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Results for “evolutionary dynamics”

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At least 973 records · Page 54Linked to original sources
PubMed1999

Instantaneous postural stability characterization using time-frequency analysis.

Postural stability assessment is critical to a more accurate understanding of sway and balance control. The center of pressure (COP) metric has been shown to be a suitable output measure for time and frequency analysis. However, the center of pressure is a non-stationary signal. Standard time and frequency analysis methods may not be adequate for monitoring the dynamic changes in the center of pressure signal. In this study a time-frequency method, based on data-adaptive evolutionary spectral estimation, is applied to monitor the dynamic changes of the center of pressure in a non-stationary environment. Metrics including the instantaneous mean frequency (IMF), instantaneous spectral bandwidth (ISB), and instantaneous average power (IAP) are analyzed to characterize the center of pressure signal in both the anterior-posterior (AP) and the medial-lateral (ML) planes. Within the confines of this study, the IMF was found to be inversely proportional to IAP. The inverse proportionality factors were calculated in both eyes-open and eyes-closed trials during upright quiet standing. These findings suggest that the time-frequency analysis provides instantaneous metrics which describe the amplitude changes and frequency shift of the center of pressure under a variety of environmental conditions, thus providing a more reliable quantification of postural control.

Adult↗
PubMed2001

Evolutionary engineering of industrially important microbial phenotypes.

The tremendous complexity of dynamic interactions in cellular systems often impedes practical applications of metabolic engineering that are largely based on available molecular or functional knowledge. In contrast, evolutionary engineering follows nature's 'engineering' principle by variation and selection. Thus, it is a complementary strategy that offers compelling scientific and applied advantages for strain development and process optimization, provided a desired phenotype is amenable to direct or indirect selection. In addition to simple empirical strain development by random mutation and direct selection on plates, evolutionary engineering also encompasses recombination and continuous evolution of large populations over many generations. Two distinct evolutionary engineering applications are likely to gain more relevance in the future: first, as an integral component in metabolic engineering of strains with improved phenotypes, and second, to elucidate the molecular basis of desired phenotypes for subsequent transfer to other hosts. The latter will profit from the broader availability of recently developed methodologies for global response analysis at the genetic and metabolic level. These methodologies facilitate identification of the molecular basis of evolved phenotypes. It is anticipated that, together with novel analytical techniques, bioinformatics, and computer modeling of cellular functions and activities, evolutionary engineering is likely to find its place in the metabolic engineer's toolbox for research and strain development. This review presents evolutionary engineering of whole cells as an emerging methodology that draws on the latest advances from a wide range of scientific and technical disciplines.

Biological Evolution↗
PubMed2004

Coupling ecology and evolution: malaria and the S-gene across time scales.

Malaria has long been a scourge to humans. The exceptionally high mortality in some regions has led to strong selection for resistance, even at the cost of increased risk of potentially fatal red blood cell deformities in some offspring. In particular, genes that confers resistance to malaria when they appear in heterozygous individuals are known to lead to sickle-cell anemia, or other blood diseases, when they appear in homozygous form. Thus, there is balancing selection against the evolution of resistance, with the strength of that selection dependent upon malaria prevalence. Over longer time scales, the increased frequency of resistance in a population might be expected to decrease the frequency of malaria and reduce selection for resistance. However, possession of the sickle-cell gene leads to longer-lasting parasitaemia in heterozygote individuals, and therefore the presence of resistance may actually increase infection prevalence. In this paper, we explore the interplay among these processes, operating over very different time scales. In particular, we show that on the fast time scale of malarial dynamics, the disease level reaches an equilibrium; on the slower, evolutionary time scale, this equilibrium tracks gene frequency. We analyze the slow time scale dynamics to investigate the impact of malaria on the evolution of resistance.

Algorithms↗
PubMed2002

The evolution of gene duplicates.

Gene and genome duplications have given rise to enormous variability among species in the number of genes within their genomes. Gene copies have in turn played important roles in adaptation, having been implicated in the evolution of the immune response, insecticide resistance, efficient protein synthesis, and vertebrate body plans. In this chapter, we discuss the life history of gene duplications, from their first appearance within a population, through the period during which they rise in frequency or disappear, to their long-term fate. At each phase, we discuss the evolutionary processes that have influenced the dynamics of gene duplications and shaped their ultimate roles within a population. We argue that there is no evidence that organisms have evolved strategies to promote gene duplication in order to permit adaptive evolution. In contrast, many mechanisms exist to silence or eliminate duplicated genes, suggesting that selection has acted largely to reduce the rate of gene duplication. We also argue that natural selection has functioned as an effective sieve, increasing the representation of beneficial gene duplicates among those that establish within a population and that play a long-term role in evolution. To refine our understanding of how selection acts on new gene duplications, we provide a model incorporating a single-copy gene, its gene duplicate, and selection either favoring heterozygotes or eliminating deleterious mutations. Although both forms of selection can increase the initial rate of spread of a gene duplicate, the efficacy with which they do so differs dramatically. Heterozygote advantage always increases the rate of spread and can have a large impact. In contrast, masking deleterious mutations never has a large effect on the rate of spread of the duplicate, and this minor effect can be negative as well as positive. In both cases, the degree of linkage between the two gene copies affects the rate of spread of the duplication. Finally, we discuss evolutionary processes that occur over longer periods after a gene duplication has become established within a population. These long-term processes include maintenance, inactivation, and diversification in function. Consideration of each of the short-term and long-term processes affecting duplicated genes illustrates the subtle ways in which selection has acted to shape genomic structure.

