PubMed Health⌕ Search

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 1,243 records · Page 69Linked to original sources
PubMed1995

The maximum information principle and the evolution of nucleotide sequences.

The probability distributions of bases in nucleotide sequences are deduced from the maximum information principle by maximizing the entropy (due to random mutation of bases) under certain constraints (Markovian entropy, G + C content, etc, due to selection). Two formulations are given with respect to different selective constraints. The deviations of theoretical distributions from experimental data are lower than 10% for most sequences. It is shown that the Lagrange multipliers change from species to species systematically--i.e. selective constraints correlate with evolution.

Animals↗
PubMed1995

Entropy, irreversibility and evolution.

The Second Law of Thermodynamics is investigated with respect to its value as an indicator of the direction of the evolutionary process. Non-thermodynamic entropy concepts and possible errors in the use of thermodynamic entropy are discussed. The importance of genuine thermodynamic potentials and their correct application for understanding processes is emphasized. There is no direct connection between evolutionary events such as speciation and thermodynamic entropy changes; the irreversibility of evolution is not a consequence of thermodynamic irreversibility.

Animals↗
PubMed1995

Analytical solutions of the dinucleotide probability after and before random mutations.

The mutation process is a classical evolutionary genetic process mainly based on the (random) substitutions of one base (A = Adenine, C = Cytosine, G = Guanine, T = Thymine) for another. Two analytical solutions derived here allow us to analyse in genes the occurrence probabilities of motifs (e.g. dinucleotides) after substitutions (in the evolutionary sense: from the past to the present) and, unexpectedly, also before substitutions (after back substitutions, in the inverse evolutionary sense: from the present to the past). We generalize on the alphabet [A, C, G, T] of the analytical solutions and of the properties derived on the alphabet [R, Y] (R = purine = A or G, Y = pyrimidine = C or T). Application of the theory is based on the analytical solution giving the probabilities of the 16 dinucleotides AA, ..., TT in the protein (coding) genes of (nuclear) eukaryotes, viruses and prokaryotes and in (eukaryotic) introns after back substitutions (called primitive genes). After back substitutions, four of 16 dinucleotides--CG, TA, GT and AC--occur with low probabilities in each of these four primitive gene populations, except for CG in the primitive prokaryotic protein genes. In the primitive eukaryotic protein genes, the dinucleotide AT has also a significant low probability. We present the properties of the two analytical solutions, and the functions which may have these five dinucleotides in primitive genes are described in terms of biological signals.

Animals↗
PubMed1996

Addition of Darwin's third dimension to phyletic trees.

A three-dimensional (3D) approach for visualizing the phyletic relationship of living animals is proposed and developed as an alternative to current two-dimensional (2D) evolutionary trees. The 3D tree enhances visualization and qualitative analysis since it simultaneously provides topological (tree-structure) and spatial information (based upon genetically measured distances). However, the meaning of the third dimension, particularly its relationship to temporal processes, and further quantitative analyses emerge as open questions. Our method consists of two phases. First, a 3D representation of the genetic relationships of a related group of extant animals is produced using an optimization algorithm developed here. Second, linear connections are added to suggest a visual representation of the differing evolutionary trajectories of the organisms involved on the basis of a 2D tree algorithm. The method is applied to a set of distantly related Caenophidian snakes, and the resulting relationships are analysed. The discussions here are meant to stimulate the generation of 3D trees in the goal of complementing standard 2D views and, perhaps ultimately, improving our classification of evolutionary relationships.

Algorithms↗
PubMed1997

Non-independence in statistical tests for discrete cross-species data.

The paper described three previously undetected effects, due to biases and non-independence, that can arise in statistical tests for associations between character states in cross-species data. One kind, which we call the family problem, is general to all known methods. In phytogenetic data, the ancestral character state from which changes occur, or below which variation is found, is likely to be the same for many regions of the tree. The family problem interacts with two kinds of non-independence that arise because of the methods of reconstruction of character states that existing tests use. Different kinds of non-independence arise in methods that reconstruct joint, or single, character states, respectively. Methods, like Ridley's (1983), that work with joint character states suffer from the problem that a character state cannot change to itself with parsimony. Other methods that work with single character states suffer from the problem that within a locally variable region of the tree it is more likely with null data that there will be two single changes in the two characters in separate branches than one double change in both; associations opposite to the locally ancestral state are therefore likely to be found in more than 50% of the variable regions. In real data sets, the family problem acts to spotlight the other kinds of bias: if the family problem is large the bias in tests due to the way they reconstruct characters will be large, whereas if it is small, the local biases tend to cancel and disappear in the aggregate.

Adaptation, Physiological↗
PubMed1999

Arms Races, Conflict Costs and Evolutionary Dynamics.

