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N-person games and the evolution of co-operation: a model based on predator inspection in fish.

Two N-person game theoretical models examining the evolution of co-operation during predator inspection in fish are presented. Predator inspection occurs in small shoals of fish, in which one to a few individuals, the "inspectors" (co-operators) break away from the shoal and cautiously approach a predator to obtain information on this potential danger. In the models presented here, remaining with the shoal and not inspecting is considered an act of defection. Both model I and II produce a stable internal polymorphism of inspectors and noninspectors. While the equilibrial frequency of inspectors can be low (i.e. less than 10%) at large shoal size, the proportion of shoals containing any inspectors--and therefore exhibiting the inspection behavior--is much greater. Both models presented here, and N-person games in general are equivalent to intrademic group selection models of evolution in structured populations, in which shoals are trait groups and co-operation evolves by between-shoal selection. While the results are cast in terms of predator inspection, the model itself is general and applies to any multi-group scenario where co-operators benefit entire groups at their own expense. The results presented here add to the mounting theoretical and empirical evidence that co-operation is frequently not a pure evolutionarily stable strategy, and that many metapopulations should be polymorphic for both co-operators and defectors.

Animals↗

Integration of shelf evolution and river basin models to simulate Holocene sediment dynamics of the Humber Estuary during periods of sea-level change and variations in catchment sediment supply.

Three modelling elements and sedimentary evidence provide an understanding of sediment characteristics, river basin processes, tidal regimes and sea-level changes to explain sediment supply to the Humber Estuary through the Holocene (the last 10,000 years). An upscaled cellular catchment model simulates water and sediment fluxes from river basins, illustrating significant variations in response to climate change, especially precipitation and vegetation changes, principally deforestation. Much of the sediment mobilised remains in stores within the catchment and only a small fraction reaches the Humber tidal system. An empirical model helps to explain sediment erosion, transport and deposition from the offshore and coastal zones through the Holocene and sea-level rise caused the transgression of the continental shelf of the North Sea. Comparison with the sediment fill of the lowlands around of the Humber estuary, that represent the extent of the estuary during the Holocene, demonstrates that most of the fill (approximately 95-98%) was derived from non-fluvial sources. A shelf evolution model, with reconstructions of sea level, palaeogeography and palaeobathymetry for 1,000 year time steps through the Holocene predicts significant changes in tidal regimes, first over wide areas of the coast as the transgression of the continental shelf progresses. The most significant changes occur with the inner reaches of the palaeo-estuaries, especially those of the Humber and the Fenland. Throughout the mid-Holocene they are characterised by significantly lower tidal ranges (MWHST approximately 2.5 m less than present) and low tidal currents. The simulated patterns of tidal currents concur with the transport of fine grain sediment from the coastal zone into the estuaries. The major tidal range changes revise estimates of late Holocene and ongoing relative sea and land level changes.

Journal Article↗

On the mod resc model and the evolution of Wolbachia compatibility types.

Cytoplasmic incompatibility (CI) is induced by the endocellular bacterium Wolbachia. It results in an embryonic mortality occurring when infected males mate with uninfected females. The mechanism involved is currently unknown, but the mod resc model allows interpretation of all observations made so far. It postulates the existence of two bacterial functions: modification (mod) and rescue (resc). The mod function acts in the males' germline, before Wolbachia are shed from maturing sperm. If sperm is affected by mod, zygote development will fail unless resc is expressed in the egg. Interestingly, CI is also observed in crosses between infected males and infected females when the two partners bear different Wolbachia strains, demonstrating that mod and resc interact in a specific manner: Two Wolbachia strains are compatible with each other only if they harbor the same compatibility type. Here we focus on the evolutionary process involved in the emergence of new compatibility types from ancestral ones. We argue that new compatibility types are likely to evolve under a wider range of conditions than previously thought, through a two-step process. First, new mod variants can arise by mutation and spread by drift. This is possible because mod is expressed in males and Wolbachia is transmitted by females. Second, once such a mod variant achieves a certain frequency, it can create the conditions for the deterministic invasion of a new resc variant, allowing the invasion of a new mod resc pair. Furthermore, we show that a stable polymorphism might be maintained in natural populations, allowing the long-term existence of "suicidal" Wolbachia strains.

