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 865 records · Page 48Linked to original sources

[Simulation of the macro-evolutionary process on computers].

The discussed model is designed for investigation of peculiarities and dynamics of the growth of evolutionary trees. The model is realized in FORTRAN, properties and principles of interaction of populations being the basis of this model. The results obtained reveal an extreme dependence of the pattern of evolutionary process from the parameters of competition, as well as the fact that evolutionary trees plotted with incomplete number of characters may be entirely different from real ones. It is concluded that many of the known evolutionary phenomena may be sufficiently described by a quantitative model based on the Darwinian principles.

Animals↗

Path costs in evolutionary tree reconstruction.

This paper describes a dynamic programming algorithm to solve a family of problems in the reconstruction of evolutionary trees from protein sequence data, that of constructing "minimal" colorings. This dynamic programming formulation can be modified to efficiently enumerate the number of minimal colorings and thereby be used to calculate the average cost of any given edge, where the average is taken over the entire set of minimal colorings. An extension of our dynamic programming formulation allows for the calculation of average path costs amongst all minimal colorings. our results resolve questions raised in (Hendy and penny, 1987); in particular, we develop polynomial time procedures to find the minimum, maximum, and average (expected) cost of an edge, and more generally of a path, for a minimal coloring. Our algorithm is distinguished in its flexibility to address further distribution and statistical questions relating to the minimal colorings. Furthermore, the more general concept of calculating statistics describing the set of optimal solutions may be of interest in other combinatorial problems.

Algorithms↗

Genome-wide identification and expression profiling of the MADS-box gene family in Lavandula angustifolia.

BACKGROUND: MADS-box genes encode transcription factors critical for plant development, particularly floral organogenesis, flowering time regulation, and adaptation to environmental stresses. Among these, the MIKCC-type genes are pivotal regulators in floral developmental processes. Although the evolutionary diversification and functional dynamics of MADS-box genes have been extensively characterized in model plants such as Arabidopsis thaliana and Oryza sativa, their evolutionary relationships and functional profiles in Lavandula angustifolia, an economically significant aromatic plant, remain poorly understood. RESULTS: Genome-wide analysis identified 173 MADS-box genes in L. angustifolia, categorized into type I (Mα: 26; Mβ: 0; Mγ: 10) and type II (MIKCC: 125; MIKC*: 12) based on phylogenetic comparisons with A. thaliana. The MIKCC subgroup was further subdivided into 12 subclasses, including genes central to the ABCDE model of floral organ specification. Structural analyses revealed distinct conserved motifs and exon-intron configurations specific to each subgroup, indicative of functional divergence. Synteny analysis demonstrated Whole Genome Duplication (WGD) and segmental duplications as major contributors to MIKCC gene family expansion, notably among genes linked to floral organ development. Expression profiling via RNA-seq and quantitative real-time PCR (qPCR) showed type II MADS-box genes exhibited higher expression levels with pronounced tissue-specific and developmental stage-specific expression patterns compared to type I genes. Many type II genes displayed significant associations with floral organogenesis, floral transition, and abiotic stress responses, underscoring their essential roles in reproductive development and environmental adaptability in L. angustifolia. CONCLUSIONS: The identification and comprehensive characterization of 173 MADS-box genes in L. angustifolia highlight the significant expansion of the MIKCC subgroup driven primarily by WGD and segmental duplications. The distinct structural features and specific expression patterns observed provide insights into the functional divergence and complexity of these genes, particularly regarding floral organogenesis and adaptation to environmental stress. This study establishes a robust molecular basis for further functional analysis and genetic improvement of aromatic plants.

MADS Domain Proteins↗

A contribution to the geographical interpretation of biological change.

"Geography" has traditionally been assigned the role of handmaiden in evolutionary studies. In this work a different understanding of the relationship between biological change and locational setting is developed: evolution as a dynamic form of spatial interaction. In the causal model presented, adaptive change is portrayed as a negative feedback response contributing to a general spatial-temporal process of resource cycle tightening involving exchanges between the two fundamental structural sectors ("abiotic" and "biotic") of the earth's surface system. As such, it is rejected as "evolution" per se. This position makes it possible to circumvent the "adaptation yields adaptation" circularity, and to view locational circumstances as being evolutionarily causal, yet not deterministic with respect to population-level change. A parallel interpretation of the relation between range and range change and evolution is also implicit; the individualistic hypothesis is thereby superceded by a model of community evolution allowing for individualistic rates of population (adaptive and) range change, but operating on the principle that populations should tend to change range in common directions (as a response to spatially-varying degrees of efficiency of turnover of resources vital to biotic sector function). This in turn leads to the possibility of normative biogeographic modelling. Comment is also made on the relationship of the present understanding to disequilibrium and dynamic equilibrium interpretations of evolutionary change, and to human cultural evolution.