In conflicts and fights, the winner is often determined by the difference in resource-holding potential, e.g. size, weaponry, strength (RHP). I model the evolution of RHP in a symmetric game with continuous strategies. I show that there is a convergence stable ESS level of RHP if the cost of the trait increases faster than linearly, and that this is the only solution if the cost increases fast enough with RHP. Otherwise with slowly increasing cost, the solution is a cyclically fluctuating level of RHP. It is also shown that if the cost increases linearly with RHP, the only solution to the game is neutrally stable cycles, the amplitude determined by the initial conditions. The cycles come about because in a population drawn into an arms race of RHP, individuals after a while suffer costs so high that mutants with the lowest possible armament level may invade. Copyright 1999 Academic Press.

Journal Article↗
PubMed1999

Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm.

The design of metabolic pathways is thought to be the result of an optimization process such that the structure of contemporary metabolic routes maximizes a particular objective function. Recently, it has been shown that some essential stoichiometric properties of glycolysis can be explained on the basis of the requirement for a high ATP production rate. Because the number of stoichiometrically feasible designs increases strongly with the number of reactions involved, a systematic analysis of all the possibilities turns out to be inaccessible beyond a certain system size. We present, therefore, an alternative approach to compute in a more efficient way the optimal design of glycolysis interacting with an external ATP-consuming reaction. The algorithm is based on the laws of evolution by natural selection, and may be viewed as a particular version of evolutionary algorithms. The following conclusions are derived: (a) evolutionary algorithms are very useful search strategies in determining optimal stoichiometries of metabolic pathways. (b) Essential topological features of the glycolytic network may be explained on the basis of flux optimization. (c) There is a strong interrelation between the optimal stoichiometries and the thermodynamic and kinetic properties of the participating reactions. (d) Some subsequences of reactions in optimal pathways are strongly conserved at variation of system parameters, which may be understood by applying principles of metabolic control analysis.

Adenosine Triphosphatases↗
PubMed2001

Evolutionary stability concepts for N-species frequency-dependent interactions.

The classical static concept of an evolutionarily stable strategy (ESS) for a single species gives rise to two new notions when there are more than two species (called an N-species ESS and RL-stability). The paper relates these to the dynamic stability of monomorphic and polymorphic evolutionary systems. It is shown that RL-stability implies the global asymptotic stability of either system with or without mutations. However, the N-species ESS only implies stability of the monomorphic system.

Animals↗
PubMed2002

Tangled nature: a model of evolutionary ecology.

We discuss a simple model of co-evolution. In order to emphasize the effect of interaction between individuals, the entire population is subjected to the same physical environment. Species are emergent structures and extinction, origination and diversity are entirely a consequence of co-evolutionary interaction between individuals. For comparison, we consider both asexual and sexually reproducing populations. In either case, the system evolves through periods of hectic reorganization separated by periods of coherent stable coexistence.

Animals↗
PubMed2002

A study of the middle-scale nucleotide clustering in DNA sequences of various origin and functionality, by means of a method based on a modified standard deviation.

The deviation from randomness in the distribution of nucleotides in genomic sequences is quantified and studied, using a modified standard deviation (MSD). This method implies a "per block" computation of the standard deviation of the nucleotide frequencies of occurrence, using local means (means taken in a neighborhood of each block). This quantity may serve as a scale-dependent measure of the nucleotide clustering. In the present work, the meso-scale of tenths of nucleotides is principally explored, by means of suitably adjusted filter parameters. This length scale is of an order of magnitude not directly affected by the grammar and syntax rules of the protein-coding procedure, remaining shorter than the scale of appearance of large-scale characteristics of the genome. MSD has been found to distinguish systematically between the sequences of different origin and functionality. The most near-random are found to be coding sequences of prokaryotes, while in intronic and intergenic regions of eukaryotic genomes, extended clustering of similar nucleotides is observed. The distributions of MSD values of large collections of sequences are found to be in most cases characteristic of their biological role and origin. Protein- and non-coding, prokaryotic and eukaryotic DNA as well as promoter, rRNA, viral and organelle sequences have been examined. The presented results corroborate a recently proposed model for genome evolution. The method is also applied for an assessment of the annotation of ORFs taken from the complete genome of Saccharomyces cerevisiae.

Animals↗
PubMed1998

Base compositional bias and phylogenetic analyses: a test of the "flying DNA" hypothesis.

