Biomedical subjects

José F Fontanari

Publications and source records attributed to José F Fontanari.

8 recordsLinked to original sources

PubMed2005

Coexistence and error propagation in pre-biotic vesicle models: a group selection approach.

Compartmentalization of unlinked, competing templates is widely accepted as a necessary step towards the evolution of complex organisms. However, preservation of information by templates confined to isolated vesicles of finite size faces much harder obstacles than by free templates: random drift allied to mutation pressure wipe out any template that does not replicate perfectly, no matter how small the error probability might be. In addition, drift alone hinders the coexistence of distinct templates in a same compartment. Here, we investigate the conditions for group selection to prevail over drift and mutation and hence to guarantee the maintenance and coexistence of distinct templates in a vesicle. Group selection is implemented through a vesicle survival probability that depends on the template composition. By considering the limit case of an infinite number of vesicles, each one carrying a finite number of templates, we were able to derive a set of recursion equations for the frequencies of vesicles with different template compositions. Numerical iteration of these recursions allows the exact characterization of the steady state of the vesicle population-a quasispecies of vesicles-thus revealing the values of the mutation and group selection intensities for which template coexistence is possible. Within the main assumption of the model-a fixed, finite or infinite, number of vesicles-we find no fundamental impediment to the coexistence of an arbitrary number of template types with the same replication rate inside a vesicle, except of course for the vesicle capacity. Group selection in the form of vesicle selection is a must for compartmentalized primordial genetic systems even in the absence of intra-genomic competition of different templates.

Animals↗

PubMed2004

Model ecosystems with random nonlinear interspecies interactions.

The principle of competitive exclusion in ecology establishes that two species living together cannot occupy the same ecological niche. Here we present a model ecosystem in which the species are described by a series of phenotypic characters and the strength of the competition between two species is given by a nondecreasing (modulating) function of the number of common characters. Using analytical tools of statistical mechanics we find that the ecosystem diversity, defined as the fraction of species that coexist at equilibrium, decreases as the complexity (i.e., number of characters) of the species increases, regardless of the modulating function. By considering both selective and random elimination of the links in the community web, we show that ecosystems composed of simple species are more robust than those composed of complex species. In addition, we show that the puzzling result that there exists either rich or poor ecosystems for a linear modulating function is not typical of communities in which the interspecies interactions are determined by a complementarity rule.

Animals↗

PubMed2004

Effect of selection on the topology of genealogical trees.

Selection is one of the factors that most influence the shape of genealogical trees. Here we report results of simulations of the infinite-sites version of Moran's model of population genetics aiming at quantifying how the presence of selection affects the branching pattern (topology) of binary genealogical trees. In particular, we consider a scenario of purifying or negative selection in which all mutations are deleterious and each new mutation reduces the fitness of the individual by the same fraction. Analysis of five statistical measures of tree balance or symmetry borrowed from taxonomy indicates that the genealogical trees of samples of populations in which selection is actuating are in the average more asymmetric than neutral trees and that this effect is enhanced by increasing the sample size. However, a quantitative evaluation of the power of these balance measures to detect a tree topology significantly distinct from the neutral one indicates that they are not useful as tests of neutrality of mutations.

Animals↗

PubMed2003

Analytical solution of the evolution dynamics on a multiplicative-fitness landscape.

In an infinite population the frequency distribution of individuals carrying a given number of mutations obeys a set of recursion equations, the equilibrium solution of which describes the mutation-selection balance. Although this solution is well-known in the case of a multiplicative-fitness landscape, where it is assumed that all mutations are deleterious and that each new mutation reduces the fitness of the individual by the same fraction, we are not aware of the existence of an analytical solution for the full dynamics. Using the generating function approach, we present here an explicit analytical solution for the frequency distribution recursion equations valid for all generations and initial conditions.

Alleles↗

PubMed2003

Phase transition and landscape statistics of the number partitioning problem.

