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 1,261 records · Page 70Linked to original sources

Mutation-based genetic neural network.

Evolving gradient-learning artificial neural networks (ANNs) using an evolutionary algorithm (EA) is a popular approach to address the local optima and design problems of ANN. The typical approach is to combine the strength of backpropagation (BP) in weight learning and EA's capability of searching the architecture space. However, the BP's "gradient descent" approach requires a highly computer-intensive operation that relatively restricts the search coverage of EA by compelling it to use a small population size. To address this problem, we utilized mutation-based genetic neural network (MGNN) to replace BP by using the mutation strategy of local adaptation of evolutionary programming (EP) to effect weight learning. The MGNN's mutation enables the network to dynamically evolve its structure and adapt its weights at the same time. Moreover, MGNN's EP-based encoding scheme allows for a flexible and less restricted formulation of the fitness function and makes fitness computation fast and efficient. This makes it feasible to use larger population sizes and allows MGNN to have a relatively wide search coverage of the architecture space. MGNN implements a stopping criterion where overfitness occurrences are monitored through "sliding-windows" to avoid premature learning and overlearning. Statistical analysis of its performance to some well-known classification problems demonstrate its good generalization capability. It also reveals that locally adapting or scheduling the strategy parameters embedded in each individual network may provide a proper balance between the local and global searching capabilities of MGNN.

Algorithms↗

Prediction and biological evolution. Concept paper.

The major issue addressed was how to introduce evolutionary thinking into epidemiology, and the appropriate approach to "evolutionary epidemiology." There was general agreement that disease emergence is not a static but a dynamic process, and that dynamic approaches should therefore be emphasized.

Biological Evolution↗

Form follows function: how muscle shape is regulated by work.

What determines the shape, size, and force output of cardiac and skeletal muscle? Chicago architect Louis Sullivan (1856-1924), father of the skyscraper, observed that "form follows function." This is as true for the structural elements of a striated muscle cell as it is for the architectural features of a building. Function is a critical evolutionary determinant, not form. To survive, the animal has evolved muscles with the capacity for dynamic responses to altered functional demand. For example, work against an increased load leads to increased mass and cross-sectional area (hypertrophy), which is directly proportional to an increased potential for force production. Thus a cell has the capacity to alter its shape as well as its volume in response to a need for altered force production. Muscle function relies primarily on an organized assembly of contractile and other sarcomeric proteins. From analysis of homogenized cells and molecular and biochemical assays, we have learned about transcription, translation, and posttranslational processes that underlie protein synthesis but still have done little in addressing the important questions of shape or regional cell growth. Skeletal muscles only grow in length as the bones grow; therefore, most studies of adult hypertrophy really only involve increased cross-sectional area. The heart chamber, however, can extend in both longitudinal and transverse directions, and cardiac cells can grow in length and width. We know little about the regulation of these directional processes that appear as a cell gets larger with hypertrophy or smaller with atrophy. This review gives a brief overview of the regulation of cell shape and the composition and aggregation of contractile proteins into filaments, the sarcomere, and myofibrils. We examine how mechanical activity regulates the turnover and exchange of contraction proteins. Finally, we suggest what kinds of experiments are needed to answer these fundamental questions about the regulation of muscle cell shape.

Adult↗

Dynamic behaviour of the B12 riboswitch.

Riboswitches are RNA segments that serve as ligand-responsive genetic control elements. They modulate the expression of certain genes in response to changing concentrations of metabolites. In this paper, we study the dynamic behaviour of the B12 riboswitch in E. coli--perhaps the most widely studied and best known of all riboswitches--through a mathematical model of its regulatory pathway. To carry this out, we simulate dynamic experiments in which the bacterial B12 uptake capacity is measured after being depleted of this vitamin for a long time. The results of these simulations compare favourably with reported experimental data. The model also predicts that an overshoot of intracellular B12 should be observed if the replenishment experiments were to be carried out for longer times. This behaviour is discussed in terms of a possible evolutionary advantage for E. coli, together with the fact that regulation at the transcriptional and translational levels is almost equivalent dynamically.