Animals↗

[The problem of organism integrity and its perspectives].

The organism integrity in onto- and phylogenesis is considered as an initial element of biosphere integrity and its evolution at the eukaryotic level. The Schmalhausen's concept of organism integrity is discussed in the context of his original strategy of evolutionary synthesis and his works on stabilizing selection. The perspectives of investigations on the problem of integrity and development of the principle of dynamic stability in contemporary evolutionary biology as integrating factors are discussed.

Animals↗

Feast and famine in plant genomes.

Plant genomes vary over several orders of magnitude in size, even among closely related species, yet the origin, genesis and significance of this variation are not clear. Because DNA content varies over a sevenfold range among diploid species in the cotton genus (Gossypium) and its allies, this group offers opportunities for exploring patterns and mechanisms of genome size evolution. For example, the question has been raised whether plant genomes have a 'one-way ticket to genomic obesity', as a consequence of retroelement accumulation. Few empirical studies directly address this possibility, although it is consistent with recent insights gleaned from evolutionary genomic investigations. We used a phylogenetic approach to evaluate the directionality of genome size evolution among Gossypium species and their relatives in the cotton tribe (Gossypieae, Malvaceae). Our results suggest that both DNA content increase and decrease have occurred repeatedly during evolution. In contrast to a model of unidirectional genome size change, the frequency of inferred genome size contraction exceeded that of expansion. In conjunction with other evidence, this finding highlights the dynamic nature of plant genome size evolution, and suggests that poorly understood genomic contraction mechanisms operate on a more extensive scale that previously recognized. Moreover, the research sets the stage for fine-scale analysis of the evolutionary dynamics and directionality of change for the full spectrum of genomic constituents.

Chromosomes↗

Herbivory promotes plant production and reproduction in nutrient-poor conditions: effects of plant adaptive phenology.

Many studies have demonstrated positive effects of herbivory on plant performance, and these encompass two categories of effects: enhancement of primary production and enhancement of reproductive success. These positive responses of plants to herbivory have been called "grazing optimization." One possible mechanism of these paradoxical phenomena is the nutrient cycling promoted by herbivory. This article models the nutrient cycling hypothesis and analyzes the evolution of plant production and reproduction enhanced by herbivores, using dynamic optimization of plant phenology. Especially when there is nutrient competition among plant individuals or nutrient transportation by herbivores, we can apply the concept of evolutionary stability for the dynamic optimization. Two types of plant responses, long-term and short-term, are examined. Long-term response is an adaptive response for a given level of herbivory pressure, while short-term response is a nonadaptive one to various levels of herbivory, different from the level to which the plant is adapted. The analysis shows that both long-term and short-term grazing optimizations in primary production can occur under poor nutrient conditions and high nutrient recycling rates. However, grazing optimization in reproduction occurs under the same conditions but requires further conditions. In particular, long-term reproductive grazing optimization occurs only when nutrient competition exists among plant individuals. Accordingly, the present analysis revealed the following points concerning grazing optimization: poor nutrient condition is necessary, nutrient competition between plant individuals can promote optimization, and the native condition of the plant is important in the short-term response.

Adaptation, Physiological↗

Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes.

Vitamin B(6) (VB6) functions as a cofactor of many diverse enzymes in amino acid metabolism. Three metabolic pathways for pyridoxal 5'-phosphate (PLP; the active form of VB6) are known: the de novo pathway, the salvage pathway, and the fungal type pathway. Most unicellular organisms and plants biosynthesize VB6 using one or two of these three biosynthetic pathways. However, animals such as insects and mammals do not possess any of the pathways and, thus, need to intake VB6 in their diet to survive. It is conceivable that breakdowns of these pathways occurred in the evolutionary lineages of insects and mammals, and one of the major reasons for this would be the loss of pertinent genes. We studied the evolution of VB6 biosynthesis from the view of the gain and loss of 10 pertinent genes in 122 species whose genome sequences were completely determined. The results revealed that each gene in the pathways was lost more than once in the entire evolutionary lineages of the 122 species. We also found the following three points regarding the evolution of PLP biosynthesis: (1) the breakdown of the PLP biosynthetic pathways occurred independently at least three times in animal lineages, (2) the de novo pathway was formed by the generation of pdxB in gamma-proteobacteria, and (3) the order of the gene loss in VB6 metabolism was conserved among different evolutionary lineages. These results suggest that the evolution of VB6 metabolism was subject to gains and frequent losses of related genes in the 122 species examined. This dynamic nature of the evolutionary changes must have been responsible for the breakdowns of the pathways, resulting in profound differentiation of heterotrophy among the species.