Animals↗
PubMed2025

Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series.

MOTIVATION: The lineage dynamics and history of cells in a population reflect the interplay of evolutionary forces they experience, including mutation, drift, and selection. When the population is polyclonal, lineage dynamics also manifest the extent of clonal competition among co-existing mutational variants. If the population exists in a community of other species, the lineage dynamics could also reflect the population's ecological interaction with the rest of the community. Recent advances in high-resolution lineage tracking via DNA barcoding, coupled with next-generation sequencing of bacteria, yeast, and mammalian cells, allow for precise quantification of clonal dynamics in these organisms. RESULTS: In this work, we introduce Doblin, an R suite for identifying dominant barcode lineages based on high-resolution lineage tracking data. We first benchmarked Doblin's accuracy using lineage data from evolutionary simulations, showing that it recovers the clones' identity and relative fitness in the simulation. Next, we applied Doblin to analyze clonal dynamics in laboratory evolutions of Escherichia coli populations undergoing antibiotic treatment and in colonization experiments of the gut microbial community. Doblin's versatility allows it to be applied to lineage time-series data across different experimental setups. AVAILABILITY AND IMPLEMENTATION: Doblin is available on CRAN (https://CRAN.R-project.org/package=doblin) and Github (https://github.com/dagagf/doblin).

DNA Barcoding, Taxonomic↗
PubMed2003

Artificial life: organization, adaptation and complexity from the bottom up.

Artificial life attempts to understand the essential general properties of living systems by synthesizing life-like behavior in software, hardware and biochemicals. As many of the essential abstract properties of living systems (e.g. autonomous adaptive and intelligent behavior) are also studied by cognitive science, artificial life and cognitive science have an essential overlap. This review highlights the state of the art in artificial life with respect to dynamical hierarchies, molecular self-organization, evolutionary robotics, the evolution of complexity and language, and other practical applications. It also speculates about future connections between artificial life and cognitive science.

Journal Article↗
PubMed2006

Uninvadability in N-species frequency models for resident-mutant systems with discrete or continuous time.

The uninvadability concept, that was originally introduced through static comparisons of individual fitness in resident-mutant systems for a single species, is developed for multi-species models with frequency-dependent fitness by extending its equivalent single-species dynamic characterization. This multi-species definition is then reinterpreted in terms of individual fitness functions based on intra and interspecific interactions. The resultant concept is discussed in relation to that of an N-species ESS (evolutionarily stable strategy) and to dynamic stability of monomorphic and polymorphic evolutionary systems.

Biological Evolution↗
PubMed2006

A mixed strategy model for the emergence and intensification of social learning in a periodically changing natural environment.

Based on a population genetic model of mixed strategies determined by alleles of small effect, we derive conditions for the evolution of social learning in an infinite-state environment that changes periodically over time. Each mixed strategy is defined by the probabilities that an organism will commit itself to individual learning, social learning, or innate behavior. We identify the convergent stable strategies (CSS) by a numerical adaptive dynamics method and then check the evolutionary stability (ESS) of these strategies. A strategy that is simultaneously a CSS and an ESS is called an attractive ESS (AESS). For certain parameter sets, a bifurcation diagram shows that the pure individual learning strategy is the unique AESS for short periods of environmental change, a mixed learning strategy is the unique AESS for intermediate periods, and a mixed learning strategy (with a relatively large social learning component) and the pure innate strategy are both AESS's for long periods. This result entails that, once social learning emerges during a transient era of intermediate environmental periodicity, a subsequent elongation of the period may result in the intensification of social learning, rather than a return to innate behavior.

Genotype↗
PubMed2000

Biodiversity: modelling angiosperms as networks.

