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Results for “evolutionary dynamics”

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At least 1,621 records · Page 90Linked to original sources
PubMed2003

Dynamic modeling of genetic networks using genetic algorithm and S-system.

MOTIVATION: The modeling of system dynamics of genetic networks, metabolic networks or signal transduction cascades from time-course data is formulated as a reverse-problem. Previous studies focused on the estimation of only network structures, and they were ineffective in inferring a network structure with feedback loops. We previously proposed a method to predict not only the network structure but also its dynamics using a Genetic Algorithm (GA) and an S-system formalism. However, it could predict only a small number of parameters and could rarely obtain essential structures. In this work, we propose a unified extension of the basic method. Notable improvements are as follows: (1) an additional term in its evaluation function that aims at eliminating futile parameters; (2) a crossover method called Simplex Crossover (SPX) to improve its optimization ability; and (3) a gradual optimization strategy to increase the number of predictable parameters. RESULTS: The proposed method is implemented as a C program called PEACE1 (Predictor by Evolutionary Algorithms and Canonical Equations 1). Its performance was compared with the basic method. The comparison showed that: (1) the convergence rate increased about 5-fold; (2) the optimization speed was raised about 1.5-fold; and (3) the number of predictable parameters was increased about 5-fold. Moreover, we successfully inferred the dynamics of a small genetic network constructed with 60 parameters for 5 network variables and feedback loops using only time-course data of gene expression.

Algorithms↗
PubMed1999

Evolution of Wolbachia pipientis transmission dynamics in insects.

Wolbachia pipientis is an intracellular bacterial parasite of arthropods that enhances its transmission by manipulating host reproduction, most commonly by inducing cytoplasmic incompatibility. The discovery of isolates with modified cytoplasmic incompatibility phenotypes and others with novel virulence properties is an indication of the potential breadth of evolutionary strategies employed by Wolbachia.

Animals↗
PubMed2002

Mathematical modelling of host-parasitoid systems: effects of chemically mediated parasitoid foraging strategies on within- and between-generation spatio-temporal dynamics.

In this paper we develop a novel discrete, individual-based mathematical model to investigate the effect of parasitoid foraging strategies on the spatial and temporal dynamics of host-parasitoid systems. The model is used to compare naïve or random search strategies with search strategies that depend on experience and sensitivity to semiochemicals in the environment. It focuses on simple mechanistic interactions between individual hosts, parasitoids, and an underlying field of a volatile semiochemical (emitted by the hosts during feeding) which acts as a chemoattractant for the parasitoids. The model addresses movement at different spatial scales, where scale of movement also depends on the internal state of an individual. Individual interactions between hosts and parasitoids are modelled at a discrete (micro-scale) level using probabilistic rules. The resulting within-generation dynamics produced by these interactions are then used to generate the population levels for successive generations. The model simulations examine the effect of various key parameters of the model on (i) the spatio-temporal patterns of hosts and parasitoids within generations; (ii) the population levels of the hosts and parasitoids between generations. Key results of the model simulations show that the following model parameters have an important effect on either the development of patchiness within generations or the stability/instability of the population levels between generations: (i) the rate of diffusion of the kairomones; (ii) the specific search strategy adopted by the parasitoids; (iii) the rate of host increase between successive generations. Finally, evolutionary aspects concerning competition between several parasitoid subpopulations adopting different search strategies are also examined.

Animals↗
PubMed1999

An evolutionary algorithm for interval solid transportation problems.

The Solid Transportation Problem arises when bounds are given on three item properties. Usually, these properties are source, destination and mode of transport (conveyance), and may be given in an interval way. This paper deals with solid transportation problems in which the data in the constraint set are expressed in an interval form, i.e. when sources, destinations and conveyances have interval values instead of point values. An arbitrary linear or nonlinear objective function is also considered. To solve the problem, an Evolutionary Algorithm which extends and generalizes other approaches considering only point values, is proposed.

Algorithms↗
PubMed2002

Sexual selection and speciation in mammals, butterflies and spiders.