Phylogenetic methods can produce biased estimates of phylogeny when base composition varies along different lineages. Pettigrew (1994, Curr. Biol. 4:277-280) has suggested that base composition bias is responsible for the apparent support for the monophyly of bats (Chiroptera: megabats and microbats) from several different nuclear and mitochondrial genes. Pettigrew's "flying DNA" hypothesis makes several predictions: (1) that metabolic constraints associated with flying result in elevated levels of adenine and thymine throughout the genome of both megabats and microbats, (2) that the resulting base compositional bias in bats is sufficient to mislead phylogenetic methods and account for the support for bat monophyly from several nuclear and mitochondrial genes, and (3) that phylogenetic analysis using pairwise distances corrected for compositional bias should eliminate the support for bat monophyly. We tested these predictions by analyzing DNA sequences from two nuclear and three mitochondrial genes. The predicted base compositional bias does not appear to exist in some of the genes, and in other genes the differences in AT content are very small. Analyses under a wide diversity of criteria and models of evolution, including analyses that take base composition into account (using log-determinant distances), all strongly support bat monophyly. Moreover, simulation analyses indicate that even extreme bias toward AT-base composition in bats would be insufficient to explain the observed levels of support for bat monophyly. These analyses provide no support for the "flying DNA" hypothesis, whereas the monophyly of bats appears to be well supported by the DNA sequence data.

Animals↗
PubMed2000

A rapid heuristic algorithm for finding minimum evolution trees.

The minimum sum of branch lengths (S), or the minimum evolution (ME) principle, has been shown to be a good optimization criterion in phylogenetic inference. Unfortunately, the number of topologies to be analyzed is computationally prohibitive when a large number of taxa are involved. Therefore, simplified, heuristic methods, such as the neighbor-joining (NJ) method, are usually employed instead. The NJ method analyzes only a small number of trees (compared with the size of the entire search space); so, the tree obtained may not be the ME tree (for which the S value is minimum over the entire search space). Different compromises between very restrictive and exhaustive search spaces have been proposed recently. In particular, the "stepwise algorithm" (SA) utilizes what is known in computer science as the "beam search," whereas the NJ method employs a "greedy search." SA is virtually guaranteed to find the ME trees while being much faster than exhaustive search algorithms. In this study we propose an even faster method for finding the ME tree. The new algorithm adjusts its search exhaustiveness (from greedy to complete) according to the statistical reliability of the tree node being reconstructed. It is also virtually guaranteed to find the ME tree. The performances and computational efficiencies of ME, SA, NJ, and our new method were compared in extensive simulation studies. The new algorithm was found to perform practically as well as the SA (and, therefore, ME) methods and slightly better than the NJ method. For searching for the globally optimal ME tree, the new algorithm is significantly faster than existing ones, thus making it relatively practical for obtaining all trees with an S value equal to or smaller than that of the NJ tree, even when a large number of taxa is involved.

Algorithms↗
PubMed2000

Tree rooting with outgroups when they differ in their nucleotide composition from the ingroup: the Drosophila saltans and willistoni groups, a case study.

Rooting is frequently the most precarious step in any phylogenetic analysis. Outgroups can become useless for rooting if they are too distantly related to the ingroup. Specifically, little attention has been paid to scenarios where outgroups have evolved different nucleotide frequencies from the ingroup. We investigate one empirical example that arose seeking to determine the phylogenetic relationship between the saltans and the willistoni groups of Drosophila (subgenus Sophophora). We have analyzed 2085 coding nucleotides from the xanthine dehydrogenase (Xdh) gene in 14 species, 6 from the saltans group and 8 from the willistoni group. We adopt a two-step strategy: (1) we investigate the phylogeny without outgroups, rooting the network by the midpoint method; (2) we reinvestigate the rooting of this phylogeny using predefined outgroups in both a parsimony- and a model-based maximum-likelihood framework. A satisfactory description of the substitution process along the Xdh region calls for six substitution types and substitution rate variation among codon positions. When the ingroup sequences are considered alone, the phylogeny obtained using this description corroborates the known relationships derived from anatomical criteria. Inclusion of the outgroups makes the root unstable, apparently because of differences between ingroups and outgroups in the substitution processes; these differences are better accounted for by a simplified model of evolution than by more complex, realistic descriptions of the substitution process.

Animals↗
PubMed2001

Molecular phylogeny of the chipmunks inferred from Mitochondrial cytochrome b and cytochrome oxidase II gene sequences.

There are currently 25 recognized species of the chipmunk genus Tamias. In this study we sequenced the complete mitochondrial cytochrome b (cyt b) gene of 23 Tamias species. We analyzed the cyt b sequence and then analyzed a combined data set of cyt b along with a previous data set of cytochrome oxidase subunit II (COII) sequence. Maximum-likelihood was used to further test the fit of models of evolution to the cyt b data. Other sciurid cyt b sequence was added to examine the evolution of Tamias in the context of other sciurids. Relationships among Tamias species are discussed, particularly the possibility of a current sorting event among taxa of the southwestern United States and the extreme divergences among the three subgenera (Neotamias, Eutamias, and Tamias).

