virulence of emerging infectious diseases.

Biological Evolution↗
PubMedDate not supplied

Parallelising a model of bacterial interaction and evolution.

Large simulations of bacterial colonies require huge amounts of computational time, the only way to achieve the necessary level of performance is with parallel computers and a suitably designed implementation that maps the problem onto the hardware. For real problems this mapping can be a non-trivial problem requiring careful consideration of the constraints in both the system being modelled and the hardware that executes that model. Here we describe an implementation of a system for modelling bacterial evolution that encompasses many physical scales. This system is composed entirely of individual entities all playing out a complex series of interactions. These individuals exist at the scale of the population of bacterial and at the gene product scale. This paper reports that it is possible to map a dynamic problem such as this onto fixed resources, for the most part making use of implicit multiplexing of resources provided by the OS and partitioning the problem to reduce communication time. Through this an efficient simulation can be created, making maximal use of the available hardware without constraining the model to require excessively specific resources.

Bacterial Physiological Phenomena↗
PubMed1999

Evolution of the rearfoot. A model of adaptation with evidence from the fossil record.

The evolution of the human foot presents an obfuscation: explanations for its occurrence and the exact nature of mechanisms of change are still not fully understood. This article outlines a model of adaptation from a primitive ape foot and presents this as a hypothesis. Evidence substantiating the hypothesis is then presented, which explains many of the large-scale features distinctive to the human foot. Further evidence is then presented that goes some way toward explaining the sequence of modification with first the lateral side becoming adapted for terrestrial function followed by the medial side. Paradoxically, this was hypothesized by Morton more than half a century ago in his "hypothetical prehuman foot," though it was not accepted favorably at the time.

Adaptation, Biological↗
PubMed1992

Phylogeny of some ascaridoid nematodes, inferred from comparison of 18S and 28S rRNA sequences.

Reverse transcription of cellular RNA was used to obtain sequences from regions of 18S and 26/28S ribosomal RNA for eight species of ascaridoid nematodes. Phylogenetic relationships among these species were inferred from the aligned sequences by maximum-parsimony and maximum-likelihood methods. Seventy-nine of the 168 sites that varied were phylogenetically informative in parsimony analysis. Phylogenetic inference based on maximum-likelihood analysis of all sequence sites yielded a tree of topology similar to that of the parsimony result. Monophyletic groups that were strongly supported by bootstrap resampling of these data included species constituting the Ascaridinae, as well as those representing the Toxocarinae. Alternative topologies that included a member of the Ascaridinae with the Toxocarinae were rejected statistically on the basis of analysis of the mean and variance of parsimony step differences between trees. The conformance of these sequence data to a molecular-clock model of evolution was evaluated statistically by a maximum-likelihood approach. The inferred rate of rRNA sequence change along the branch leading to Parascaris equorum is not consistent with a clocklike model of evolution.

Animals↗
PubMed2000

The possible role of reaction-diffusion in leaf shape.

We consider mechanisms that may determine certain simple leaf shapes. Compared with other aspects of plant morphogenesis, such as phyllotaxis or spiral leaf arrangement, rather little is known about leaf-shape-determining mechanisms. We develop mathematical models for the gross pattern of leaf shape based on reaction diffusion systems. These models are consistent with what is known about factors that might determine leaf shape. They show that diverse leaf shapes may be obtained from a single reaction diffusion system. This has implications in terms of both convergent and divergent evolution. The models make predictions that can be tested experimentally. We predict the form of pre-patterns of growth promoters in leaf primordia of different sizes when the morphogens either diffuse into the primordia or are produced locally. We also predict the effects on leaf shape of removing parts of primordia at different times. The models can also predict the effects on leaf shape of the topical application of activators and inhibitors to leaf primordia.

Biological Evolution↗
PubMed2005

A gamma mixture model better accounts for among site rate heterogeneity.

MOTIVATION: Variation of substitution rates across nucleotide and amino acid sites has long been recognized as a characteristic of molecular sequence evolution. Evolutionary models that account for this rate heterogeneity usually use a gamma density function to model the rate distribution across sites. This density function, however, may not fit real datasets, especially when there is a multimodal distribution of rates. Here, we present a novel evolutionary model based on a mixture of gamma density functions. This model better describes the among-site rate variation characteristic of molecular sequence evolution. The use of this model may improve the accuracy of various phylogenetic methods, such as reconstructing phylogenetic trees, dating divergence events, inferring ancestral sequences and detecting conserved sites in proteins. RESULTS: Using diverse sets of protein sequences we show that the gamma mixture model better describes the stochastic process underlying protein evolution. We show that the proposed gamma mixture model fits protein datasets significantly better than the single-gamma model in 9 out of 10 datasets tested. We further show that using the gamma mixture model improves the accuracy of model-based prediction of conserved residues in proteins. AVAILABILITY: C++ source codes are available from the authors upon request.

