SEARCH · PubMed Health

Results for “Models of evolution”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 1,135 records · Page 63Linked to original sources

PubMed2001

Chloroplast sharing in the Tasmanian eucalypts.

The biogeographic pattern of chloroplast DNA (cpDNA) haplotypes in Eucalyptus on the island of Tasmania is consistent with reticulate evolution, involving at least 12 Tasmanian species from the subgenus Symphyomyrtus. Intraspecific cpDNA polymorphism in 14 of 17 species is coupled with extensive sharing of identical haplotypes across populations of different species in the same geographic area. Haplotype diversity is lowest in central regions of Tasmania formerly occupied by alpine vegetation during glacial intervals and in northern regions that were periodically linked to continental Australia by land bridges. The observed distribution of several cpDNA haplotypes unique to Tasmania coincides with modeled locations of glacial refugia in coastal areas of Tasmania and shows the power of cpDNA in unraveling the complex history of past distributions of Eucalyptus. The results suggest that the model of evolution of the eucalypts should be reassessed to allow for the anastomosing effects of interspecific hybridization and introgression.

Base Sequence↗

PubMed2003

Toward a realistic model of mutations affecting fitness.

Analysis of a recent mutation accumulation (MA) experiment has led to the suggestion that as many as one-half of spontaneous mutations in Arabidopsis are advantageous for fitness. We evaluate this in the light of data from other MA experiments, along with molecular evidence, that suggest the vast majority of new mutations are deleterious.

Animals↗

PubMed2004

Kin discrimination and sex ratios in a parasitoid wasp.

Sex ratio theory provides a clear and simple way to test if nonsocial haplodiploid wasps can discriminate between kin and nonkin. Specifically, if females can discriminate siblings from nonrelatives, then they are expected to produce a higher proportion of daughters if they mate with a sibling. This prediction arises because in haplodiploids, inbreeding (sib-mating) causes a mother to be relatively more related to her daughters than her sons. Here we formally model this prediction for when multiple females lay eggs in a patch, and test it with the parasitoid wasp Nasonia vitripennis. Our results show that females do not adjust their sex ratio behaviour dependent upon whether they mate with a sibling or nonrelative, in response to either direct genetic or a range of indirect environmental cues. This suggests that females of N. vitripennis cannot discriminate between kin and nonkin. The implications of our results for the understanding of sex ratio and social evolution are discussed.

Animals↗

PubMed2000

Flower color variation: a model for the experimental study of evolution.

We review the study of flower color polymorphisms in the morning glory as a model for the analysis of adaptation. The pathway involved in the determination of flower color phenotype is traced from the molecular and genetic levels to the phenotypic level. Many of the genes that determine the enzymatic components of flavonoid biosynthesis are redundant, but, despite this complexity, it is possible to associate discrete floral phenotypes with individual genes. An important finding is that almost all of the mutations that determine phenotypic differences are the result of transposon insertions. Thus, the flower color diversity seized on by early human domesticators of this plant is a consequence of the rich variety of mobile elements that reside in the morning glory genome. We then consider a long history of research aimed at uncovering the ecological fate of these various flower phenotypes in the southeastern U.S. A large body of work has shown that insect pollinators discriminate against white phenotypes when white flowers are rare in populations. Because the plant is self-compatible, pollinator bias causes an increase in self-fertilization in white maternal plants, which should lead to an increase in the frequency of white genes, according to modifier gene theory. Studies of geographical distributions indicate other, as yet undiscovered, disadvantages associated with the white phenotype. The ultimate goal of connecting ecology to molecular genetics through the medium of phenotype is yet to be attained, but this approach may represent a model for analyzing the translation between these two levels of biological organization.

Journal Article↗

PubMed2006

Mean curvature versus normality: a comparison of two approximations of Fisher's geometrical model.

Fisher's geometrical model amounts to a description of mutation and selection for individuals characterised by a number of quantitative traits. In the present work the fitness landscape is not assumed to be spherically symmetric, hence different points, i.e. phenotypes, on a surface of constant fitness generally have different curvatures. We investigate two different approximations of Fisher's geometrical model that have appeared in the literature. One approximation uses the average curvature of the fitness surface at the parental phenotype. The other approach is based on a normal approximation of a distribution associated with new mutations. Analytical results and simulations are used to compare the accuracy of the two approximations.