Animals↗

A computational study into the evolution of dual-route dynamics for affective processing.

The evolutionary justification by LeDoux (1996) for his dual-route model of fear processing was analyzed computationally by applying genetic algorithms to artificial neural networks. The evolution was simulated of a neural network controlling an agent that gathered food in an artificial world and that was occasionally menaced by a predator. Connections could not change in the agent's "lifetime," so there was no learning in the simulations. Only if the smells of food and predator were hard to distinguish and the fitness reflected time pressures in escaping from the predator did the type of dual processing postulated by LeDoux emerge in the surviving agents. Processing in the "quick and dirty" pathway of the fear system ensured avoidance of both predators and food, but a distinction between food and predator was made only in the long pathway. Elaborate processing inhibited the avoidance reaction and reversed it into an approach reaction to food, but strengthened the avoidance reaction to predators (and more finely tuned the direction of escape). It is suggested that "computational neuroethology" (Beer, 1990) may help constrain reasoning in evolutionary psychology, particularly when applied to specific neurobiological models, and in the future may even generate new hypotheses for cognitive neuroscience.

Adaptation, Biological↗

Analyzing evolutionary patterns in amniote embryonic development.

Heterochrony (differences in developmental timing between species) is a major mechanism of evolutionary change. However, the dynamic nature of development and the lack of a universal time frame makes heterochrony difficult to analyze. This has important repercussions in any developmental study that compares patterns of morphogenesis and gene expression across species. We describe a method that makes it possible to quantify timing shifts in embryonic development and to map their evolutionary history. By removing a direct dependence on traditional staging series, through the use of a relative time frame, it allows the analysis of developmental sequences across species boundaries. Applying our method to published data on vertebrate development, we identified clear patterns of heterochrony. For example, an early onset of various heart characters occurs throughout amniote evolution. This suggests that advanced (precocious) heart development arose in evolutionary history before endothermy. Our approach can be adapted to analyze other forms of comparative dynamic data, including patterns of developmental gene expression.

Age Factors↗

Drive theory revisited.

Fallacious energic formulations and phylogenetic oversimplifications have led drive theory into disfavor. However, the advantages of a drive concept based on evolutionary principles outweigh the disadvantages. A psychological drive concept best captures the innately endowed, self-enhancing motivational push compatible with evolutionary principles, while at the same time being consonant with the intrapsychic dynamics of psychoanalytic observation. Current evolutionary principles and their implications are discussed. Incorporating these principles as cogent theoretical postulates is a crucial part of maintaining a link to the natural sciences and thereby to our involvement in the great enterprise of elaborating a comprehensive psychology. To exclude these concepts is to promote a detachment from our involvement in the natural sciences and to lose a powerful heuristic guide for our theoretical endeavors.

Aggression↗

Evolutionary predictions should be based on individual-level traits.

Recent theoretical studies have analyzed the evolution of habitat specialization using either the logistic or the Ricker equation. These studies have implemented evolutionary change directly in population-level parameters such as habitat-specific intrinsic growth rates r or carrying capacities K. This approach is a shortcut to a more detailed analysis where evolutionary change is studied in underlying morphological, physiological, or behavioral traits at the level of the individual that contribute to r or K. Here we describe two pitfalls that can occur when such a shortcut is employed. First, population-level parameters that appear as independent variables in a population dynamical model might not be independent when derived from processes at the individual level. Second, patterns of covariation between individual-level traits are usually not conserved when mapped to the level of demographic parameters. Nonlinear mappings constrain the curvature of trade-offs that can sensibly be assumed at the population level. To illustrate these results, we derive a two-habitat version of the logistic and Ricker equations from individual-level processes and compare the evolutionary dynamics of habitat-specific carrying capacities with those of underlying individual-level traits contributing to the carrying capacities. Finally, we sketch how our viewpoint affects the results of earlier studies.

Animals↗

Why homeodynamics, not homeostasis?