The phase transition in the number partitioning problem (NPP), i.e., the transition from a region in the space of control parameters in which almost all instances have many solutions to a region in which almost all instances have no solution, is investigated by examining the energy landscape of this classic optimization problem. This is achieved by coding the information about the minimum energy paths connecting pairs of minima into a tree structure, termed a barrier tree, the leaves and internal nodes of which represent, respectively, the minima and the lowest energy saddles connecting those minima. Here we apply several measures of shape (balance and symmetry) as well as of branch lengths (barrier heights) to the barrier trees that result from the landscape of the NPP, aiming at identifying traces of the easy-hard transition. We find that it is not possible to tell the easy regime from the hard one by visual inspection of the trees or by measuring the barrier heights. Only the difficulty measure, given by the maximum value of the ratio between the barrier height and the energy surplus of local minima, succeeded in detecting traces of the phase transition in the tree. In addition, we show that the barrier trees associated with the NPP are very similar to random trees, contrasting dramatically with trees associated with the p spin-glass and random energy models. We also examine critically a recent conjecture on the equivalence between the NPP and a truncated random energy model.

Journal Article↗

PubMed2003

Spatial dynamics and the evolution of enzyme production.

We re-examine the problem of the evolution of protein synthesis or enzyme production using a stochastic cellular automaton model, where the replicators are fixed in the sites of a two-dimensional square lattice. In contrast with the classical chemical kinetics or mean-field predictions, we show that a small colony of mutant, protein-mediated (enzymatic) replicators has an appreciable probability to take over a resident population of simpler, direct-template replicators. In addition, we argue that the threshold phenomenon corresponding to the onset of invasion can be described quantitatively within the physics framework of nonequilibrium phase transitions. We study also the invasion of a resident population of enzymatic replicators by more efficient replicators of the same kind, and show that although slightly more efficient mutants cannot invade, invasion is a likely event if the productivity advantage of the mutants is large. In this sense, the establishment of a population of enzymatic replicators is not a 'once-forever' evolutionary decision.

Animals↗

PubMed2002

Multifractal analysis of DNA walks and trails.

The characterization of the long-range order and fractal properties of DNA sequences has proved a difficult though rewarding task mainly due to the mosaic character of DNA consisting of many interwoven patches of various lengths with different nucleotide constitutions. We apply here a recently proposed generalization of the detrended fluctuation analysis method to show that the DNA walk construction, in which the DNA sequence is viewed as a time series, exhibits a monofractal structure regardless of the existence of local trends in the series. In addition, we point out that the monofractal structure of the DNA walks carries over to an apparently alternative graphical construction given by the projection of the DNA walk into the d spatial coordinates, termed DNA trails. In particular, we calculate the fractal dimension D(t) of the DNA trails using a well-known result of fractal theory linking D(t) to the Hurst exponent H of the corresponding DNA walk. Comparison with estimates obtained by the standard box-counting method allows the evaluation of both finite-length and local trends effects.

Biophysical Phenomena↗

PubMed2002

Genealogical process on a correlated fitness landscape.

We study with extensive numerical simulation the genealogical process of 2N haploid genetic sequences. The sequences are under selective pressure, and fitness values are assigned at random, but with a tunable degree of correlation to the fitness values of closely related sequences. The genealogies that we observe can be classified into three different categories, corresponding to different regimes of the mutation rate. At low mutation rates, the sequences remain localized around a small number of central sequences, which leads to trees with short pairwise distances and slow turnover of the most recent common ancestor of the population. At high mutation rates, we observe trees similar (but not identical) to those of neutral evolution. In this regime, the population drifts rapidly, and selection does not influence the distribution of fitness values in the population. The third regime, for intermediate mutation rates, is only found in strongly correlated landscapes. It resembles the one for high mutation rates in that the population drifts rapidly, but nevertheless selection still shapes the distribution of fitness values.

Animals↗