Adaptation, Biological↗

PubMed2006

Adaptive dynamics: Modelling Darwin's divergence principle.

A model illustrating Darwin's divergence principle is presented. It shows how competition for resources can explain evolutionary branching. It is based on an assumption of degenerate competition. Mathematically, it is a partial differential equation with an integral term, and it describes a new mechanism of self-organization.

Adaptation, Biological↗

PubMed1977

A new index for the intensity of natural selection.

A new index for the intensity of natural selection is proposed, based upon the double exponential model for fitness functions. This index is defined as a variance and is such that a value of zero indicates no selection while a value of one indicates quite strong selection. The use of the index is demonstrated using published data on the survival of human infants with different birth weights and gestation times.

Biological Evolution↗

PubMed1984

A model for human colon carcinoma evolution based on the differential response of cultured preneoplastic, premalignant, and malignant cells to 12-O-tetradecanoylphorbol-13-acetate.

Small colonic adenocarcinomas can be found in focal areas within benign tumors (adenomas), strongly suggesting an adenoma-to-carcinoma sequence. The induction of plasminogen activator (PA) secretion by the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) has been used to order histologically distinct classes of human colonic adenomas in primary culture into a sequence from the most benign to the most advanced premalignant state. This ordering is based on the observation that each of five carcinomas examined in an earlier study by E. A. Friedman (Cancer Res., 41: 4588-4599, 1981) and each of seven carcinomas tested in this study released PA in response to TPA, inducing easily scored morphological alterations. Benign tumors either resembled carcinomas in their response to TPA or exhibited no morphological changes. The most benign adenomas by histopathology criteria were the small pure tubular adenomas without dysplasia. Six of seven of these adenomas did not secrete PA in response to TPA. We concluded that malignant cells had acquired the ability to respond to TPA by PA secretion, while tubular adenoma cells were not an advanced enough preneoplastic stage to so respond. TPA treatment of two cultured villous adenomas, one with infiltrating carcinoma and one with focus of moderately dysplastic cells, in the presence of low serum to decrease the plasmin concentration, demonstrated that only a subpopulation of cells secreted PA. Local areas of the monolayer were morphologically altered by the protease, forming clusters of cells loosely attached to the dish. The presence of such subpopulations within cultured adenomas was demonstrated by screening an additional five villous adenomas, 15 villotubular adenomas, and 11 tubular adenomas. The presence of dysplastic cells in 23 of 24 cases correlated with PA secretion. A subpopulation of villous cells, in the absence of dysplastic cells in each of three cases, also secreted PA. We conclude that, during tumor evolution, this villous subpopulation is the first preneoplastic cell type to acquire responsiveness to TPA by PA secretion. This property is maintained as the cells further evolve through premalignant dysplastic stages to carcinoma.

Adenoma↗

PubMed2006

Evolution of resistance to cancer therapy.

Acquired drug resistance is a major limitation for successful treatment of cancer. Resistance emerges due to drug exclusion, drug metabolism and alteration of the drug target by mutation or overexpression. Depending on therapy, the type of cancer and its stage, one or several genetic or epigenetic alterations are necessary to confer resistance to treatment. The fundamental question is the following: if a genetically diverse population of replicating cancer cells is subjected to chemotherapy that has the potential to eradicate it, what is the probability of emergence of resistance? Here, we review a general mathematical framework based on multi-type branching processes designed to study the dynamics of escape of replicating organisms from selection pressures. We apply the general model to evolution of resistance of cancer cells and discuss examples for diverse mechanisms of resistance. Our theory shows how to estimate the probability of success for any treatment regimen.

Animals↗

PubMed2005

Temporal analysis of tissue displacement induced by a transient ultrasound radiation force.

One of the stress sources that can be used in dynamic elastography imaging methods is the acoustic radiation force. However, displacements of the medium induced by this stress field are generally not fully understood in terms of spatial distribution and temporal evolution. A model has been developed based on the elastodynamic Green's function describing the different acoustic waves generated by focused ultrasound. The function is composed of three terms: two far-field terms, which correspond to a purely longitudinal compression wave and a purely transverse shear wave, and a coupling near-field term which has a longitudinal component and a transverse component. For propagation distances in the shear wavelength range, the predominant term is the near field term. The displacement duration corresponds to the propagation duration of the shear wave between the farthest source point and the observation point. This time therefore depends on the source size and the local shear modulus of the tissue. Evolution of the displacement/time curve profile, which is directly linked to spatial and temporal source profiles, is computed at different radial distances, for different durations of force applications and different shear elastic coefficients. Experimental results performed with an optical interferometric method in a homogeneous tissue-mimicking phantom agreed with the theoretical profiles.