Algorithms↗

Tandemly repeated satellite DNA of Dolichopoda schiavazzii: a test for models on the evolution of highly repetitive DNA.

Three specific satellite DNA families can be detected in the genome of the cave cricket Dolichopoda schiavazzii. The pDoP102 and the pDsPv400 families are species specific for D. schiavazzii; the pDoP500 family is probably present in all Dolichopoda species. The three satellite DNA families were characterized from individuals of three isolated populations of D. schiavazzii with respect to nucleotide sequence, sequence complexity, sequence variability, and copy number. This unique data set on satellite DNAs of D. schiavazzii seems to allow one to test the significance of theoretical approaches to the mode of evolution of noncoding, tandemly arranged satellite DNA. At least for satellite DNAs of D. schiavazzii two clear trends were observed: (1) sequence variability increases with copy number and (2) the repeat length decreases with copy number. The first trend is in good agreement with the theory but the second is not. Thus, a revision of the models is proposed.

Animals↗

Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa.

Multicellular animals, or Metazoa, appear in the fossil records between 575 and 509 million years ago (MYA). At odds with paleontological evidence, molecular estimates of basal metazoan divergences have been consistently older than 700 MYA. However, those date estimates were based on the molecular clock hypothesis, which is almost always violated. To relax this hypothesis, we have implemented a Bayesian approach to describe the change of evolutionary rate over time. Analysis of 22 genes from the nuclear and the mitochondrial genomes under the molecular clock assumption produced old date estimates, similar to those from previous studies. However, by allowing rates to vary in time and by taking small species-sampling fractions into account, we obtained much younger estimates, broadly consistent with the fossil records. In particular, the date of protostome-deuterostome divergence was on average 582 +/- 112 MYA. These results were found to be robust to specification of the model of rate change. The clock assumption thus had a dramatic effect on date estimation. However, our results appeared sensitive to the prior model of cladogenesis, although the oldest estimates (791 +/- 246 MYA) were obtained under a suboptimal model. Bayes posterior estimates of evolutionary rates indicated at least one major burst of molecular evolution at the end of the Precambrian when protostomes and deuterostomes diverged. We stress the importance of assumptions about rates on date estimation and suggest that the large discrepancies between the molecular and fossil dates of metazoan divergences might partly be due to biases in molecular date estimation.

Algorithms↗

Heavy-chain variable regions in carcharhine sharks: development of a comprehensive model for the evolution of VH domains among the gnathanstomes.

We determined the sequence of 18 DNA clones encoding VH regions of sandbar shark and bull shark. All of these sequences exhibit key structural coding features characteristic of known VH genes of higher vertebrates. These VH sequences disclosed considerable diversity, and can be divided into six families according to the criterion of 80% DNA sequence identity. The overlapping of some VH gene clones to two or more families is a particular feature found in carcharhine sharks, which suggests that VH diversification is a continuing process. The basic sequence patterns of heavy-chain V regions found in all representative gnathanstomes and in VH of the shark heavy immunoglobulin IgW provides evidence for selection of canonical residues in all VH structures. Elasmobranch VH sequences can be divided into two classes or clans, one comprising the 'classical' VH set and the other comprising VHS related to those of IgW (V omega). Phylogenetic analyses place the VH cluster as the root of all the classic VHS and indicates that the V omega set is most probably that of the primordial heavy chain.

Amino Acid Sequence↗

A theoretical model of the evolution of virulence in sexually transmitted HIV/AIDS.

INTRODUCTION: The evolution of virulence in host-parasite relationships has been the subject of several publications. In the case of HIV virulence, some authors suggest that the evolution of HIV virulence correlates with the rate of acquisition of new sexual partners. In contrast some other authors argue that the level of HIV virulence is independent of the sexual activity of the host population. METHODS: Provide a mathematical model for the study of the potential influence of human sexual behaviour on the evolution of virulence of HIV is provided. RESULTS: The results indicated that, when the probability of acquisition of infection is a function both of the sexual activity and of the virulence level of HIV strains, the evolution of HIV virulence correlates positively with the rate of acquisition of new sexual partners. CONCLUSION: It is concluded that in the case of a host population with a low (high) rate of exchange of sexual partners the evolution of HIV virulence is such that the less (more) virulent strain prevails.

Acquired Immunodeficiency Syndrome↗

Behavioral drive versus behavioral inertia in evolution: a null model approach.

