SEARCH · PubMed Health

Results for “Models of evolution”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 577 records · Page 32Linked to original sources

PubMed2004

Know when to walk away: contingent movement and the evolution of cooperation.

Models of the evolution of cooperation suggest that an important characteristic of successful strategies is the ability to respond contingently to the social environment. A number of mechanisms by which this can be accomplished have been suggested, some of which require relatively complex information processing systems. This research explores relaxing the requirements on information processing while preserving the evolvability of a cooperative strategy. The agent-based computer simulations reported here show that 'Walk Away,' a behavioral rule of extremely limited complexity (move after partner defects), can outperform more complex strategies under a number of conditions. Previous simulations of exit strategies have not examined the effect of implicit and explicit movement costs, different error rates, or the simultaneous presence of TFT and PAVLOV. The simulations reported here establish that the Walk Away strategy resists invasion and can invade a population of defectors at a lower initial frequency than any other strategy. The Walk Away strategy was successful, despite its simplicity, because it exploited aspects of the physical and social environment.

Animals↗

PubMed2004

Microscale simulation of martensitic microstructure evolution.

A new model for the evolution of multivariant martensitic microstructure in single crystals and polycrystals is developed. In contrast with Landau-Ginzburg models, which are limited in practice to nanoscale specimens, this new scale-free model is valid for length scales greater than 100 nm and without an upper bound. It is based on a thermodynamic potential in the volume fractions of the martensitic variants that exhibits an instability resulting in microstructure formation. Simulated microstructures in elastic single crystals and polycrystals under uniaxial loading are in qualitative agreement with those observed experimentally.

Journal Article↗

PubMed1991

A model for development and evolution of complex morphological structures.

How 'complex' or composite morphological structures like the mammalian craniomandibular region arise during development and how they are altered during evolution are two major unresolved questions in biology. Herein, we have described a model for the development and evolution of complex morphological structures. The model assumes that natural selection acts upon an array of phenotypes generated by variation in a variety of underlying genetic and epigenetic controlling factors. Selection refines the integration of the various morphogenetic components during ontogeny in order to produce a functioning structure and to adapt the organisms to differing patterns of environmental heterogeneity. The model was applied to the development and evolution of the mammalian mandible (which is used as a paradigm of complex morphological structures). The embryology of the mandible was examined in detail in order to identify the fundamental developmental units which are necessary to assemble the final morphological structure. The model is quite general since equivalent units exist for the development of many other biological structures. This model could be applied to many other developing morphological structures as well as other groups of organisms. For example, it can be applied to cell parameters during Drosophila development (Atchley, 1987). The model as discussed in this paper assumes that morphological changes in the mandible result from evolutionary changes in its underlying developmental units. The developmental units relate to characteristics of cellular condensations which are produced from the differentiation of embryonic neural crest cells. The developmental units include: the number of stem cells in preskeletal condensations (n), the time of initiation of condensation formation (t), the fraction of cells that is mitotically active within a condensation (f), the rate of division of these cells (r), and their rate of cell death (d). These units and their derivative structures are discussed in terms of types of tissue differentiation (chondrogenesis, osteogenesis, primary/secondary osteogenesis, intramembranous/endochondral ossification) and growth properties of major morphological regions of the mandible. Variation in these five units provides the developmental basis for ontogenetic and phylogenetic modification of mandibular morphology. We have discussed how these developmental units are influenced by (a) the cell lineage from which they arise, (b) epithelial-mesenchymal (inductive tissue) interactions, (c) regulation of cell differentiation, and (d) extrinsic factors such as muscles, teeth and hormones. Evidence was provided that variation in mandibular morphology is heritable, subject to modification by natural selection, and that divergence among different genetic stocks has apparently occurred through changes in these developmental units and their derivative structures.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1975

On the evolution of the physiological model.