In the neotropics, one of the last biological frontiers, the major ecological concern should not involve local strategies, but global effects often responsible for irreparable damage. For a holistic approach, angiosperms are ideal model systems dominating most land areas of the present world in an astonishing variety of form and function. Recognition of biogeographical patterns requires new methodologies and entails several questions, such as their nature, dynamics and mechanism. Demographical patterns of families, modelled via species dominance, reveal the existence of South American angiosperm networks converging at the central Brazilian plateau. Biodiversity of habitats, measured via taxonomic uniqueness, reveal higher creative power at this point of convergence than in more peripheral regions. Compositional affinities of habitats, measured via bioconnectivity, reveal the decisive role of ecotones in the exchange or redistribution of information, energy and organisms among the ecosystems. Forming dynamic boundaries, ecotones generate and relay evolutionary novelty, and integrate all neotropical ecosystems into a single vegetation net. Connectivity in such plant webs may depend on mycorrhizal links. If sufficiently general such means of metabolic transfer will require revision of the chemical composition of many plants.

Conservation of Natural Resources↗
PubMed2006

Positive selection in the evolution of cancer.

We hypothesize that forms of antagonistic coevolution have forged strong links between positive selection at the molecular level and increased cancer risk. By this hypothesis, evolutionary conflict between males and females, mothers and foetuses, hosts and parasites, and other parties with divergent fitness interests has led to rapid evolution of genetic systems involved in control over fertilization and cellular resources. The genes involved in such systems promote cancer risk as a secondary effect of their roles in antagonistic coevolution, which generates evolutionary disequilibrium and maladaptation. Evidence from two sources: (1) studies on specific genes, including SPANX cancer/testis antigen genes, several Y-linked genes, the pem homebox gene, centromeric histone genes, the breast cancer gene BRCA1, the angiogenesis gene ANG, cadherin genes, cytochrome P450 genes, and viral oncogenes; and (2) large-scale database studies of selection on different functional categories of genes, supports our hypothesis. These results have important implications for understanding the evolutionary underpinnings of cancer and the dynamics of antagonistically-coevolving molecular systems.

Animals↗
PubMed2006

Why animals lie: how dishonesty and belief can coexist in a signaling system.

We develop and apply a simple model for animal communication in which signalers can use a nontrivial frequency of deception without causing listeners to completely lose belief. This common feature of animal communication has been difficult to explain as a stable adaptive outcome of the options and payoffs intrinsic to signaling interactions. Our theory is based on two realistic assumptions. (1) Signals are "overheard" by several listeners or listener types with different payoffs. The signaler may then benefit from using incomplete honesty to elicit different responses from different listener types, such as attracting potential mates while simultaneously deterring competitors. (2) Signaler and listener strategies change dynamically in response to current payoffs for different behaviors. The dynamic equations can be interpreted as describing learning and behavior change by individuals or evolution across generations. We explain how our dynamic model differs from other solution concepts from classical and evolutionary game theory and how it relates to general models for frequency-dependent phenotype dynamics. We illustrate the theory with several applications where deceptive signaling occurs readily in our framework, including bluffing competitors for potential mates or territories. We suggest future theoretical directions to make the models more general and propose some possible experimental tests.

Animal Communication↗
PubMed1999

Production of fertile unreduced sperm by hybrid males of the Rutilus alburnoides complex (Teleostei, cyprinidae). An alternative route to genome tetraploidization in unisexuals.

The hybrid minnow Rutilus alburnoides comprises diploid and polyploid females and males. Previous studies revealed that diploid and triploid females exhibit altered oogenesis that does not involve random segregation and recombination of the genomes of the two ancestors, constituting unisexual lineages. In the present study, we investigated the reproductive mode of hybrid males from the Tejo basin, using experimental crosses and flow cytometric analysis of blood and sperm. The results suggest that diploid hybrids produced fertile unreduced sperm, transmitting their hybrid genome intact to offspring. Triploid hybrids also produced unreduced sperm, but it was not possible to obtain data concerning their fertility. Finally, tetraploid hybrids produced fertile diploid sperm, which exhibited Mendelian segregation. Tetraploid R. alburnoides may reestablish biparental reproduction, as individuals of both sexes with the appropriate constitution for normal meiosis (two haploid genomes from each parental species) are likely to occur in natural populations. Tetraploids probably have arisen from syngamy of diploid eggs and diploid sperm produced by diploid hybrid males. Diploid hybrid males may therefore play a significant role in the dynamics of the complex, starting the evolutionary process that may ultimately lead to a new sexually reproducing species.

Animals↗
PubMed1983

Manifestations of consciousness and the developmental phenomenon of death.

Recent developments in nursing science include the development of theoretic structures that focus on the developmental nature of the human life process. According to Rogers, this life process represents a unitary phenomenon within which change is constant and evolutionary. Such change occurs through a dynamic, rhythmic interaction between the person and the environment. A theoretic framework derived from conceptualizations of the life process with its associated manifestation of consciousness and the developmental phenomenon of death is presented. The concepts and identified propositions are related to specific empiric indicators for testing or measurement. Implications of the proposed relationships between state of consciousness and resolution of death anxiety for nursing practice are also discussed.

