Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “evolutionary dynamics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 793 records · Page 44Linked to original sources
PubMed1997

End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences.

MOTIVATION: Phylogenetic trees constructed from molecular sequences contain information about the evolutionary or population dynamical processes that created them. Here we describe a computer package (End-Epi) that uses graphical methods to allow researchers to make inferences about these processes from their data. Statistical analyses can be performed to test the consistency of the data with various competing hypotheses. AVAILABILITY: End-Epi can be obtained by WWW from http://evolve.zoo.ox.ac.uk/ and by anonymous FTP from ftp://evolve.zoo.ox.ac.uk/packages/End-Epi10.hqx. This file contains the compiled application, the manual and a test tree.

Algorithms↗
PubMed1995

Evolutionary cycling in predator-prey interactions: population dynamics and the red queen.

This paper describes the coevolution of phenotypes in a community comprising a population of predators and of prey. It is shown that evolutionary cycling is a likely outcome of the process. The dynamical systems on which this description is based are constructed from microscopic stochastic birth and death events, together with a process of random mutation. Births and deaths are caused in part by phenotype-dependent interactions between predator and prey individuals and therefore generate natural selection. Three outcomes of evolution are demonstrated. A community may evolve to a state at which the predator becomes extinct, or to one at which the species coexist with constant phenotypic values, or the species may coexist with cyclic changes in phenotypic values. The last outcome corresponds to a Red Queen dynamic, in which the selection pressures arising from the predator-prey interaction cause the species to evolve without ever reaching an equilibrium phenotypic state. The Red Queen dynamic requires an intermediate harvesting efficiency of the prey by the predator and sufficiently high evolutionary rate constant of the prey, and is robust when the model is made stochastic and phenotypically polymorphic. A cyclic outcome lies outside the contemporary focus on evolutionary equilibria, and argues for an extension to a dynamical framework for describing the asymptotic states of evolution.

Animals↗
PubMedDate not supplied

On the evolutionary coexistence of parasite strains.

Classical models of parasite competition show that coexistence is impossible if different strains give complete cross-immunity. However, parasite coexistence is possible if some of the model assumptions are changed. For instance, coexistence is impossible if density-dependence operates only in hosts' fertility, but surprisingly becomes possible if hosts' mortality is density-dependent. Parasite strains can also coexist if a host already infected with one strain may become infected by another strain (superinfection). I examine here if these reasons for coexistence carry over to evolutionary timescales: in other words, suppose that potentially a continuum of parasite strains may arise by mutations; will evolution arrive at a halt? in that case, will only one or several strains persist? The paradigm and methods of adaptive dynamics are used in this study. It is found, under reasonably general assumptions, that a unique evolutionarily stable state for virulence, alpha(*), exist for both models. However, the pattern of the invasibility plots depends on the shape of the trade-off (between virulence and transmissibility, or superinfection rates) functions, and on the host demography. In many cases, the state alpha(*) is evolutionarily stable only with respect to small mutations, not to larger ones; hence, evolutionary dynamics will bring virulence to alpha(*) only if mutations are sufficiently small; for larger mutations, evolutionary dynamics are more complex and still mainly unresolved.

Animals↗
PubMed2006

Evolutionary prisoner's dilemma game with dynamic preferential selection.

We study a modified prisoner's dilemma game taking place on two-dimensional disordered square lattices. The players are pure strategists and can either cooperate or defect with their immediate neighbors. In the generations each player updates its strategy by following one of the neighboring strategies with a probability dependent on the payoff difference. The neighbor selection obeys a dynamic preferential rule, i.e., the more frequently a neighbor's strategy was adopted by the focal player in the previous rounds, the larger probability it will be chosen to refer to in the subsequent rounds. It is found that cooperation is substantially promoted due to this simple selection mechanism. Corresponding analysis is provided by the investigation of the distribution of the players' impact weights, persistence, and correlation function.

Journal Article↗
PubMed2006

Stochasticity and evolutionary stability.

In stochastic dynamical systems, different concepts of stability can be obtained in different limits. A particularly interesting example is evolutionary game theory, which is traditionally based on infinite populations, where strict Nash equilibria correspond to stable fixed points that are always evolutionarily stable. However, in finite populations stochastic effects can drive the system away from strict Nash equilibria, which gives rise to a new concept for evolutionary stability. The conventional and the new stability concepts may apparently contradict each other leading to conflicting predictions in large yet finite populations. We show that the two concepts can be derived from the frequency dependent Moran process in different limits. Our results help to determine the appropriate stability concept in large finite populations. The general validity of our findings is demonstrated showing that the same results are valid employing vastly different co-evolutionary processes.