Some biologists embrace the classical view that changes in behavior inevitably initiate or drive evolutionary changes in other traits, yet others note that behavior sometimes inhibits evolutionary changes. Here we develop a null model that quantifies the impact of regulatory behaviors (specifically, thermoregulatory behaviors) on body temperature and on performance of ectotherms. We apply the model to data on a lizard (Anolis cristatellus) and show that thermoregulatory behaviors likely inhibit selection for evolutionary shifts in thermal physiology with altitude. Because behavioral adjustments are commonly used by ectotherms to regulate physiological performance, regulatory behaviors should generally constrain rather than drive evolution, a phenomenon we call the "Bogert effect." We briefly review a few other examples that contradict the classical view of behavior as the inevitable driving force in evolution. Overall, our analysis and brief review challenge the classical view that behavior is invariably the driving force in evolution, and instead our work supports the alternative view that behavior has diverse--and sometimes conflicting--effects on the directions and rates at which other traits evolve.

Altitude↗

Mutation and recombination in cattle satellite DNA: a feedback model for the evolution of satellite DNA repeats.

The cattle genome contains several distinct centromeric satellites with interrelated evolutionary histories. We compared these satellites in Bovini species that diverged 0.2 to about 5 Myr ago. Quantification of hybridization signals by phosphor imaging revealed a large variation in the relative amounts of the major satellites. In the genome of water buffalo this has led to the complete deletion of satellite III. Comparative sequencing and PCR-RFLP analysis of satellites IV, 1.711a, and 1.711b from the related Bos and Bison species revealed heterogeneities in 0.5 to 2% of the positions, again with variations in the relative amounts of sequence variants. Restriction patterns generated by double digestions suggested a recombination of sequence variants. Our results are compatible with a model of the life history of satellites during which homogeneity of interacting repeat units is both cause and consequence of the rapid turnover of satellite DNA. Initially, a positive feedback loop leads to a rapid saltatory amplification of homogeneous repeat units. In the second phase, mutations inhibit the interaction of repeat units and coexisting sequence variants amplify independently. Homogenization by the spreading of one of the variants is prevented by recombination and the satellite is eventually outcompeted by another, more homogeneous tandem repeat sequence.

Animals↗

Relatedness in trait group models of social evolution.

Genetic relatedness is a central concept in the study of social evolution. Though originally defined in terms of genealogy, the modern version of relatedness accommodates genetic similarity of any origin. This paper examines relatedness in group structured modes, in which a trait affects the fitness of all group members. Such traits can be divided into two types, based on whether their group fitness effects encompass all group members including the actor ("whole-group traits"), or only group members other than the actor ("other-only traits"). Both trait types are common in nature as well as in theoretical models, but they have rarely been distinguished clearly. The average relatedness of recipients to actors differs for the two trait types within the same population and even the same individual, leading to different selection pressures and evolutionary outcomes. Total relatedness in group-structured models can be partitioned into two components: structural relatedness due to the size and number of groups in the population, and assortative relatedness due to the distribution of genotypes among groups. Each component differs for whole-group vs. other-only traits, both in terms of their values and the factors that influence them. Some key differences include: positive relatedness requires positive assortment for other-only but not for whole-group traits; negative relatedness is possible for other-only but not whole-group traits; relatedness depends on average group size for whole-group but not other-only traits, and non-random assortment into groups affects relatedness more strongly for other-only than whole-group traits. Recognizing the distinction between these trait types resolves some apparent contradictions in the literature, and clarifies the limits of some previous results.

Animals↗

Score-dependent fertility model for the evolution of cooperation in a lattice.

The evolution of cooperation is studied in a lattice-structured population, in which each individual plays the iterated Prisoner's Dilemma game with its neighbors. The population includes Tit-for-Tat (TFT, a cooperative strategy) and All Defect (AD, a selfish strategy) distributed over the lattice points. An individual dies randomly, and the vacant site is filled immediately by a copy of one of the neighbors in which the probability of colonization success by a particular neighbor is proportional to its score accumulated in the game. This "score-dependent fertility model" (or fertility model) behaves very differently from score-dependent viability model (viability model) studied in a previous paper. The model on a one-dimensional lattice is a analysed by invasion probability analysis, pair-edge method mean-field approximation, pair approximation, and computer simulation. Results are: (1) TFT players come to form tight clusters. When the probability of iteration w is large, initially rare TFT can invade and spread in a population dominated by AD, unlike in the complete mixing model. The condition for the increase of TFT is accurately predicted by all the techniques except mean-field approximation; (2) fertility model is much more favorable for the spread of TFT than the corresponding viability model, because spiteful killing of neighbors is favored in the viability model but not in the fertility model; (3) eight lattice games on two-dimensional lattice with different assumptions are examined. Cooperation and defects can coexist in the models of deterministic state change but not in the models of stochastic state change.