Anxiety↗
PubMed2006

Evolutionary responses of natives to introduced species: what do introductions tell us about natural communities?

Biological invasions dramatically affect the distribution, abundance and reproduction of many native species. Because of these ecological effects, exotic species can also influence the evolution of natives exposed to novel interactions with invaders. Evolutionary changes in natives in response to selection from exotics are usually overlooked, yet common responses include altered anti-predator defenses, changes in the spectrum of resources and habitats used, and other adaptations that allow native populations to persist in invaded areas. Whether a native population is capable of responding evolutionarily to selection from invaders will depend on the demographic impact of the invader, the genetic architecture and genetic variability of the native population and potentially the history of previous invasions. In some cases, natives will fail to evolve or otherwise adapt, and local or global extinction will result. In other cases, adaptive change in natives may diminish impacts of invaders and potentially promote coexistence between invaders and natives. Here, we review the evidence for evolutionary responses of native species to novel community members. We also discuss how the effects of introduced species may differ from those caused by natural range expansions of native species. Notably, introduced species may come from remote biotas with no previous evolutionary history with the native community. In addition, the rate of addition of introduced species into communities is much greater than all but the most extreme cases of historical biotic exchange. Understanding the evolutionary component of exotic/native species interactions is critical to recognizing the long-term impacts of biological invasions, and to understanding the role of evolutionary processes in the assembly and dynamics of natural communities.

Animals↗
PubMed1978

Synchronies in mental development: an epigenetic perspective.

Early mental development is analyzed from an evolutionary viewpoint and related to the dynamic interplay of genetic programming, maturational status, and environmental influence. Data are reported from a large sample of twins and siblings who have been tested longitudinally from 3 months to 6 years of age. Monozygotic twins became increasingly concordant with age and also paralleled each other for the spurts and lags in development. Dizygotic twins became less concordant with age and eventually matched their singleton siblings as closely as one another. The overall results suggested that the course of mental development is guided by the intrinsic scheduling of the genetic program acting in concert with maturational status and environmental influence.

Behavior↗
PubMed2006

Optimum tracking with evolution strategies.

Evolutionary algorithms are frequently applied to dynamic optimization problems in which the objective varies with time. It is desirable to gain an improved understanding of the influence of different genetic operators and of the parameters of a strategy on its tracking performance. An approach that has proven useful in the past is to mathematically analyze the strategy's behavior in simple, idealized environments. The present paper investigates the performance of a multiparent evolution strategy that employs cumulative step length adaptation for an optimization task in which the target moves linearly with uniform speed. Scaling laws that quite accurately describe the behavior of the strategy and that greatly contribute to its understanding are derived. It is shown that in contrast to previously obtained results for a randomly moving target, cumulative step length adaptation fails to achieve optimal step lengths if the target moves in a linear fashion. Implications for the choice of population size parameters are discussed.

Adaptation, Biological↗
PubMed2005

Combinatorial chemistry and fragment screening--two unlike siblings?

Efficiently scouting the chemical space is one of the major challenges for lead discovery for drug development. In recent times some shifts have been made away from HTS and combinatorial chemistry to more focused approaches. Combinatorial chemistry was the starting point for the development of synthesis concepts that were intended to cover and explore the chemical space without having to prepare every individual compound. In this review, these lead finding approaches will be discussed comparing virtual and synthesized libraries. In addition we discuss the concepts and relationships of evolutionary libraries using genetic algorithms and dynamic combinatorial chemistries, as well as templated fragment ligation concepts. Taking a more abstract view of all approaches, the concepts may loop back into Combinatorial Chemistry allowing a more educated choice of building blocks and chemistries.

Combinatorial Chemistry Techniques↗
PubMed1999

[Scientific languages and the science of complexity].

For centuries the goal of galileian and newtonian science has been the discovery of the universal laws of nature governing all natural phenomena. But, starting with the sixties of this century, advanced research has concentrated on the study of the characteristic aspects of irregular and unrepeatable evolutionary processes. Signs of this change are the rediscovery of Poincaré's results on the dynamics of non linear systems, and the extraordinary development of evolutionary thinking. Three properties characterize complex systems: the multiplicity of their levels of organization, the presence of self-referential loops of internal communication, and the irreducible nature of their past history to structural properties. The traditional cartesian gap between mind and body therefore falls down, as argued at length by the works of Gregory Bateson. His arguments are further strengthened by the neurologist Antonio Damasio in his book on reason, emotion and human brain, whose title is L'errore di Cartesio (The error of Descartes), where the negative consequences of this error on the development of science in general and on contemporary medicine in particular, are illustrated.

Biological Evolution↗