Chromosome Mapping↗
PubMed2026

Decoding glioblastoma evolution and heterogeneity through mechanistic modeling: implications for clinical translation.

Glioblastoma (GBM) is one of the most aggressive and lethal primary brain tumors in adults, characterized by dynamic clonal evolution and extensive genomic, cellular, spatial, and microenvironmental heterogeneity. Multi-omics studies have revealed that GBM follows complex evolutionary trajectories involving genetic, epigenetic, transcriptional, and immune-microenvironmental remodeling as tumors grow, adapt to the brain microenvironment, and acquire therapeutic resistance. Increasing evidence suggests that GBM may originate from aberrant neural stem or progenitor cells, including those residing in the subventricular zone, and that glioblastoma stem cells (GSCs) contribute to tumor propagation, heterogeneity, and recurrence. A key conceptual challenge is to reconcile hierarchical cancer stem cell models, in which GSCs are viewed as relatively stable tumor-propagating subpopulations, with dynamic state plasticity models, in which stem-like properties can be reversibly acquired or lost during transitions among proneural-like, mesenchymal-like, invasive, and therapy-tolerant states. Recent advances in single-cell profiling, spatial transcriptomics, lineage tracing, organoid culture, 3D bioprinting, genetically engineered models, and artificial intelligence (AI)-assisted computational modeling have substantially improved the ability to study these processes. However, no currently available model fully recapitulates human GBM heterogeneity, recurrence, treatment history, and tumor-microenvironment interactions. Therefore, model selection should be guided by clearly defined mechanistic questions rather than by reliance on any single platform. This review summarizes current advances in in vitro, ex vivo, in vivo, and computational models for studying GBM evolution and heterogeneity, and discusses how integrated model pipelines may improve preclinical drug testing, treatment-response prediction, and precision neuro-oncology.

Humans↗
PubMed2003

The analysis of asthma control under a Markov assumption with use of covariates.

In studies of disease states and their relation to evolution, data on the state are usually obtained at in frequent time points during follow-up. Moreover in many applications, there are measured covariates on each individual under study and interest centres on the relationship between these covariates and the disease evolution. We developed a continuous-time Markov model with use of time-dependent covariates and a Markov model with piecewise constant intensities to model asthma evolution. Methods to estimate the effect of covariates on transition intensities, to test the assumption of time homogeneity and to assess goodness-of-fit are proposed. We apply these methods to asthma control. We consider a three-state model and we discuss in detail the analysis of asthma control evolution.

Asthma↗
PubMed2003

Laboratory models of the thermal evolution of the mantle during rollback subduction.

The subduction of oceanic lithosphere plays a key role in plate tectonics, the thermal evolution of the mantle and recycling processes between Earth's interior and surface. Information on mantle flow, thermal conditions and chemical transport in subduction zones come from the geochemistry of arc volcanoes, seismic images and geodynamic models. The majority of this work considers subduction as a two-dimensional process, assuming limited variability in the direction parallel to the trench. In contrast, observationally based models increasingly appeal to three-dimensional flow associated with trench migration and the sinking of oceanic plates with a translational component of motion (rollback). Here we report results from laboratory experiments that reveal fundamental differences in three-dimensional mantle circulation and temperature structure in response to subduction with and without a rollback component. Without rollback motion, flow in the mantle wedge is sluggish, there is no mass flux around the plate and plate edges heat up faster than plate centres. In contrast, during rollback subduction flow is driven around and beneath the sinking plate, velocities increase within the mantle wedge and are focused towards the centre of the plate, and the surface of the plate heats more along the centreline.

Journal Article↗
PubMed2002

Mutation, specialization, and hypersensitivity in highly optimized tolerance.

We introduce a model of evolution in which competing organisms are represented by percolation lattice models. Fitness is based on the number of occupied sites remaining after removing a cluster connected to a randomly selected site. High-fitness individuals arising through mutation and selection must trade off density versus robustness to loss, and are characterized by cellular barrier patterns that prevent large cascading losses to common disturbances. This model shows that Highly Optimized Tolerance (HOT), which links complexity to robustness in designed systems, arises naturally through Darwinian mechanisms. Although the model is a severe abstraction of biology, it produces a surprisingly wide variety of micro- and macroevolutionary features strikingly similar to real biological evolution.

Biological Evolution↗
PubMed1994

Long-lived planetary vortices and their evolution: Conservative intermediate geostrophic model.