Biophysics↗

The radiography essentials: an evolutionary perspective.

A review of all the Radiography Essentials since their inception in 1944 provides an insightful look into the history and dynamics of entry-level educational standards in radiography. As successive Essentials have been revised, more attention has been given to the clinical environment, a broadened and strengthened curricula and due process. Additionally, radiographers have gained greater autonomy in delivering professional entry-level education in radiography.

Curriculum↗

Micro-Mar: a database for dynamic representation of marine microbial biodiversity.

BACKGROUND: The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes. DESCRIPTION: The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for biogeographical and ecological analyses. The database currently includes 11874 sequences corresponding to high resolution taxonomic genes (16S rRNA, ITS and 23S rRNA) and many other genes including CDS of marine prokaryotes together with available biogeographical and ecological information. CONCLUSION: The database aims to integrate molecular data and taxonomic affiliation with biogeographical and ecological features that will allow to have a dynamic representation of the marine microbial diversity embedded in a user friendly web interface. It is available online at http://egg.umh.es/micromar/.

Base Sequence↗

Concerted motions in the photoactive yellow protein.

Molecular dynamics simulations have been performed with the aim of identifying concerted backbone motions in the photoactive yellow protein. Application of the essential dynamics method revealed large, chromophore-linked fluctuations of the protein in the ground state, as well as in a form containing the isomerized chromophore. Various loops become more mobile upon isomerization of the chromophore, including a loop which is part of the PAS domain motif, found in light perception proteins. The hinge points identified in these fluctuations correlate with the positions of evolutionary conserved glycines. The results derived from the simulations directly correlate with available experimental data, provide a framework for understanding the dynamic behaviour of the yellow protein and give clues to subsequent steps in the signal transduction pathway.

Amino Acid Sequence↗

The evolutionary origin of genetic instability in cancer development.

The standard model of carcinogenesis is currently being questioned. The main controversy concerns genetic instability and has links to fundamental questions in evolutionary biology. This paper aims to clarify the underlying conflict between the linear configuration of the standard model and the non-linear dynamics of Darwinian evolution. It addresses the problem of applying the concept of clonal selection to genetically unstable cells and presents an alternative perspective based on the principles of molecular evolution. This model explains genetic instability in terms of competition between genetic strategies and draws lines to basic aspects of evolutionary biology.

Animals↗

Complex limiting behaviour of multilocus genetic systems in cyclical environments.

Here we demonstrate that complex limiting behaviour (supercycles and chaotic-like phenomena) may arise in a rather broad and natural class of multilocus systems, both haploid and diploid, experiencing stabilizing selection with cyclically varying optima over a short period. These include loci with purely additive, dominant, or semidominant effects, with different types of their chromosome distribution. The observed complex dynamics appeared to manifest a certain stability with respect to disturbances of parameters specifying the structure of the selected system and environmental characteristics. This mode of multilocus dynamics by far exceeds the potential attainable under ordinary selection models resulting in simple behaviour. It may represent a novel evolutionary mechanism increasing genetic diversity over long time periods. This novel mechanism could contribute to the observation that biological diversity has increased over geological time regardless of the well-known massive extinctions.

Animals↗

Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family.

Molecular dynamics simulations of representative mesophilic and psycrophilic elastases have been carried out at different temperatures to explore the molecular basis of cold adaptation inside a specific enzymatic family. The molecular dynamics trajectories have been compared and analyzed in terms of secondary structure, molecular flexibility, intramolecular and protein-solvent interactions, unravelling molecular features relevant to rationalize the efficient catalytic activity of psychrophilic elastases at low temperature. The comparative molecular dynamics investigation reveals that modulation of the number of protein-solvent interactions is not the evolutionary strategy followed by the psycrophilic elastase to enhance catalytic activity at low temperature. In addition, flexibility and solvent accessibility of the residues forming the catalytic triad and the specificity pocket are comparable in the cold- and warm-adapted enzymes. Instead, loop regions with different amino acid composition in the two enzymes, and clustered around the active site or the specificity pocket, are characterized by enhanced flexibility in the cold-adapted enzyme. Remarkably, the psycrophilic elastase is characterized by reduced flexibility, when compared to the mesophilic counterpart, in some scattered regions distant from the functional sites, in agreement with hypothesis suggesting that local rigidity in regions far from functional sites can be beneficial for the catalytic activity of psychrophilic enzymes.