Most of us who have concerned ourselves with models can perceive outlines like those above to catalog the future evolution of the expository function of models. In the context of a single class of computerized mathematical models of respiratory physiology, we can observe at once the burgeoning interest among scientists, and the similarities between model activity and the general organization of scientific information for use. Although physiological models have become quite advanced in their subject control, there is relatively little coordinated activity in the mechanization of the purposes and philosophical potential of automata. The outlines, however, are visible. An assiduous pursuit of the notion of "explanation" by machine is a major evolutionary step next to occur. It appears to us that various diagrams similar to Figures 5 or 6 can be created and investigated in terms of their relation to the human mind and in terms of formalizing rules for traversing from one plane to the next. The evolution of models will require program-making programs which can decide when and how to aggregate for deductive inference, and how far to penetrate top-down for explanation. The rules for identifying "second order" effects must be established. The decision to ignore or use these rules will be crucial. These are the means whereby the systems are traversed from plane to plane. In a word, models need to synthesize the means to ignore, "forget," and gloss over; only then will we have useful tools for taking informed action in physiology, diagnosis in medicine, or the writing of "scholarly" reviews.

Computers↗

PubMed2001

Ordering dynamics of the driven lattice-gas model.

The evolution of a two-dimensional driven lattice-gas model is studied on an LxxL(y) lattice. Scaling arguments and extensive numerical simulations are used to show that starting from random initial configuration the model evolves via two stages: (a) an early stage in which alternating stripes of particles and vacancies are formed along the direction y of the driving field, and (b) a stripe coarsening stage, in which the number of stripes is reduced and their average width increases. The number of stripes formed at the end of the first stage is shown to be a function of L(x)/L(straight phi)(y), with straight phi approximately 0.2. Thus, depending on this parameter, the resulting state could be either single or multistriped. In the second, stripe coarsening stage, the coarsening time is found to be proportional to L(y), becoming infinitely long in the thermodynamic limit. This implies that the multistriped state is thermodynamically stable. The results put previous studies of the model in a more general framework.

Journal Article↗

PubMed1996

New statistical tests of neutrality for DNA samples from a population.

The purpose of this paper is to develop statistical tests of the neutral model of evolution against a class of alternative models with the common characteristic of having an excess of mutations that occurred a long time ago or a reduction of recent mutations compared to the neutral model. This class of population genetics models include models for structured populations, models with decreasing effective population size and models of selection and mutation balance. Four statistical tests were proposed in this paper for DNA samples from a population. Two of these tests, one new and another a modification of an existing test, are based on EWENS' sampling formula, and the other two new tests make use of the frequencies of mutations of various classes. Using simulated samples and regression analyses, the critical values of these tests can be computed from regression equations. This approach for computing the critical values of a test was found to be appropriate and quite effective. We examined the powers of these four tests using simulated samples from structured populations, populations with linearly decreasing sizes and models of selection and mutation balance and found that they are more powerful than existing statistical tests of the neutral model of evolution.

Biological Evolution↗

PubMed1983

A laboratory model for interstellar chemical evolution.

The chemistry in a supersonic plasma source flow was studied as a laboratory model for interstellar chemical evolution. It is important to match the similarity parameters for cosmic and laboratory conditions, which connect the temporal and spatial scales of the two cases. The apparatus simulated the conditions in a molecular cloud with respect to molecular-ionic reaction fraction, temperature, and non-equilibrium kinetics. The plasma flow was found to be cold enough, by the radical expansion, to produce polyatomic molecules. From the simple atomic plasma as reactant, cyanopolyyne and unsaturated hydrocarbons were synthesized in the present experiment. These molecules are also inherent in molecular clouds. The reaction mechanism is discussed.

Computer Simulation↗

PubMed1988

The use of Markov chain models in studying the evolution of the proteins.

In a recent paper Giulio & Caldararo (1987) used a Markov chain model to study the evolution of proteins. Unfortunately, their use of a first-order Markov chain model at the amino acid level is incorrect. The model has to be applied at the codon level [Jorre & Curnow (1975a)] followed by amalgamation of the codon states corresponding to each amino acid and of the three codons specifying termination. The model is correctly applied in this paper. The results obtained do not differ substantially from those obtained by Giulio & Caldararo (1987). The interpretation of the results as supporting the neutralist view of protein evolution is criticized.

Amino Acids↗

PubMed2004

Modeling of elastic modulus evolution of cirrhotic human liver.

A micromechanics-based composite model is developed for the elastic behavior and its modulus evolution of cirrhotic human liver correlated with different pathological stages. Microstructurally, the cirrhotic liver is hypothesized to be pathologically elastic nodules embedded in the soft tissue matrix whose hyperelastic behavior is controlled by the Veronda-Westmann model. Under finite deformation, the total strain energy of the liver is collected through the combination of that in nodule particles and that in the tissue matrix. The overall constitutive relation of the pathological liver can further be established through the nonlinear hyperelasticity theory. Predictions of the elastic modulus and its pathological evolution are compared with available experimental data.