Ideas of homeostasis derive from the concept of the organism as an open system. These ideas can be traced back to Heraclitus. Hopkins, Bernard, Hill, Cannon, Weiner and von Bertalanffy developed further the mechanistic basis of turnover of biological components, and Schoenheimer and Rittenberg were pioneers of experimental approaches to the problems of measuring pool sizes and dynamic fluxes. From the second half of the twentieth century, a biophysical theory mainly founded on self-organisation and Dynamic Systems Theory allowed us to approach the quantitative and qualitative analysis of the organised complexity that characterises living systems. This combination of theoretical framework and more refined experimental techniques revealed that feedback control of steady states is a mode of operation that, although providing stability, is only one of many modes and may be the exception rather than the rule. The concept of homeodynamics that we introduce here offers a radically new and all-embracing concept that departs from the classical homeostatic idea that emphasises the stability of the internal milieu toward perturbation. Indeed, biological systems are homeodynamic because of their ability to dynamically self-organise at bifurcation points of their behaviour where they lose stability. Consequently, they exhibit diverse behaviour; in addition to monotonic stationary states, living systems display complex behaviour with all its emergent characteristics, i.e., bistable switches, thresholds, waves, gradients, mutual entrainment, and periodic as well as chaotic behaviour, as evidenced in cellular phenomena such as dynamic (supra)molecular organisation and flux coordination. These processes may proceed on different spatial scales, as well as across time scales, from the very rapid processes within and between molecules in membranes to the slow time scales of evolutionary change. It is dynamic organisation under homeodynamic conditions that make possible the organised complexity of life.

Hemodynamics↗

Origin and evolution of sleep: roles of vision and endothermy.

The origin of both sleep and memory appears to be closely associated with the evolution of mechanisms of enhancement and maintenance of synaptic efficacy. After the origin of activity-dependent synaptic plasticity, whereby single activations of synapses led to short-term efficacy enhancements, lengthy maintenance of the enhancements probably was achieved by repetitive activations ("dynamic stabilization"). These are thought to have occurred either in the course of frequent functional use, or to have been induced spontaneously within the brain to maintain synaptic efficacies in circuits that were in infrequent use. The latter repetitive activations are referred to as 'non-utilitarian' dynamic stabilization. With the evolution of increasing repertories and complexities of behavioral and sensory capabilities-with vision usually being the vastly preeminent sense-brain complexity increased markedly. Accompanying the greater complexity, needs for storage and maintenance of hereditary and experimental information (memories) also increased greatly. It is suggested that these increases led to conflicts between sensory input processing during restful waking and concomitant 'non-utilitarian' dynamic stabilization of infrequently used memory circuits. The selective pressure for the origin of primitive sleep may have been a need to achieve greater depression of central processing of sensory inputs-largely complex visual information-than occurs during restful waking. The electrical activities of the brain during sleep (aside from those that subserve autonomic activities) may function largely to maintain sleep and to dynamically stabilize infrequently used circuitry encoding memories. Sleep may not have been the only evolutionary adaptation to conflicts between dynamic stabilization and sensory input processing. In some ectothermic vertebrates, sleep may have been postponed or rendered unnecessary by a more readily effected means of resolution of the conflicts, namely, extensive retinal processing of visual information during restful waking. By this means, processing of visual information in central regions of the brain may have been maintained at a sufficiently low level to allow adequate concomitant dynamic stabilization. As endothermy evolved, the skeletal muscle hypotonia of primitive sleep may have become insufficient to prevent sleep-disrupting skeletal muscle contractions during 'non-utilitarian' dynamic stabilization of motor circuitry at the accompanying higher body temperatures and metabolic rates. Selection against such disruption during dynamic stabilization of motor circuitry may have led to the inhibition of skeletal muscle tone during a portion of primitive sleep, the portion designated as "rapid-eye-movement sleep." Many marine mammals that are active almost continuously engage only in unihemispheric non-rapid-eye-movement sleep. They apparently do not require rapid-eye-movement sleep and accompanying 'non-utilitarian' dynamic stabilization of motor circuitry because this circuitry is in virtually continuous use. Studies of hibernation by arctic ground squirrels suggest that each hour of sleep stabilizes brain synapses for as long as four hours.

Animals↗

Pattern Categorization and Generalization with a Virtual Neuromolecular Architecture.