Acclimatization↗

Emerging pathogens: the epidemiology and evolution of species jumps.

Novel pathogens continue to emerge in human, domestic animal, wildlife and plant populations, yet the population dynamics of this kind of biological invasion remain poorly understood. Here, we consider the epidemiological and evolutionary processes underlying the initial introduction and subsequent spread of a pathogen in a new host population, with special reference to pathogens that originate by jumping from one host species to another. We conclude that, although pathogen emergence is inherently unpredictable, emerging pathogens tend to share some common traits, and that directly transmitted RNA viruses might be the pathogens that are most likely to jump between host species.

Journal Article↗

Density-dependent host choice by disease vectors: epidemiological implications of the ideal free distribution.

The proportion of vector blood meals taken on humans (the human blood index, h) appears as a squared term in classical expressions of the basic reproduction ratio (R(0)) for vector-borne infections. Consequently, R(0) varies non-linearly with h. Estimates of h, however, constitute mere snapshots of a parameter that is predicted, from evolutionary theory, to vary with vector and host abundance. We test this prediction using a population dynamics model of river blindness assuming that, before initiation of vector control or chemotherapy, recorded measures of vector density and human infection accurately represent endemic equilibrium. We obtain values of h that satisfy the condition that the effective reproduction ratio (R(e)) must equal 1 at equilibrium. Values of h thus obtained decrease with vector density, decrease with the vector:human ratio and make R(0) respond non-linearly rather than increase linearly with vector density. We conclude that if vectors are less able to obtain human blood meals as their density increases, antivectorial measures may not lead to proportional reductions in R(0) until very low vector levels are achieved. Density dependence in the contact rate of infectious diseases transmitted by insects may be an important non-linear process with implications for their epidemiology and control.

Animals↗

Genes and the physics of the DNA double-helix.

The processing of the genetic information stored in the double-helical DNA implies the separation of the two strands, the physics of which is described by the helix-coil transition model. Is there a relationship between genetic maps and DNA physical stability maps that plot the sequence-specific propensity for the thermal disruption of the double-helix? Here, with appropriate methodological formulations, such maps are derived for a large set of sequences, including complete genomes. The superposition of the two maps leads to a contrasted picture with correlations ranging between two extremes: from almost perfect (with the genes precisely delineated as stable regions) to more or less complete unrelatedness. The simplest explanation for the results is that the observed striking correlations correspond to the relics of a primeval organisation of the genetic message, with the physics of DNA playing a role in the delimitation of coding regions. In order to trace the evolutionary fate of this signal further, a detailed study of the yeast complete genome is performed. In this study, the superposition of the genetic and physical stability maps is examined in the light of information concerning gene duplication. On the basis of this analysis it is concluded that the 'signature' associated with the supposed archaic signal is in the process of being erased, most probably because the underlying feature is no longer under selective pressure. There are many evolutionary implications for the results presented and for their proposed interpretations, notably concerning models of mutational dynamics in relation to erasure processes.

Algorithms↗

The life of form. Emergent patterns of morphological transformation.

The problem of biological form remains unresolved despite the known details of gene activities in embryonic development. Segmentation is discussed in connection with observed gene activities and the question of generic regularities across phyla. The sciences of complexity and nonlinear dynamics are considered as contexts for the exploration of constraints at both the level of genetic networks and morphogenesis. A new model of morphogenetic constraints coupled to dynamic attractors is proposed as an approach to the question--how to unite the contingencies of evolutionary genetic changes with the emergent regularities of organismic morphologies?