Large, long-lived vortices, surviving during many turnaround times and far longer than the dispersive linear Rossby wave packets, are abundant in planetary atmospheres and oceans. Nonlinear effects which prevent dispersive decay of intense cyclones and anticyclones and provide their self-propelling propagation are revised here using shallow water equations and their balanced approximations. The main physical mechanism allowing vortical structures to be long-lived in planetary fluid is the quick fluid rotation inside their cores which prevents growth in the amplitude of asymmetric circulation arising due to the beta-effect. Intense vortices of both signs survive essentially longer than the linear Rossby wave packet if their azimuthal velocity is much larger than the Rossby wave speed. However, in the long-time evolution, cyclonic and anticyclonic vortices behave essentially differently that is illustrated by the conservative intermediate geostrophic model. Asymmetric circulation governing vortex propagation is described by the azimuthal mode m=1 for the initial value problem as well as for steadily propagating solutions. Cyclonic vortices move west-poleward decaying gradually due to Rossby wave radiation while anticyclonic ones adjust to non-radiating solitary vortices. Slow weakening of an intense cyclone with decreasing of its size and shrinking of the core is described assuming zero azimuthal velocity outside the core while drifting poleward. The poleward tendency of the cyclone motion relative to the stirring flow corresponds to characteristic trajectories of tropical cyclones in the Earth's atmosphere. The asymmetry in dispersion-nonlinear properties of cyclones and anticyclones is thought to be one of the essential reasons for the observed predominance of anticyclones among long-lived vortices in the atmospheres of the giant planets and also among intrathermoclinic eddies in the ocean.

Journal Article↗
PubMed1985

Autocatalysis in cultural ecology: model ecosystems and the dynamics of biocultural evolution.

Using a well-known mathematical model frequently applied in theoretical population dynamics, certain ecological mechanisms are investigated that are inherent in the organic evolution of cultural capacities in man. Culture is argued to involve ecological interactions exhibiting analogies to the interaction of chemical species in autocatalytic biomolecular reactions. In the model, biocultural evolution proceeds by more and more broadening ecological niches and, thus, releasing competitive selection pressure on the populations involved. This, in turn, facilitates the maintenance of polymorphism in these populations as well as the individual acquisition of organic traits through learning and cultural transmission. The result is that the genetic variance in phenotypic expressions decreases at an accelerated rate.

Cultural Evolution↗
PubMed1988

Evolution of a steam atmosphere during Earth's accretion.

We have modeled the evolution of an impact-generated steam atmosphere surrounding an accreting Earth. The model assumes Safronov accretion; it includes degassing of planetesimals upon impact, thermal blanketing by a steam atmosphere, interchange of water between the surface and the interior, shock heating and convective cooling of Earth's interior, and hydrogen escape, both by a solar extreme ultraviolet (EUV) powered planetary wind and by impact erosion (atmospheric cratering). The model does not include atmophiles other than water, chemical reaction of water with metallic iron, core formation, compression, and spatial and temporal inhomogeneity of accretion. If the incoming planetesimals were too dry or the EUV flux too high, very little water would accumulate at the surface. Essentially all water retained by such a planet would be through rehydration of silicates. If rehydration were inefficient, very little water would be retained in any form. Degassing of wetter planetesimals produces a steam atmosphere over a magma ocean, the energy of accretion being sufficient to maintain a runaway greenhouse atmosphere. The mass of the atmosphere is limited by water's solubility in the (partial) melt. This type of solution is produced for a wide range of model parameters. During accretion, approximately 30 bars of water could have kept the surface at 1500 degrees K. As the accretional energy input declined below the runaway greenhouse threshold, the steam atmosphere rained out. Outgassing of dissolved water at the close of accretion is quantitatively important. These models can leave from approximately 100 to more than 300 bars of water at the surface at the close of accretion. In general, most of the water accreted remains dissolved in the mantle. H2 could have escaped as rapidly as it formed only if the planetesimals were relatively dry. Consequently H2 should have accumulated until it reached chemical equilibrium with water vapor. Impact erosion (escape caused by impact) is a critical but poorly understood process. It can prevent the accumulation of a steam atmosphere if the planetesimals are sufficiently dry, or for wetter impactors if it is much more effective than we have assumed. Impact erosion of a steam atmosphere is less important; it is equivalent to a slightly drier rain of impactors. If a hypothetical Moon-forming impact took place before the collapse of the runaway greenhouse, relatively little water (approximately 30-100 bars) would have been in the atmosphere; hence little could have been lost. If the event took place later, the potential damage could have been greater.

Atmosphere↗
PubMed1998

Assessing the impact of secondary structure and solvent accessibility on protein evolution.

Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution-both above and below the species level-will not be well understood until the physical constraints that affect protein evolution are identified and characterized.

Databases, Factual↗