Acoustics↗

PubMed1991

Demographic predisposition to the evolution of eusociality: a hierarchy of models.

I present a hierarchy of models that illustrate, within the framework of inclusive fitness theory, how demographic factors can predispose a species to the evolution of eusociality. Delayed reproductive maturation lowers the inclusive fitness of a solitary foundress relative to that of a worker. Variation in age at reproductive maturity makes the worker strategy more profitable to some individuals than to others and thus predicts the coexistence of single-foundress and multiple-foundress nesting associations. Delayed reproductive maturation and variation in age at reproductive maturity also select for mixed reproductive strategies so that some individuals whose reproductive maturation is expected to be delayed can first act as workers and later switch over to the role of a queen or foundress. Assured fitness returns shows how identical mortality rates can have different consequences for workers and solitary nest foundresses because a solitary foundress will have to necessarily survive for the entire duration of development of her brood, whereas a worker can hope to get proportional fitness returns for short periods of work. In concert with assured fitness returns, delayed reproductive maturation and variation in age at reproductive maturity become more powerful in selecting for worker behavior, and mixed reproductive strategies become available to a wider range of individuals. These phenomena provide a consistently more powerful selective advantage for the worker strategy than do genetic asymmetries created by haplodiploidy.

Animals↗

PubMed2005

A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome.

Most reported examples of change in vertebrate mitochondrial (mt) gene order could be explained by a tandem duplication followed by random loss of redundant genes (tandem duplication-random loss [TDRL] model). Under this model of evolution, independent loss of genes arising from a single duplication in an ancestral species are predicted, and remnant pseudogenes expected, intermediate states that may remain in rearranged genomes. However, evidence for this is rare and largely scattered across vertebrate lineages. Here, we report new derived mt gene orders in the vertebrate "WANCY" region of four closely related caecilian amphibians. The novel arrangements found in this genomic region (one of them is convergent with the derived arrangement of marsupials), presence of pseudogenes, and positions of intergenic spacers fully satisfy predictions from the TDRL model. Our results, together with comparative data for the available vertebrate complete mt genomes, provide further evidence that the WANCY genomic region is a hotspot for gene order rearrangements and support the view that TDRL is the dominant mechanism of gene order rearrangement in vertebrate mt genomes. Convergent gene rearrangements are not unlikely in hotspots of gene order rearrangement by TDRL.

Amphibians↗

PubMed1993

The origin of genetic information: viruses as models.

A living entity can be described as a complex adaptive system which differs from any, however complex, chemical structure by its capability of functional self-organization based on the processing of information. If one asks, where does this information come from and what is its primary semantics, the answer is: information generates itself in feedback loops via replication and selection, the objective being 'to be or not to be'. This paper describes the theoretical framework of information-generating systems and provides experimental clues for some basic forms of genetic organization, such as molecular quasi-species, hypercyclic and compartmentalized RNA-protein assemblies. The results are primarily obtained with RNA viruses and virus-like systems. The experiments are carried out with the help of automated, computer-controlled bioreactors, called 'evolution machines', that may form the basis of a new 'evolutionary biotechnology'.

Base Sequence↗

PubMed2004

ADAPT: a developmental, asemantic, and procedural model for transcoding from verbal to arabic numerals.

This article presents a new model of transcoding numbers from verbal to arabic form. This model, called ADAPT, is developmental, asemantic, and procedural. The authors' main proposal is that the transcoding process shifts from an algorithmic strategy to the direct retrieval from memory of digital forms. Thus, the model is evolutive, adaptive, and particularly suited to account for learning and development. ADAPT, which has been implemented in a computer program, accounts for existing and new developmental data, for new data in adolescents with mild retardation, and for the neuropsychological cases described in the literature.

Aphasia↗

PubMed1989

Evolution of alpha-satellite DNA on human acrocentric chromosomes.