Recently refined evolutionary theories propose that sexual selection and reproductive conflict could be drivers of speciation. Male and female reproductive optima invariably differ because the potential reproductive rate of males almost always exceeds that of females: females are selected to maximize mate 'quality', while males can increase fitness through mate 'quantity'. A dynamic, sexually selected conflict therefore exists in which 'competitive' males are selected to override the preference tactics evolved by 'choosy' females. The wide variation across taxa in mating systems therefore generates variance in the outcome of intrasexual conflict and the strength of sexual selection: monandry constrains reproductive heterozygosity and allows female choice to select and maintain particular (preferred) genes; polyandry promotes reproductive heterozygosity and will more likely override female choice. Two different theories predict how sexual selection might influence speciation. Traditional ideas indicate that increased sexual selection (and hence conflict) generates a greater diversity of male reproductive strategies to be counteracted by female mate preferences, thus providing elevated potentials for speciation as more evolutionary avenues of male-female interaction are created. A less intuitively obvious theory proposes that increased sexual selection and conflict constrains speciation by reducing the opportunities for female mate choice under polyandry. We use a comparative approach to test these theories by investigating whether two general measures of sexual selection and the potential for sexual conflict have influenced speciation. Sexual size dimorphism (across 480 mammalian genera, 105 butterfly genera and 148 spider genera) and degree of polyandry (measured as relative testes size in mammals (72 genera) and mating frequency in female butterflies (54 genera)) showed no associations with the variance in speciosity. Our results therefore show that speciation occurs independently of sexual selection.

Animals↗
PubMed2026

Loss, persistence and reversal of phenotypic traits.

The irreversibility of complex trait loss has long been a tenet of evolutionary biology. However, this idea is increasingly at odds with the numerous documented exceptions across the Tree of Life. We synthesise this growing body of evidence across a diverse array of taxa and traits, exploring the evolutionary conditions that enable evolutionary reversal. By integrating macroevolutionary, genetic, and developmental information, we argue that trait reversal is commonly fostered by some form of persistence in the generative developmental pathway of the lost trait. We identify three overarching modes of trait reversal and support them with multiple case studies: by pleiotropy (the involvement of the same generative components in other traits and/or functions), by plasticity (environment-dependent expression of the trait) and by hemiplasy (persistence in another lineage, followed by reticulate evolution). We also examine important affinities between trait reversal and evolutionary novelties, undermining a neat distinction between what is old and what is new in evolution. This survey may provide a useful framework for future explorations of the developmental mechanisms underlying these still overlooked macroevolutionary dynamics.

Phenotype↗
PubMed2000

Dynamics of dominance of a dipeptide insertion in reverse transcriptase of HIV-1 from patients subjected to prolonged therapy.

A small proportion (0.8%) of individuals of a cohort of HIV-1 infected patients subjected to prolonged therapy with nucleoside analogues included a recently recognised dipeptide insertion in their RT (Ser-Ser or Ser-Gly between RT codons 69 and 70). To study the dynamics of dominance of genomes with this genetic change, sequential HIV-1 isolates from two patients were analyzed with regard to consensus sequences and complexity of mutant spectra. The two patients displayed completely different, complex evolutionary patterns leading to temporary dominance of dipeptide insertions. In one patient, a virus very closely related to an ancestor virus from the same patient overtook the population at late times, displacing genomes encoding a Ser-Ser insertion. In another patient the sequential dominance of genomes with Ser-Ser insertion-->no insertion-->Ser-Gly insertion was observed. These three types of genomes coexisted in the mutant spectrum of one HIV-1 isolate. Complexity was also reflected in the shape of phylogenetic trees derived with genomes from the mutant spectrum at each time point. The results suggest that HIV-1 genomes encoding a dipeptide insertion between RT codons 69 and 70 do not show a clear selective advantage over other genomes lacking the insertion. Such an absence of a clear selective advantage will favor that such genomes encoding this RT insertion become dominant only in a transient fashion, and following disparate kinetics in different patients.

Adult↗
PubMed2004

Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models.