Animals↗

Cloning of inversion breakpoints in the Anopheles gambiae complex traces a transposable element at the inversion junction.

Anopheles arabiensis, one of the two most potent malaria vectors of the gambiae complex, is characterized by the presence of chromosomal paracentric inversions. Elucidation of the nature and the dynamics of these inversions is of paramount importance for the understanding of the population genetics and evolutionary biology of this mosquito and of the impact on malaria epidemiology. We report here the cloning of the breakpoints of the naturally occurring polymorphic inversion 2Rd' of A. arabiensis. A cDNA clone that cytologically mapped on the proximal breakpoint was the starting material for the isolation of a cosmid clone that spanned the breakpoint. Analysis of the surrounding sequences demonstrated that adjacent to the distal breakpoint lies a repetitive element that exhibits distinct distribution in different A. arabiensis strains. Sequencing analysis of that area revealed elements characteristic of transposable element terminal repeats. We called this presumed transposable element Odysseus. The presence of Odysseus at the junction of the naturally occuring inversion 2Rd' suggests that the inversion may be the result of the transposable element's activity. Characteristics of Odysseus' terminal region as well as its cytological distribution in different strains may indicate a relatively recent activity of Odysseus.

Animals↗

Private and collective interests; conflicts and solutions: the central theme of current thinking in evolutionary biology.

The statement made by the population geneticist Theodosius Dobzhansky (1973): "Nothing in Biology Makes Sense Except in the Light of Evolution", is often quoted as a crucially important generalization on the nature of biology. I am inclined to consider as equally important the statement: "Nothing in Evolutionary Biology Makes Sense Except in the Light of Conflicts between Parts and Systems." This generalization takes account of the dynamic nature of biological phenomena, but also of the fact that the study of transitions from autonomous units to cooperative systems has become one of the most exciting and scientifically rewarding enterprises in all of organismic biology. The problems encountered and the speculations generated in the course of this enterprise will be either of the more unit-centered or of the more system-centered type, most biologists tending to lean towards one or the other. This explains why evolutionary biology is fraught with so many antagonistic attitudes and polarizing points of view. In this essay I want specifically to draw attention to and discuss the following issues which in recent years have polarized biologists: the dual nature of genes; the logic of Hamilton's rule; the relationship between kin selection, signalling networks and systemic manipulation; the semantic problem of progress in evolution; and the evolutionary consequences of the vastly differing time scales over which genotypic and phenotypic information processing occurs in higher animals.

Journal Article↗

Genomic erosion in the assessment of species' extinction risk and recovery potential.

Many species are undergoing rapid population declines and environmental deterioration, leading to genomic erosion. Here we define genomic erosion as the loss of genetic diversity, accumulation of deleterious mutations, maladaptation, and introgression, all of which can undermine individual fitness and long-term population viability. Critically, this process continues even after demographic recovery due to a time-lagged impact of genetic drift, which is known as drift debt. Current conservation assessments, such as the International Union for Conservation of Nature Red List, focus on short-term extinction risk and do not capture the long-term consequences of genomic erosion. Likewise, the longer-term assessments of the International Union for Conservation of Nature Green Status may overestimate population recovery by failing to account for the enduring effects of genomic erosion. As genome sequencing becomes increasingly accessible, there is a growing opportunity to quantify genomic erosion and integrate it into conservation planning. Here, we use genomic simulations to illustrate how different genomic metrics are sensitive to the drift debt. We test how ancestral effective population size (Ne) and bottleneck history influence the tempo and severity of genomic erosion. Furthermore, we demonstrate how these dynamics shape genetic load and additive genetic variation, which are key indicators of long-term evolutionary potential. Finally, we present a proof-of-concept for a Genomic Green Status framework that aligns genomic metrics with conservation impact assessments, laying the foundation for genomics-informed strategies to support species recovery.

Extinction, Biological↗