Computer Simulation↗

PubMed2004

Immunity promotes virulence evolution in a malaria model.

Evolutionary models predict that host immunity will shape the evolution of parasite virulence. While some assumptions of these models have been tested, the actual evolutionary outcome of immune selection on virulence has not. Using the mouse malaria model, Plasmodium chabaudi, we experimentally tested whether immune pressure promotes the evolution of more virulent pathogens by evolving parasite lines in immunized and nonimmunized ("naïve") mice using serial passage. We found that parasite lines evolved in immunized mice became more virulent to both naïve and immune mice than lines evolved in naïve mice. When these evolved lines were transmitted through mosquitoes, there was a general reduction in virulence across all lines. However, the immune-selected lines remained more virulent to naïve mice than the naïve-selected lines, though not to immunized mice. Thus, immune selection accelerated the rate of virulence evolution, rendering parasites more dangerous to naïve hosts. These results argue for further consideration of the evolutionary consequences for pathogen virulence of vaccination.

Animals↗

PubMed1986

Natural selection and the molecular clock.

This paper concludes that the statistical properties of protein evolution are compatible with a particular model of evolution by natural selection. The argument begins with a statistical description of the molecular clock based on a Poisson process with a randomly varying tick rate. If the time scale of the change of the tick rate of the molecular clock is assumed to be much less than the average time between substitutions, then it is shown that the substitution process must be episodic, with bursts of substitutions being separated by long periods of time with no substitutions. This analysis generalizes the recent work of Gillespie (1984a). The second part of the argument shows that a simple model of evolution by natural selection--one that incorporates a changing environment, the molecular landscape, and a simple form of epistasis--exhibits dynamics that are identical to those inferred from the statistical analysis. This leads to the conclusion that natural selection is a viable explanation for protein evolution. In addition, a correction formula for multiple substitutions is given that does not require that the substitution process be a Poisson process, and some comments on the inability of the neutral allele theory to account for the dynamics of the substitution process are presented.

Animals↗

PubMed2005

Multistep skin cancer in mice as a model to study the evolution of cancer cells.

Although much of cancer research relies on Nowell's clonal evolution hypothesis as a conceptual framework, large gaps remain in understanding how tumors develop. The multistage skin cancer model in mice provides continuing insight on fundamental aspects of tumor evolution. In this model, mutation of the oncogene Hras is frequently the initiating event while mutation of the tumor suppressor p53 is a late event, associated with malignant progression. Recent evidence demonstrates that intracellular signaling from the initial Hras mutation leads directly to the activation of p53, creating selective pressure in favor of cells with mutant p53. Thus, selection for subsequent mutations is mechanistically linked to the initial mutation, explaining the preferred order of mutational events observed. Analysis of this model also reveals that a diverse array of signals can selectively impair or enhance clonal expansion of Ras mutant cells into a visible neoplasm. These modifiers can be genetic, physiological, or environmental and are often highly specific to tumor cells. This indicates that tumor cells have an inherent reduced capacity to buffer against perturbations. Reduced buffering may play an important role in both tumor evolution and therapy response and may be a hallmark of cancer cells.

Animals↗

PubMed2004

Nutrient enrichment and food chains: can evolution buffer top-down control?

We show how evolutionary dynamics can alter the predictions of classical models of the effects of nutrient enrichment on food webs. We compare an ecological nutrient-plant-herbivore food-chain model without evolution with the same model, including herbivore evolution, plant evolution, or both. When only herbivores are allowed to evolve, the predictions are similar to those of the ecological model without evolution, i.e., plant biomass does not change with nutrient addition. When only plants evolve, nutrient enrichment leads to an increase in the biomass of all compartments. In contrast, when plants and herbivores are allowed to coevolve, although these two classical patterns are common, a wide variety of other responses is possible. The form of the trade-offs that constrain evolution of the two protagonists is then critical. This stresses the need for experimental data on phenotypic traits, their costs and their influence on the interactions between organisms and the rest of the community.