BACKGROUND: The size distribution of gene families in a broad range of genomes is well approximated by a generalized Pareto function. Evolution of ensembles of gene families can be described with Birth, Death, and Innovation Models (BDIMs). Analysis of the properties of different versions of BDIMs has the potential of revealing important features of genome evolution. RESULTS: In this work, we extend our previous analysis of stochastic BDIMs. In addition to the previously examined rational BDIMs, we introduce potentially more realistic logistic BDIMs, in which birth/death rates are limited for the largest families, and show that their properties are similar to those of models that include no such limitation. We show that the mean time required for the formation of the largest gene families detected in eukaryotic genomes is limited by the mean number of duplications per gene and does not increase indefinitely with the model degree. Instead, this time reaches a minimum value, which corresponds to a non-linear rational BDIM with the degree of approximately 2.7. Even for this BDIM, the mean time of the largest family formation is orders of magnitude greater than any realistic estimates based on the timescale of life's evolution. We employed the embedding chains technique to estimate the expected number of elementary evolutionary events (gene duplications and deletions) preceding the formation of gene families of the observed size and found that the mean number of events exceeds the family size by orders of magnitude, suggesting a highly dynamic process of genome evolution. The variance of the time required for the formation of the largest families was found to be extremely large, with the coefficient of variation >> 1. This indicates that some gene families might grow much faster than the mean rate such that the minimal time required for family formation is more relevant for a realistic representation of genome evolution than the mean time. We determined this minimal time using Monte Carlo simulations of family growth from an ensemble of simultaneously evolving singletons. In these simulations, the time elapsed before the formation of the largest family was much shorter than the estimated mean time and was compatible with the timescale of evolution of eukaryotes. CONCLUSIONS: The analysis of stochastic BDIMs presented here shows that non-linear versions of such models can well approximate not only the size distribution of gene families but also the dynamics of their formation during genome evolution. The fact that only higher degree BDIMs are compatible with the observed characteristics of genome evolution suggests that the growth of gene families is self-accelerating, which might reflect differential selective pressure acting on different genes.

Birth Rate↗
PubMed2006

Insights into cytoskeletal behavior from computational modeling of dynamic microtubules in a cell-like environment.

Microtubule dynamic instability plays a fundamental role in cell biology, enabling microtubules to find and interact with randomly distributed cargo and spatially localized signals. In vitro, microtubules transition between growth and shrinkage symmetrically, consistent with the theoretical understanding of the mechanism of dynamic instability. In vivo, however, microtubules commonly exhibit asymmetric dynamic instability, growing persistently in the cell interior and experiencing catastrophe near the cell edge. What is the origin of this behavior difference? One answer is that the cell edge causes the asymmetry by inducing catastrophe in persistently growing microtubules. However, the origin of the persistent growth itself is unclear. Using a simplified coarse-grained stochastic simulation of a system of dynamic microtubules, we provide evidence that persistent growth is a predictable property of a system of nucleated, dynamic, microtubules containing sufficient tubulin in a confined space--MAP activity is not required. Persistent growth occurs because cell-edge-induced catastrophe increases the concentration of free tubulin at steady-state. Our simulations indicate that other aspects of MT dynamics thought to require temporal or spatial changes in MAP activity are also predictable, perhaps unavoidable, outcomes of the "systems nature" of the cellular microtubule cytoskeleton. These include the mitotic increase in microtubule dynamics and the observation that defects in nucleation cause changes in the behavior of microtubule plus ends. These predictions are directly relevant to understanding of the microtubule cytoskeleton, but they are also attractive from an evolutionary standpoint because they provide evidence that apparently complex cellular behaviors can originate from simple interactions without a requirement for intricate regulatory machinery.

Cell Shape↗
PubMed2004

Echolocation clicks of two free-ranging, oceanic delphinids with different food preferences: false killer whales Pseudorca crassidens and Risso's dolphins Grampus griseus.