In situ hybridization of five new and one previously described alpha-satellite sequences isolated from chromosome 21 libraries gave the following chromosomal distribution patterns: (a) two sequences (pTRA-1 and -4) hybridizing to chromosomes 13, 14, 15, 21, and 22 (also 19 and 20); (b) one sequence (pTRA-7) hybridizing to chromosome 14; and (c) three sequences (pTRA-2, -11 and -15) hybridizing to chromosomes 13, 14, and 21, with significant but weaker signals on 15 and 22. These results suggested the sharing of alphoid domains between different acrocentric chromosomes and the coexistence of multiple domains on each chromosome. Analysis of somatic cell hybrids carrying a single human acrocentric chromosome using pTRA-2 demonstrated a higher-order repeating structure common to chromosomes 13, 14, and 21, but not to 15 and 22, providing direct evidence for sequence homogenization in this domain among the former three chromosomes. We present a model of evolution and genetic exchange of alpha sequences on the acrocentric chromosomes which can satisfactorily explain these and previous observations of (a) two different alphoid subfamilies, one common to chromosomes 13 and 21 and the other common to chromosomes 14 and 22, (b) a different alphoid subfamily on chromosome 22, and (c) nonrandom participation of chromosomes 13 and 14, and 14 and 21 in Robertsonian translocations.

Blotting, Southern↗

PubMed2006

Payoff-monotonic game dynamics and the maximum clique problem.

Evolutionary game-theoretic models and, in particular, the so-called replicator equations have recently proven to be remarkably effective at approximately solving the maximum clique and related problems. The approach is centered around a classic result from graph theory that formulates the maximum clique problem as a standard (continuous) quadratic program and exploits the dynamical properties of these models, which, under a certain symmetry assumption, possess a Lyapunov function. In this letter, we generalize previous work along these lines in several respects. We introduce a wide family of game-dynamic equations known as payoff-monotonic dynamics, of which replicator dynamics are a special instance, and show that they enjoy precisely the same dynamical properties as standard replicator equations. These properties make any member of this family a potential heuristic for solving standard quadratic programs and, in particular, the maximum clique problem. Extensive simulations, performed on random as well as DIMACS benchmark graphs, show that this class contains dynamics that are considerably faster than and at least as accurate as replicator equations. One problem associated with these models, however, relates to their inability to escape from poor local solutions. To overcome this drawback, we focus on a particular subclass of payoff-monotonic dynamics used to model the evolution of behavior via imitation processes and study the stability of their equilibria when a regularization parameter is allowed to take on negative values. A detailed analysis of these properties suggests a whole class of annealed imitation heuristics for the maximum clique problem, which are based on the idea of varying the parameter during the imitation optimization process in a principled way, so as to avoid unwanted inefficient solutions. Experiments show that the proposed annealing procedure does help to avoid poor local optima by initially driving the dynamics toward promising regions in state space. Furthermore, the models outperform state-of-the-art neural network algorithms for maximum clique, such as mean field annealing, and compare well with powerful continuous-based heuristics.

Journal Article↗

PubMed2002

Potential applications and pitfalls of Bayesian inference of phylogeny.

Only recently has Bayesian inference of phylogeny been proposed. The method is now a practical alternative to the other methods; indeed, the method appears to possess advantages over the other methods in terms of ability to use complex models of evolution, ease of interpretation of the results, and computational efficiency. However, the method should be used cautiously. The results of a Bayesian analysis should be examined with respect to the sensitivity of the results to the priors used and the reliability of the Markov chain Monte Carlo approximation of the probabilities of trees.

Bayes Theorem↗

PubMed1985

Chromatographic separation as selection process for prebiotic evolution and the origin of the genetic code.

A model for the evolution of a translation apparatus has been suggested where oligonucleotides in a hairpin conformation act as primordial adapters. Specifically activated amino acids are assumed to be attached to these hairpin molecules. For the specific activation, a chromatographic separation of, e.g. ala and CMP from gly and GMP can be accomplished on silica (e.g. of volcanic origin) with aqueous salt solutions. Other adsorbents like clays (kaolin, bentonite, montmorillonite), different silicates (florisil, magnesium trisilicate, calcium silicate, talc), hydroxyapatite, barium sulfate, calcium carbonate, calcium fluoride and titanoxide have been examined as model systems for the separation of nucleotides, nucleosides and amino acids on mineral surfaces. The possible role of chromatographic separation of amino acids for the formation of proteinoids, composed of selected amino acids, is also considered.

Amino Acids↗