A multilevel neuromolecular computing architecture has been developed that provides a rich platform for evolutionary learning. The architecture comprises a network of neuron-like modules with internal dynamics modeled by cellular automata. The dynamics are motivated by the hypothesis that molecular processes operative in real neurons (in particular processes connected with second messenger signals and cytoskeleton-membrane interactions) subserve a signal integrating function. The objective is to create a repertoire of special purpose dynamic pattern processors through an evolutionary search algorithm and then to use memory manipulation algorithms to select combinations of processors from the repertoire that are capable of performing coherent pattern recognition/neurocontrol tasks. The system consists of two layers of cytoskeletally controlled (enzymatic) neurons and two layers of memory access neurons (called reference neurons) divided into a collection of functionally comparable subnets. Evolutionary learning can occur at the intraneuronal level through variations in the cytoskeletal structures responsible for the integration of signals in space and time, through variations in the location of elements that represent readin or readout proteins, and through variations in the connectivity of the neurons. The memory manipulation algorithms that orchestrate the repertoire of neuronal processors also use evolutionary search procedures. The network is capable of performing complicated pattern categorization tasks and of doing so in a manner that balances specificity and generalization. Copyright 1996 Elsevier Science Ltd.

Journal Article↗

Learning dynamics in social dilemmas.

The Nash equilibrium, the main solution concept in analytical game theory, cannot make precise predictions about the outcome of repeated mixed-motive games. Nor can it tell us much about the dynamics by which a population of players moves from one equilibrium to another. These limitations, along with concerns about the cognitive demands of forward-looking rationality, have motivated efforts to explore backward-looking alternatives to analytical game theory. Most of the effort has been invested in evolutionary models of population dynamics. We shift attention to a learning-theoretic alternative. Computational experiments with adaptive agents identify a fundamental solution concept for social dilemmas--stochastic collusion--based on a random walk from a self-limiting noncooperative equilibrium into a self-reinforcing cooperative equilibrium. However, we show that this solution is viable only within a narrow range of aspiration levels. Below the lower threshold, agents are pulled into a deficient equilibrium that is a stronger attractor than mutual cooperation. Above the upper threshold, agents are dissatisfied with mutual cooperation. Aspirations that adapt with experience (producing habituation to stimuli) do not gravitate into the window of viability; rather, they are the worst of both worlds. Habituation destabilizes cooperation and stabilizes defection. Results from the two-person problem suggest that applications to multiplex and embedded relationships will yield unexpected insights into the global dynamics of cooperation in social dilemmas.

Adaptation, Psychological↗

Recursive use of evolutionary conservation data in molecular modeling of membrane proteins A model of the multidrug H+ antiporter emrE.

Membrane proteins are currently the most biomedically important family of proteins, serving as targets for the majority of pharmaceutical agents. It is also clear that they are invariably abundant in all of the genomes sequence so far, representing up to a third of all open reading frames. Finally, and regrettably, it is clear that they are highly resistant to structural elucidation, representing less than 0.2% of the Protein Data Bank. Recent accomplishments in genome sequencing efforts, however, may help offset this imbalance through the availability of evolutionary conservation data. Herein, we develop a novel approach, utilizing a combination of evolutionary conservation data and global searching molecular dynamics simulations to model membrane proteins, deriving a model for the multidrug H+ antiporter EmrE, a transmembrane four-helix bundle. Structures resulting from an extensive, rotational molecular dynamics search, were evaluated by comparing the residue specific interaction energy and the evolutionary conservation data. Subsequent rounds of molecular dynamics, in which confinement of the search space was undertaken in order to achieve a self consistent result, point to a structure that best satisfies the evolutionary conservation data. As the conservation patterns calculated for each of the helices suggested that the different conservation pattern for helix 3 (as well as being the most conserved) might be due to the oligomeric nature of EmrE, a dodecamer of helices was constructed based on the result of a search of helix 3 as a trimer. The resulting interaction energy per residue in the final model is in reasonable agreement with the evolutionary data and consistent with recent site directed mutagenesis experiments, pointing to the strength of this method as a general tool.

Amino Acid Sequence↗

A prolegomenon for a viable evolutionary psychology--the myth and the reality: comment on Lickliter and Honeycutt (2003).

R. Lickliter and H. Honeycutt (2003) attempted to create a dynamic developmental systems theory of evolutionary psychology. In this commentary, the author argues that the quality of their reasoning, their conflation of evolution and evolution by natural selection, their failure to explain the relative importance of multilevel, epigenetic interactions, their lack of population thinking, and their failure to define adaptation undermines their endeavor.

Biological Evolution↗