Toothed whales (Odontoceti, Cetacea) navigate and locate prey by means of active echolocation. Studies on captive animals have accumulated a large body of knowledge concerning the production, reception and processing of sound in odontocete biosonars, but there is little information about the properties and use of biosonar clicks of free-ranging animals in offshore habitats. This study presents the first source parameter estimates of biosonar clicks from two free-ranging oceanic delphinids, the opportunistically foraging Pseudorca crassidens and the cephalopod eating Grampus griseus. Pseudorca produces short duration (30 micro s), broadband (Q=2-3) signals with peak frequencies around 40 kHz, centroid frequencies of 30-70 kHz, and source levels between 201-225 dB re. 1 micro Pa (peak to peak, pp). Grampus also produces short (40 micro s), broadband (Q=2-3) signals with peak frequencies around 50 kHz, centroid frequencies of 60-90 kHz, and source levels between 202 and 222 dB re. 1 micro Pa (pp). On-axis clicks from both species had centroid frequencies in the frequency range of most sensitive hearing, and lower peak frequencies and higher source levels than reported from captive animals. It is demonstrated that sound production in these two free-ranging echolocators is dynamic, and that free-ranging animals may not always employ biosonar signals comparable to the extreme signal properties reported from captive animals in long-range detection tasks. Similarities in source parameters suggest that evolutionary factors other than prey type determine the properties of biosonar signals of the two species. Modelling shows that interspecific detection ranges of prey types differ from 80 to 300 m for Grampus and Pseudorca, respectively.

Animal Communication↗
PubMed1996

Paleobiology, community ecology, and scales of ecological pattern.

The fossil record provides a wealth of data on the role of regional processes and historical events in shaping biological communities over a variety of time scales. The Quaternary record with its evidence of repeated climatic change shows that both terrestrial and marine species shifted independently rather than as cohesive assemblages over scales of thousands of years. Larger scale patterns also show a strong individualistic component to taxon dynamics; assemblage stability, when it occurs, is difficult to separate from shared responses to low rates of environmental change. Nevertheless, the fossil record does suggest that some biotic interactions influence large-scale ecological and evolutionary patterns, albeit in more diffuse and protracted fashions than those generally studied by community ecologists. These include: (1) the resistance by incumbents to the establishment of new or invading taxa, with episodes of explosive diversification often appearing contingent on the removal of incumbents at extinction events; (2) steady states of within-habitat and global diversity at longer time scales (10(7)-l0(8) yr), despite enormous turnover of taxa; and (3) morphological and biogeographic responses to increased intensities of predation and substratum disturbance over similarly long time scales. The behavior of species and communities over the array of temporal and spatial scales in the fossil record takes on additional significance for framing conservation strategies, and for understanding recovery of species, lineages, and communities from environmental changes.

Animals↗
PubMed1995

Evolving mobile robots in simulated and real environments.

The problem of the validity of simulation is particularly relevant for methodologies that use machine learning techniques to develop control systems for autonomous robots, as, for instance, the artificial life approach known as evolutionary robotics. In fact, although it has been demonstrated that training or evolving robots in real environments is possible, the number of trials needed to test the system discourages the use of physical robots during the training period. By evolving neural controllers for a Khepera robot in computer simulations and then transferring the agents obtained to the real environment we show that (a) an accurate model of a particular robot-environment dynamics can be built by sampling the real world through the sensors and the actuators of the robot; (b) the performance gap between the obtained behaviors in simulated and real environments may be significantly reduced by introducing a "conservative" form of noise; (c) if a decrease in performance is observed when the system is transferred to a real environment, successful and robust results can be obtained by continuing the evolutionary process in the real environment for a few generations.

Algorithms↗
PubMed2002

Order in ectoparasite communities of marine fish is explained by epidemiological processes.

Two kinds of community structure referred to, nestedness and bimodal distribution, have been observed or were searched for in parasite communities. We investigate here the relation between these two kinds of organisation, using marine fishes as a model, in order to show that parasite population dynamics may parsimoniously explain the patterns of ectoparasite species distribution and abundance. Thirty six assemblages of metazoan ectoparasites on the gills and heads of marine fish showed the following patterns: a positive relationship between abundance and the variance of abundance; a positive relationship between abundance and prevalence of infection; a bimodal pattern of the frequency distribution of prevalence of infection; nestedness as indicated by Atmar and Patterson's thermodynamic measure (a mean of 7.9 degrees C); a unimodal distribution of prevalence in parasite assemblages with a temperature lower than the mean, and a bimodal distribution in assemblages with a temperature higher than the mean. We conclude that patterns are the result of characteristics of the parasite species themselves and that interspecific competition is not necessary to explain them. We emphasize that a holistic approach, taking all evidence jointly into account, is necessary to explain patterns of community structure. Ectoparasite assemblages of marine fish are among the animal groups that have been most thoroughly examined using many different methods, and all evidence supports the view that these animals live under non-equilibrium conditions, in largely non-saturated niche space in which interspecific competition occurs but is of little evolutionary importance.