Adaptation, Biological↗

PubMed2005

Symbiosis versus competition in plant virus evolution.

Darwin's theory of evolution by natural selection has been supported by molecular evidence and by experimental evolution of viruses. However, it might not account for the evolution of all life, and an alternative model of evolution through symbiotic relationships also has gained support. In this review, the evolution of plant viruses has been reinterpreted in light of these two seemingly opposing theories by using evidence from the earliest days of plant virology to the present. Both models of evolution probably apply in different circumstances, but evolution by symbiotic association (symbiogenesis) is the most likely model for many evolutionary events that have resulted in rapid changes or the formation of new species. In viruses, symbiogenesis results in genomic reassortment or recombination events among disparate species. These are most noticeable by phylogenetic comparisons of extant viruses from different taxonomic groups.

Evolution, Molecular↗

PubMed2006

A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution.

Variations of nucleotidic composition affect phylogenetic inference conducted under stationary models of evolution. In particular, they may cause unrelated taxa sharing similar base composition to be grouped together in the resulting phylogeny. To address this problem, we developed a nonstationary and nonhomogeneous model accounting for compositional biases. Unlike previous nonstationary models, which are branchwise, that is, assume that base composition only changes at the nodes of the tree, in our model, the process of compositional drift is totally uncoupled from the speciation events. In addition, the total number of events of compositional drift distributed across the tree is directly inferred from the data. We implemented the method in a Bayesian framework, relying on Markov Chain Monte Carlo algorithms, and applied it to several nucleotidic data sets. In most cases, the stationarity assumption was rejected in favor of our nonstationary model. In addition, we show that our method is able to resolve a well-known artifact. By Bayes factor evaluation, we compared our model with 2 previously developed nonstationary models. We show that the coupling between speciations and compositional shifts inherent to branchwise models may lead to an overparameterization, resulting in a lesser fit. In some cases, this leads to incorrect conclusions, concerning the nature of the compositional biases. In contrast, our compound model more flexibly adapts its effective number of parameters to the data sets under investigation. Altogether, our results show that accounting for nonstationary sequence evolution may require more elaborate and more flexible models than those currently used.

Animals↗

PubMed2000

The evolution of duplicated genes considering protein stability constraints.

We model the evolution of duplicated genes by assuming that the gene's protein message, if transcribed and translated, must form a stable, folded structure. We observe the change in protein structure over time in an evolving population of lattice model proteins. We find that selection of stable proteins conserves the original structure if the structure is highly designable, that is, if a large fraction of all foldable sequences form that structure. This effect implies the relative number of pseudogenes can be less than previously predicted with neutral evolution models. The data also suggests a reason for lower than expected ratios of non-synonymous to synonymous substitutions in pseudogenes.

Computer Simulation↗

PubMed2001

Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1).

The blind use of models of nucleotide substitution in evolutionary analyses is a common practice in the viral community. Typically, a simple model of evolution like the Kimura two-parameter model is used for estimating genetic distances and phylogenies, either because other authors have used it or because it is the default in various phylogenetic packages. Using two statistical approaches to model fitting, hierarchical likelihood ratio tests and the Akaike information criterion, we show that different viral data sets are better explained by different models of evolution. We demonstrate our results with the analysis of HIV-1 sequences from a hierarchy of samples; sequences within individuals, individuals within subtypes, and subtypes within groups. We also examine results for three different gene regions: gag, pol, and env. The Kimura two-parameter model was not selected as the best-fit model for any of these data sets, despite its widespread use in phylogenetic analyses of HIV-1 sequences. Furthermore, the model complexity increased with increasing sequence divergence. Finally, the molecular-clock hypothesis was rejected in most of the data sets analyzed, throwing into question clock-based estimates of divergence times for HIV-1. The importance of models in evolutionary analyses and their repercussions on the derived conclusions are discussed.

Databases, Factual↗

PubMed2003

Biphasic constitutive laws for biological interface evolution.

A model of tissue differentiation at the bone-implant interface is proposed. The basic hypothesis of the model is that the mechanical environment determines the tissue differentiation. The stimulus chosen is related to the bone-implant micromotions. Equations governing the evolution of the interfacial tissue are proposed and combined with a finite element code to determine the evolution of the fibrous tissue around prostheses. The model is applied to the case of an idealized hip prosthesis.

Algorithms↗