Biological Evolution↗
PubMed1995

Evolutionary predictions from invariant physical measures of dynamic processes.

The invariant physical measure of a dynamic process comprises the information necessary to compute statistical quantities of the system. It allows us to replace time averages over the system's trajectory by integrals over state-space. In particular, it allows us to compute the long-term growth rate of a fluctuating population and hence to make evolutionary predictions. This is explained here using a one-dimensional difference equation. The invariant physical measure reflects three types of selection in this model: K-selection when the resident has a stable equilibrium; r-selection when the resident exhibits complex dynamics; and c-selection, i.e. selection for lower complexity when the resident undergoes large fluctuations. For all three evolutionary scenarios the interaction of the physical measure with the higher moments of the distribution of offspring numbers is crucial. It is also shown how stochastic noise can affect the invariant physical measure and the evolutionary predictions made from it.

Animals↗
PubMed1999

Experimental evolution of Ebg enzyme provides clues about the evolution of catalysis and to evolutionary potential.

The ebg (evolved beta-galactosidase) operon of Escherichia coli has been used since 1974 as a model system to dynamically study the evolutionary processes which have led to catalytic efficiency and substrate specificity in enzymes. Wild-type ebg beta-galactosidase, encoded by ebgA, is a catalytically feeble enzyme that does not hydrolyze lactose or other beta-galactosidase efficiently enough to permit growth on those substrates. Each of two specific base substitutions at widely separated sites increases catalytic activity sufficiently to permit growth, and the combination of the two mutations further increases catalytic effectiveness and expands the substrate range of the enzyme in a non-additive fashion. Experimental studies suggested that in the 3126 bp coding region those two substitutions were the only mutations capable of increasing activity toward lactose sufficiently to permit growth. Alignment of EbgA with the LacZ beta-galactosidase showed that both mutations were in active site amino acids. Multiple alignment and phylogenetic analysis of EbgA, LacZ, and 12 other related beta-galactosidases showed that EbgA and LacZ diverged from a common ancestor at least 2.2 billion years ago, that they belonged to different subclasses of the family of 14 beta-galactosidases, that the two subclasses differed at 12 of the 15 active site residues, and confirmed that the two previously identified mutations in ebgA are the only ones that can lead to enzyme with sufficient activity on lactose to permit growth. Studies of the catalytic mechanism of Ebg beta-galactosidase have allowed the widely accepted Albery and Knowles model for the evolution of catalysis to be rejected.

Amino Acid Sequence↗
PubMed2005

Adaptive evolution of phytoplankton cell size.

We present a simple nutrient-phytoplankton-zooplankton (NPZ) model that incorporates adaptive evolution and allometric relations to examine the patterns and consequences of adaptive changes in plankton body size. Assuming stable environmental conditions, the model makes the following predictions. First, phytoplankton should evolve toward small sizes typical of picoplankton. Second, in the absence of grazers, nutrient concentration is minimized as phytoplankton reach their fitness maximum. Third, increasing nutrient flux tends to increase phytoplankton cell size in the presence of phytoplankton-zooplankton coevolution but has no effect in the absence of zooplankton. Fourth, phytoplankton reach their fitness maximum in the absence of grazers, and the evolutionary nutrient-phytoplankton system has a stable equilibrium. In contrast, phytoplankton may approach their fitness minimum in the evolutionary NPZ system where phytoplankton and zooplankton are allowed to coevolve, which may result in oscillatory (unstable) dynamics of the evolutionary NPZ system, compared with the otherwise stable nonevolutionary NPZ system. These results suggest that evolutionary interactions between phytoplankton and zooplankton may have contributed to observed changes in phytoplankton sizes and associated biogeochemical cycles over geological time scales.

Adaptation, Physiological↗
PubMed2005

When do mixotrophs specialize? Adaptive dynamics theory applied to a dynamic energy budget model.