Analysis of Variance↗
PubMed2004

Dynamic subset selection based on a fitness case topology.

A large training set of fitness cases can critically slow down genetic programming, if no appropriate subset selection method is applied. Such a method allows an individual to be evaluated on a smaller subset of fitness cases. In this paper we suggest a new subset selection method that takes the problem structure into account, while being problem independent at the same time. In order to achieve this, information about the problem structure is acquired during evolutionary search by creating a topology (relationship) on the set of fitness cases. The topology is induced by individuals of the evolving population. This is done by increasing the strength of the relation between two fitness cases, if an individual of the population is able to solve both of them. Our new topology-based subset selection method chooses a subset, such that fitness cases in this subset are as distantly related as is possible with respect to the induced topology. We compare topology-based selection of fitness cases with dynamic subset selection and stochastic subset sampling on four different problems. On average, runs with topology-based selection show faster progress than the others.

Algorithms↗
PubMed1983

Human behavioral development and genetics.

Behavioral development during childhood is examined in relation to recent concepts and data from evolutionary theory and developmental genetics. The epigenetic framework of Waddington is proposed as a powerful tool for analyzing the progressions in behavior, particularly for recognizing that development involves coordinated pathways of change over time. Many of these pathways appear to depend upon the activity of timed gene-action systems that switch off and on according to a predetermined plan. Behavioral development thus gives expression to the dynamics of preprogrammed change; and in this perspective, behavioral discontinuities may be as strongly rooted in the epigenetic ground plan as the continuities are. The present paper aims to pull together some common themes from different areas that bear on the central issues of behavioral development--the neural foundations, the time course followed, the interplay of maturation and experience, the extent of preorganization furnished by the genetic program, and the adaptive significance of such behaviors in an evolutionary perspective. The final section touches on some hypotheses drawn from developmental neurobiology and developmental genetics that may enrich the analyses of human behavioral development.

Biological Evolution↗
PubMed1997

On the evolution of density dependent dispersal in a spatially structured population model.

A simple metapopulation lattice model of two competing phenotypes is presented, where one phenotype reacts more sensitively to overcrowding by migrating to neighbouring local habitats. The sensitivity is formulated by means of a threshold density of the subpopulations, above which dispersal is triggered off. If this threshold density is not very far from the local carrying capacity, an increased mobility provides benefits on the metapopulation level. At a surprisingly small difference between migrational triggering thresholds, the phenotype of larger mobility (or lower threshold) squeezes out the less mobile one from the whole system in a wide parameter range. Evolutionary considerations give an optimal threshold level for our model metapopulation.

Animals↗
PubMed2002

Dysregulation of neuronal differentiation and cell cycle control in Alzheimer's disease.

Degeneration in Alzheimer's disease primarily occurs in those neurons that in the adult brain retain, a high degree of structural plasticity and, is associated with the activation of mitogenic signaling and cell cycle activation. Brain areas affected by neurofibrillary degeneration in Alzheimer's disease are structures involved in the regulation of "higher brain functions" that become increasingly predominant as the evolutionary process of encephalization progresses. The functions these areas subserve require a life-long adaptive reorganization of neuronal connectivity. With the increasing need during evolution to organize brain structures of increasing complexity, these processes of dynamic stabilization and de-stabilization become more and more important but might also provide the basis for an increasing rate of failure. The hypothesis is put forward that it is the labile state of differentiation of a subset of neurons in the adult brain that allows for ongoing morphoregulatory processes after development is completed but at the same time renders these neurons particularly vulnerable. Interferring with neuronal differentiation control might, thus, be a potential strategy to prevent neurodegeneration in Alzheimer's disease and related disorders.

Aged↗