arXiv subjects

S. Moss de Oliveira

Publications and source records attributed to S. Moss de Oliveira.

At least 19 recordsLinked to original sources

arXiv2009

Modelling survival and allele complementation in the evolution of genomes with polymorphic loci

We have simulated the evolution of sexually reproducing populations composed of individuals represented by diploid genomes. A series of eight bits formed an allele occupying one of 128 loci of one haploid genome (chromosome). The environment required a specific activity of each locus, this being the sum of the activities of both alleles located at the corresponding loci on two chromosomes. This activity is represented by the number of bits set to zero. In a constant environment the best fitted individuals were homozygous with alleles' activities corresponding to half of the environment requirement for a locus (in diploid genome two alleles at corresponding loci produced a proper activity). Changing the environment under a relatively low recombination rate promotes generation of more polymorphic alleles. In the heterozygous loci, alleles of different activities complement each other fulfilling the environment requirements. Nevertheless, the genetic pool of populations evolves in the direction of a very restricted number of complementing haplotypes and a fast changing environment kills the population. If simulations start with all loci heterozygous, they stay heterozygous for a long time.

q-bio.GN↗

arXiv2008

Simulated self-organisation of death by inherited mutations

An agent-based computer simulation of death by inheritable mutations in a changing environment shows a maximal population, or avoids extinction, at so intermediate mutation rate of the individuals. Thus death seems needed to al for evolution of the fittest, as required by a changing environment.

q-bio.PE↗

arXiv2007

Does Sex Induce a Phase Transition?

We discovered a dynamic phase transition induced by sexual reproduction. The dynamics is a pure Darwinian rule with both fundamental ingredients to drive evolution: 1) random mutations and crossings which act in the sense of increasing the entropy (or diversity); and 2) selection which acts in the opposite sense by limiting the entropy explosion. Selection wins this competition if mutations performed at birth are few enough. By slowly increasing the average number m of mutations, however, the population suddenly undergoes a mutational degradation precisely at a transition point mc. Above this point, the "bad" alleles spread over the genetic pool of the population, overcoming the selection pressure. Individuals become selectively alike, and evolution stops. Only below this point, m < mc, evolutionary life is possible. The finite-size-scaling behaviour of this transition is exhibited for large enough "chromosome" lengths L. One important and surprising observation is the L-independence of the transition curves, for large L. They are also independent on the population size. Another is that mc is near unity, i.e. life cannot be stable with much more than one mutation per diploid genome, independent of the chromosome length, in agreement with reality. One possible consequence is that an eventual evolutionary jump towards larger L enabling the storage of more genetic information would demand an improved DNA copying machinery in order to keep the same total number of mutations per offspring.

q-bio.PE↗

arXiv2007

Child mortality in Penna ageing model

Assuming the deleterious mutations in the Penna ageing model to affect mainly the young ages, we get an enhanced mortality at very young age, followed by a minimum of the mortality, and then the usual exponential increase of mortality with age.

q-bio.PE↗

arXiv2007

Computer simulations on the sympatric speciation modes for the Midas cichlid species complex

Cichlid fishes are one of the best model system for the study of evolution of the species. Inspired by them, in this paper we simulated the splitting of a single species into two separate ones via random mutations, with both populations living together in sympatry, sharing the same habitat. We study the ecological, mating and genetic conditions needed to reproduce the polychromatism and polymorphism of three species of the Midas Cichlid species complex. Our results show two scenarios for the A. Citrinellus speciation process, one with and the other without disruptive natural selection. In the first scenario, the ecological and genetic conditions are sufficient to create two new species, while in the second the mating and genetic conditions must be synchronized in order to control the velocity of genetic drift.

q-bio.PE↗

arXiv2006

Bit-strings and other modifications of Viviane model for language competition

The language competition model of Viviane de Oliveira et al is modified by associating with each language a string of 32 bits. Whenever a language changes in this Viviane model, also one randomly selected bit is flipped. If then only languages with different bit-strings are counted as different, the resulting size distribution of languages agrees with the empirically observed slightly asymmetric log-normal distribution. Several other modifications were also tried but either had more free parameters or agreed less well with reality.

physics.soc-ph↗

arXiv2006

Thermodynamic behavior of a phase transition in a model for sympatric speciation

We investigate the macroscopic effects of the ingredients that drive the origin of species through sympatric speciation. In our model, sympatric speciation is obtained as we tune up the strength of competition between individuals with different phenotypes. As a function of this control parameter, we can characterize, through the behavior of a macroscopic order parameter, a phase transition from a non-speciation to a speciation state of the system. The behavior of the first derivative of the order parameter with respect to the control parameter is consistent with a phase transition and exhibits a sharp peak at the transition point. For different resources distribution, the transition point is shifted, an effect similar to pressure in PVT system. The inverse of the parameter related to sexual selection strength behaves like an external field in the system and, as thus, is also a control parameter. The macroscopic effects of the biological parameters used in our model reveal thus fingerprints typical of thermodynamic quantities in a phase transition of an equilibrium physical system.