Biological Evolution↗

Can weighting improve bushy trees? Models of cytochrome b evolution and the molecular systematics of pipits and wagtails (Aves: Motacillidae).

Among-site rate variation (alpha) and transition bias (kappa) have been shown, most often as independent parameters, to be important dynamics in DNA evolution. Accounting for these dynamics should result in better estimates of phylogenetic relationships. To test this idea, we simultaneously estimated overall (averaged over all codon positions) and codon-specific values of alpha and kappa, using maximum likelihood analyses of cytochrome b data from all genera of pipits and wagtails (Aves: Motacillidae), and six outgroup species, using initial trees generated with default values. Estimates of alpha and kappa were robust to initial tree topology and suggested substantial among-site rate variation even within codon classes; alpha was lowest (large among-site rate variation) at second-codon and highest (low among-site rate variation) at third-codon positions. When overall values were applied, there were shifts in tree topology and dramatic and statistically significant improvements in log-likelihood scores of trees compared with the scores from application of default values. Applying codon-specific values resulted in yet another highly significant increase in likelihood. However, although incorporating substitution dynamics into maximum likelihood, maximum parsimony, and neighbor-joining analyses resulted in increases in congruence among trees, there were only minor improvements in phylogenetic signal, and none of the successive approximations tree topologies were statistically distinguishable from one another by the data. We suggest that the bushlike nature of many higher-level phylogenies in birds makes estimating the dynamics of DNA evolution less sensitive to tree topology but also less susceptible to improvement via weighting.

Animals↗

Estimating the rate of evolution of the rate of molecular evolution.

A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.

Algorithms↗

Model for the genetic evolution of human solid tumors.

A conceptual model is proposed for the genetic evolution of many human solid tumors that is based on the observations that cancer cells may spontaneously double their chromosome number; that cells with excessive chromosome numbers may be cytogenetically unstable, both losing chromosomes randomly during subsequent cell divisions, and often developing structural abnormalities in the chromosomes that are retained; and that some structural chromosome abnormalities may activate growth-promoting genes. The sequence of tetraploidization with chromosome loss can occur repeatedly in a given tumor. The available evidence supporting the model is reviewed. A computer simulation system that embodies these concepts is described and the model is used to generate distributions of chromosome number/cell under various simulated conditions and in a variety of simulated biological settings. A simulation of the time course of changes in chromosome number per cell that accompany the spontaneous neoplastic transformation of mouse fibroblasts in vitro is described. The best fit to the data was obtained when provision was made for the activation of at least two growth-promoting genes. The conditions for generating discrete aneuploid peaks in cytogenetic and flow cytometric studies were explored; our modeling studies suggest that the activation of a growth promoting gene is required in order to produce a discrete aneuploid peak. Our modeling studies suggest that the overrepresentation of individual oncogene-bearing chromosomes in aneuploid cell lines may require the activation of gene dose-dependent growth-promoting genes and is not likely to occur in cell lines in which at least two copies of each normal chromosome are required for cell survival. Overall, the results obtained using the model are consistent with a wide variety of flow cytometric and cytogenetic studies in human solid tumors.

Animals↗

Challenging the trade-off model for the evolution of virulence: is virulence management feasible?

Progress in understanding the evolution of infectious diseases has inspired proposals to manage the evolution of pathogen (including parasite) virulence. A common view is that social interventions that lower pathogen transmission will indirectly select lower virulence because of a trade-off between transmission and virulence. Here, we argue that there is little theoretical justification and no empirical evidence for this plan. Although a trade-off model might apply to some pathogens, the mechanism appears too weak for rapid selection of substantial changes in virulence. Direct selection against virulence itself might be a more rewarding approach to managing the evolution of virulence.

Animals↗