In evolutionary history, several events have occurred at which mixotrophs specialized into pure autotrophs and heterotrophs. We studied the conditions under which such events take place, using the Dynamic Energy Budget (DEB) theory for physiological rules of the organisms' metabolism and Adaptive Dynamics (AD) theory for evolutionary behavior of parameter values. We modeled a population of mixotrophs that can take up dissolved inorganic nutrients by autotrophic assimilation and detritus by heterotrophic assimilation. The organisms have a certain affinity for both pathways; mutations that occur in the affinities enable the population to evolve. One of the possible evolutionary outcomes is a branching point which provides an opportunity for the mixotrophic population to split up and specialize into separate autotrophs and heterotrophs. Evolutionary branching is not a common feature of the studied system, but is found to occur only under specific conditions. These conditions depend on intrinsic properties such as the cost function, the level of the costs and the boundaries of the trait space: only at intermediate cost levels and when an explicit advantage exists to pure strategies over mixed ones may evolutionary branching occur. Usually, such an advantage (and hence evolutionary branching) can be induced by interference between the two affinities, but this result changes due to the constraints on the affinities. Now, only some of the more complicated cost functions give rise to a branching point. In contrast to the intrinsic properties, extrinsic properties such as the total nutrient content or light intensity were found to have no effect on the evolutionary outcomes at all.

Adaptation, Physiological↗
PubMed2004

Investigating the dynamic behavior of biochemical networks using model families.

MOTIVATION: Supporting the evolutionary modeling process of dynamic biochemical networks based on sampled in vivo data requires more than just simulation. In the course of the modeling process, the modeler is typically concerned not only with a single model but also with sequences, alternatives and structural variants of models. Powerful automatic methods are then required to assist the modeler in the organization and the evaluation of alternative models. Moreover, the structure and peculiarities of the data require dedicated tool support. SUMMARY: To support all stages of an evolutionary modeling process, a new general formalism for the combinatorial specification of large model families is introduced. It allows for automatic navigation in the space of models and excludes biologically meaningless models on the basis of elementary flux mode analysis. An incremental usage of the measured data is supported by using splined data instead of state variables. With MMT2, a versatile tool has been developed as a computational engine intended to be built into a tool chain. Using automatic code generation, automatic differentiation for sensitivity analysis and grid computing technology, a high performance computing environment is achieved. MMT2 supplies XML model specification and several software interfaces. The performance of MMT2 is illustrated by several examples from ongoing research projects. AVAILABILITY: http://www.simtec.mb.uni-siegen.de/ CONTACT: wiechert@simtec.mb.uni-siegen.de.

Algorithms↗
PubMed2005

The application of statistical physics to evolutionary biology.

A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations. The analogy with statistical physics also reveals that, contrary to a basic tenet of the nearly neutral theory of molecular evolution, the frequencies of adaptive and deleterious substitutions at steady state are equal. Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift.

Adaptation, Biological↗
PubMed2002

Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics.

Biotic recoveries following mass extinctions are characterized by a process in which whole ecologies are reconstructed from low-diversity systems, often characterized by opportunistic groups. The recovery process provides an unexpected window to ecosystem dynamics. In many aspects, recovery is very similar to ecological succession, but important differences are also apparently linked to the innovative patterns of niche construction observed in the fossil record. In this paper, we analyse the similarities and differences between ecological succession and evolutionary recovery to provide a preliminary ecological theory of recoveries. A simple evolutionary model with three trophic levels is presented, and its properties (closely resembling those observed in the fossil record) are compared with characteristic patterns of ecological response to disturbances in continuous models of three-level ecosystems.

Animals↗
PubMed2002

Genomic biodiversity, phylogenetics and coevolution in proteins.

Comprehensive sampling of genomic biodiversity is fast becoming a reality for some genomic regions and complete organelle genomes. Genomic biodiversity is defined as large genomic sequences from many species, and here some recent work is reviewed that demonstrates the potential benefits of genomic biodiversity for molecular evolutionary analysis and phylogenetic reconstruction. This work shows that using likelihood-based approaches, taxon addition can dramatically improve phylogenetic reconstruction. Features or dynamics of the evolutionary process are much more easily inferred with large numbers of taxa, and large numbers are essential for discriminating differences in evolutionary patterns between sites. Accurate prediction of site-specific patterns can improve phylogenetic reconstruction by an amount equivalent to quadrupling sequence length. Genomic biodiversity is particularly central to research relating patterns of evolution, adaptation and coevolution to structural and functional features of proteins. Research on detecting coevolution between amino acid residues in proteins demonstrates a clear need for much greater numbers of closely related taxa to better discriminate site-specific patterns of interaction, and to allow more detailed analysis of coevolutionary interactions between subunits in protein complexes. It is argued that parsing out coevolutionary and other context-dependent substitution probabilities is essential for discriminating between coevolution and adaptation, and for more realistically modelling the evolution of proteins. Also reviewed is research that argues for increasing the efficiency of acquiring genomic biodiversity, and suggests that this might be done by simultaneously shotgun cloning and sequencing genomic mixtures from many species. Increased efficiency is a prerequisite if genomic biodiversity levels are to rapidly increase by orders of magnitude, and thus lead to dramatically improved understanding of interactions between protein structure, function and sequence evolution.