Animals↗
PubMed2002

Bacteriophages: evolution of the majority.

The dsDNA-tailed bacteriophages are probably the largest evolving group in the Biosphere and they are arguably very ancient. Comparative examination of genomes indicates that the hallmark of phage evolution is horizontal exchange of sequences. This is accomplished, first, by rampant non-homologous recombination between different genomes and, second, by reassortment of the variant sequences so created through homologous recombination. The comparative analysis suggests mechanisms by which new genes can be added to phage genomes and by which genes with novel functions may be assembled from parts. Horizontal exchange of sequences occurs most frequently among closely related phages, but it also extends across the entire global population at lower frequency. Bacteriophages also have probable ancestral connections with viruses of eukaryotes and archaea.

Bacteriophages↗
PubMed1997

Evolutionary dynamics of cucumber mosaic virus satellite RNA during natural epidemics in Italy.

The evolutionary dynamics of 22 variants of cucumber mosaic virus satellite RNA (CMV satRNA) isolated in Italy during virus epidemics from 1988 to 1993 were investigated on the basis of their primary structure and biological properties. Most of the variants were amplified from total nucleic acid preparations extracted from field-infected plants, thus representing wild isolates of CMV satRNA. Eleven variants were associated with subgroup II CMV strains, 10 with subgroup I and 1 with a mixed infection by both strains. When inoculated onto tomato seedlings, the variants induced the phenotype (necrogenic or ameliorative) predicted by their nucleotide sequence. Phylogenetic relationships between the satRNA variants were determined using the stationary Markov model, a stochastic model for evolution. For each satRNA, the Markov analysis gave a good correlation between position in the phylogenetic tree and biological properties. The variants with ameliorative and necrogenic phenotypes in tomato followed two different evolutionary dynamics in nature. Tfn-satRNA, a 390-nt-long molecule, followed a third type of evolutionary dynamic far apart from that of the shorter satRNA molecules (i.e., those in the 334- to 340-nt-length class). Average values of the mean constant rate of nucleotide substitutions/site (Ksubs/site) indicated that in nature the variants tend to keep their heterogeneity unchanged from one epidemic episode to the other, even if the outbreaks occur in places very far from each other. This seems to be in agreement with the proposed maintenance of a functional molecular structure as a constraint to CMV satRNA evolution.

Computer Simulation↗
PubMed1976

A critical review of the 'neugliederung' concept in relation to the development of the vertebral column.

The literature on the early embryonic development of the vertebral column in various animal species was analyzed to evaluate so many unrelated or contradictory observations. The recurring problems are described. One of the first was the lack of correspondence between the metameric boundaries of the 'primitive vertebral bodies' arising from the somites and those of the adult vertebral bodies, as presumably shown by their relationship to the vertebral processes and spinal nerves. A century ago, Remak introduced the concept of 'Neugliederung', according to which the ultimate vertebral body boundaries are determined by a shift of a half segment in comparison with the earlier segment boundaries. Another question was about the nature of the structures the primitive segments give rise to (axial skeletal tissue and/or muscular tissue and/or nervous tissue), which led to the fundamental problem which system (skeleton or musculature) retains its segmentation. The observation of what was called the intervertebral fissure led to a far-reaching modification of the 'Neugliederung' concept, making a regrouping of parts of the primitive vertebral bodies both possible and probable. The functional necessity for the alternation of muscle and skeleton primordia was also assumed. Although the difference in rostro-caudal level between the boundaries of the somites and the definitive vertebral bodies, measured for instance in relation to the position of the intersegmental vessels, does not support a resegmentation of the vertebral column, because the somite is not a precursor of the adult vertebra, few authors have rejected this view. Subsequently, the discussion focussed on the problem of a) the animal species in which and b) the time at which the intervertebral fissure occurs, and the relationship of this fissure to the primitive vertebral cavity. Under the influence of comparative embryology, a number of authors concentrated mainly on identifying certain embryonic primordia as homologues of phylogenetic vertebral elements, and also on attempting to determine the recombination by which such elements could form a definitive vertebra. According to these authors, not only the vertebral bodies but also the arches and ribs undergo a 'Neugliederung'. Another variant of the 'Neugliederung' concept envisages a gradual shift of the original boundaries of the somites with respect to the transverse level of the definitive vertebrae with or without migration of cellular material. A critical consideration of the concepts at issue, and notably of the 'Neugliederung' concept, is presented. Certain phenomena held to be pillars of the 'Neugliederung' theory could not be confirmed. The functional interpretation of the resegmentation was also reduced to its proper proportions by the analysis. A development of the axial skeleton without resegmentation is just as conceivable in functional terms as one in which resegmentation occurs. A functionally meaningful relationship between muscles and skeletal elements is possible in both cases...

Animals↗