q-bio.PE↗

arXiv2005

Phase transition in a mean-field model for sympatric speciation

We introduce an analytical model for population dynamics with intra-specific competition, mutation and assortative mating as basic ingredients. The set of equations that describes the time evolution of population size in a mean-field approximation may be decoupled. We find a phase transition leading to sympatric speciation as a parameter that quantifies competition strength is varied. This transition, previously found in a computational model, occurs to be of first order.

q-bio.PE↗

arXiv2004

Simple Bit-String Model for Lineage Branching

We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die, keeping the population constant. An offspring has the same genome as its (randomly chosen) parent, except for a small amount of (also random) mutations. Chance may thus generate a newborn with a genome that is better than that of its parent, and the newborn will have a smaller death probability. When this happens, this individual is a would-be founder of a new lineage. A new lineage is considered created if its alive descendence grows above a certain previously defined threshold. The time evolution of populations evolving under these rules is followed by computer simulations and the probability densities of lineage duration and size, among others, are computed. These densities show a scale-free behaviour, in accordance with some conjectures in paleoevolution, and suggesting a simple mechanism as explanation for the ubiquity of these power-laws.

cond-mat.stat-mech↗

arXiv2003

Penna bit-string model with constant population

We removed from the Penna model for biological ageing any random killing Verhulst factor. Deaths are due only to genetic diseases and the population size is fixed, instead of fluctuating around some constant value. We show that these modifications give qualitatively the same results obtained in an earlier paper, where the random killings (used to avoid an exponential increase of the population) were applied only to newborns.

cond-mat.stat-mech↗

arXiv2003

Positive mutations and mutation-dependent Verhulst factor in Penna ageing model

We twice modify the Penna model for biological ageing. First we introduce back (good) mutations and a memory for them into the model. It allows us to observe an improvement of the species fitness over long time scales as well as punctuated equilibrium. Second we adopt a food/space competition factor that depends on the number of accumulated mutations in the individuals genomes, and get rid of the fixed limiting number of allowed mutations. Besides reproducing the main results of the standard model, we also observe a mortality maximum for the oldest old.

cond-mat.stat-mech↗

arXiv2002

The evolutionary advantage of diploid sex

We modify the Penna Model for biological aging, which is based on the mutation-accumulation theory, in order to verify if there would be any evolutionary advantage of triploid over diploid organisms. We show that this is not the case, and that usual sex is always better than that involving three individuals.

cond-mat.stat-mech↗

arXiv2002

Simulating Male Selfish Strategy in Reproduction Dispute

We introduce into the Penna Model for biological ageing one of the possible male mechanisms used to maximize the ability of their sperm to compete with sperm from other males. Such a selfish mechanism increases the male reproduction success but may decrease the survival probability of the whole female population, depending on how it acts. We also find a dynamic phase transition induced by the existence of an absorbing state where no selfish males survive.

cond-mat↗

arXiv2002

Bit-String Models for Parasex

We present different bit-string models of haploid asexual populations in which individuals may exchange part of their genome with other individuals (parasex) according to a given probability. We study the advantages of this parasex concerning population sizes, genetic fitness and diversity. We find that the exchange of genomes always improves these features.

cond-mat.stat-mech↗

arXiv2001

Applications and Sexual Version of a Simple Model for Biological Ageing

We use a simple model for biological ageing to study the mortality of the population, obtaining a good agreement with the Gompertz law. We also simulate the same model on a square lattice, considering different strategies of parental care. The results are in agreement with those obtained earlier with the more complicated Penna model for biological ageing. Finally, we present the sexual version of this simple model.

cond-mat.stat-mech↗

arXiv2001

Simulated ecology-driven sympatric speciation

We introduce a multi-locus genetically acquired phenotype, submitted to mutations and with selective value, in an age-structured model for biological aging. This phenotype describes a single-trait effect of the environment on an individual, and we study the resulting distribution of this trait among the population. In particular, our simulations show that the appearance of a double phenotypic attractor in the ecology induces the emergence of a stable polymorphism, as observed in the Galapagos finches. In the presence of this polymorphism, the simulations generate short-term speciation, when mating preferences are also allowed to suffer mutations and acquire selective value.

cond-mat.stat-mech↗

arXiv2001

An Unusual Antagonistic Pleiotropy in the Penna Model for Biological Ageing

We combine the Penna Model for biological aging, which is based on the mutation-accumulation theory, with a sort of antagonistic pleiotropy. We show that depending on how the pleiotropy is introduced, it is possible to reproduce both the humans mortality, which increases exponentially with age, and fruitfly mortality, which decelerates at old ages, allowing the appearance of arbitrarily old Methuselah's.

cond-mat.stat-mech↗

arXiv2000

Computer Simulations for Biological Ageing and Sexual Reproduction

The sexual version of the Penna model of biological ageing, simulated since 1996, is compared here with alternative forms of reproduction as well as with models not involving ageing. In particular we want to check how sexual forms of life could have evolved and won over earlier asexual forms hundreds of million years ago. This computer model is based on the mutation-accumulation theory of ageing, using bits-strings to represent the genome. Its population dynamics is studied by Monte Carlo methods.

cond-mat.stat-mech↗