Biodiversity↗
PubMed2025

Lineage-specific targets of positive selection in three leaf beetles correspond with defence capacity against their shared parasitoid wasp.

Parasitoid wasps are major causes of mortality of many species, making host immune defences a common target of adaptive evolution, though such targets outside model species are poorly understood. In this study, we used two tests of positive selection to compare across three closely related Galerucella leaf beetles that show substantial differences in their phenotypic response to the shared parasitoid wasp Asecodes parviclava, their main natural enemy. Using a codon-based test, which detects excess amino acid fixations per locus along each species' lineage, we found more evidence of positive selection on parasitoid-relevant immune genes in the species with the strongest immunocompetence (G. pusilla) compared with the species having weaker immunocompetence (G. tenella and G. calmariensis). Moreover, genes coding for the early phases in the immune response cascade were predominantly among the positively selected immune genes, providing targets for future functional genomic study to pin-point connections between genotypic and phenotypic differences in defences towards a parasitoid wasp. In contrast, genome-wide analyses of the haplotype frequency spectrum, which quantify selection over recent evolutionary time scales, revealed similar signatures of positive selection on immune genes across species. These results advance the field of host-parasitoid dynamics by providing novel insights into the tempo and mode of insect host evolutionary dynamics, and offering a framework for making genotype to phenotype connections for immunocompetence phenotypes.

Animals↗
PubMed2003

Toward an ecological synthesis: a case for habitat selection.

Habitat selection, and its associated density and frequency-dependent evolution, has a profound influence on such vital phenomena as population regulation, species interactions, the assembly of ecological communities, and the origin and maintenance of biodiversity. Different strategies of habitat selection, and their importance in ecology and evolution, can often be revealed simply by plots of density in adjacent habitats. For individual species, the strategies are closely intertwined with mechanisms of population regulation, and with the persistence of populations through time. For interacting species, strategies of habitat selection are not only responsible for species coexistence, but provide one of the most convenient mechanisms for measuring competition, and the various community structures caused by competitive interactions. Other kinds of interactions, such as those between predators and prey, demonstrate that an understanding of the coevolution of habitat-selection strategies among strongly interacting species is essential to properly interpret their spatial and temporal dynamics. At the evolutionary scale, the frequency dependence associated with habitat selection may often allow populations to diverge and diversify into separate species. Habitat selection thereby demonstrates how we can map microevolutionary strategies in behavior onto their population and community consequences, and from there, onto macroevolutionary patterns of speciation and adaptive radiation. We can anticipate that future studies of habitat selection will not only help us complete those maps, but that they will also continue to enrich the panoply of ideas that shape evolutionary ecology.

Animals↗
PubMed1987

Studies on evolutionary and selective properties of hypercycles using a Monte Carlo method.

The most relevant properties of hypercycles were previously studied mainly from a theoretical point of view. We have developed a Monte Carlo method simulating hypercyclic organization to obtain information about the dynamics of this prebiotic organization. Nucleation, growth, and selective properties have been tested and the results obtained are in good agreement with those of the theoretical predictions. The influence of hypercyclic organization on the "error threshold" has also been studied. As a consequence of the emergence of a hypercycle, the value of this threshold decreases. The amount of this decrease depends on the population size. Moreover, for some interval of quality factor values, either the hypercycle organization or an error catastrophe can be produced, depending on the initial conditions. The influence of these phenomena on both the dynamic behavior and evolutionary advantages of the hypercycle, as well as their decisive roles on genome size, are discussed.

Biological Evolution↗
PubMed2002

Evolutionary ecology of plant diseases in natural ecosystems.

Plant pathogens cause mortality and reduce fecundity of individual plants, drive host population dynamics, and affect the structure and composition of natural plant communities. Pathogens are responsible for both numerical changes in host populations and evolutionary changes through selection for resistant genotypes. Linking such ecological and evolutionary dynamics has been the focus of a growing body of literature on the effects of plant diseases in natural ecosystems. A guiding principle is the importance of understanding the spatial and temporal scales at which plants and pathogens interact. This review summarizes the effects of diseases on populations of wild plants, focusing in particular on the mediation of plant competition and succession, the maintenance of plant species diversity, as well as the process of rapid evolutionary changes in host-pathogen symbioses.

Adaptation, Physiological↗