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If in the sexual Penna ageing model conditions are applied leading to complementary bit-strings, then marriages between brothers and sisters, or between close cousins, may lead to more offspring than for unrelated couples., Comment: 7 pages, 7 figures

We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination processes are not effective enough to ensure an independent assortment of linked genes and larger clusters of genes could be inherited as the genetic units. There are whole clusters of genes which tend to complement in such conditions instead of single pairs of alleles like in the case of purifying selection. Computer simulations have shown that switching in-between complementation and purification strategies has a character of a phase transition. This is also responsible for specific distribution of recombination events observed along eukaryotic chromosomes - higher recombination rate is observed in subtelomeric regions than in central parts of chromosomes - for sympatric speciation and probably for non-monotonous relation between reproduction potential and genetic distance between parents., Comment: 29 pages, 18 figures

In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been observed that the recombination events are distributed unevenly along the chromosomes. We have found that many of such recombination properties can be predicted by computer simulations of population evolution based on the Monte Carlo methods. For example, these simulations have shown that the probability of acceptance of the recombination events by selection is higher at the ends of chromosomes and lower in their middle parts. The regions of high coding density are more prone to enter the strategy of haplotype complementation and to form clusters of genes which are "recombination deserts". The phenomenon of switching in-between the purifying selection and haplotype complementation has a phase transition character, and many relations between the effective population size, coding density, chromosome size and recombination frequency are those of the power law type., Comment: 26 pages, 7 figures

We have simulated the evolution of age structured populations whose individuals represented by their diploid genomes were distributed on a square lattice. The environmental conditions on the whole territory changed simultaneously in the same way by switching on or off some requirements. Mutations accumulated in the genes dispensable during a given period of time were neutral, but they could cause a genetic death of individuals if the environment required their functions again. Populations survived due to retaining some surplus of genetic information in the individual genomes. The changes of the environment caused the fluctuations of the population size. Since the simulations were performed with individuals spatially distributed on the lattice and the maximal distance between mating partners was set as a parameter of the model, the inbreeding coefficient in populations changed unevenly, following the fluctuation of population size and enhancing the speciation phenomena., Comment: 15 pages, 7 figures

Background: Hybridogenesis is a very interesting example of reproduction which seems to integrate the sexual and clonal processes in one system. In a case of frogs, described in the paper, two parental species - Rana lessonae and Rana ridibunda can form fertile hybrid individuals - Rana esculenta. Hybrid individuals eliminate one parental haplotype from their germ line cells before meiosis (end before recombination) which implicates clonal reproduction of the haplotype transferred to the gametes. All three "species" are called "complex species". To study the evolution of genomes in the hybridogenetic fraction of this complex species we have used the Monte Carlo based model rendering the age structured populations. The model enables the analysis of distribution of defective alleles in the individual genomes as well as in the genetic pool of the whole populations. Results: We have shown that longer isolation of hybrids' populations leads to the speciation through emerging the specific sets of complementing haplotypes in their genetic pool. The fraction of defective alleles increases but the defects are complemented in the heterozygous loci. Nevertheless, even small supply of new hybrids generated by the two parental species or crossbreeding between hybrids and one of the parental species prevents the speciation and changes the strategy of the genome evolution from the complementing to the purifying Darwinian selection., Comment: 17 pages, 5 figures

Intragenomic recombination (crossover) is a very important evolutionary mechanism. The crossover events are not evenly distributed along the natural chromosomes. Monte Carlo simulations revealed that frequency of recombinations decides about the strategy of chromosomes' and genomes' evolution. In large panmictic populations, under high recombination rate the Darwinian purifying selection operates keeping the fraction of defective genes at the relatively low level. In small populations and under low recombination rate the strategy of complementing haplotypes seems to be more advantageous. Switching between the two strategies has a character of phase transition - it depends on inbreeding coefficient and crossover rate. The critical recombination rate depends also on the size of chromosome. It is also possible, that in one genome some chromosomes could be under complementing while some other under purifying selection. Such situation stabilizes genome evolution and reproduction strategy. It seems that this phenomenon can be responsible for the positive correlation between kinship and fecundity, recently found in the Islander population. When large population is forced to enter the complementing strategy, the phenomenon of sympatric speciation is observed., Comment: 32 pages, 19 figures

We describe the simulation method of modelling the population evolution using Monte Carlo based on the Penna model. Individuals in the populations are represented by their diploid genomes. Genes expressed after the minimum reproduction age are under a weaker selection pressure and accumulate more mutations than those expressed before the minimum reproduction age. The generated gradient of defective genes determines the ageing of individuals and age-structured populations are very similar to the natural, sexually reproducing populations. The genetic structure of a population depends on the way how the random death affects the population. The improvement of the medical care and healthier life styles are responsible for the increasing of the life expectancy of humans during the last century. Introducing a noise into the relations between the genotype, phenotype, and environment, it is possible to simulate some other effects, like the role of immunological systems and a mother care. One of the most interesting results was the evolution of sex chromosomes. Placing the male sex determinants on one chromosome of a pair of sex chromosomes is enough to condemn it for shrinking if the population is panmictic (random-mating is assumed). If males are indispensable for taking care of their offspring and have to be faithful to their females, the male sex chromosome does not shrink., Comment: 35 pages, 19 figures

We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have described the differences of mutational pressure connected with replication of the leading and lagging DNA strands. We have shown how the asymmetric replication of DNA affects the structure of genomes, positions of genes, their function and amino acid composition. Results of Monte Carlo simulations of evolution of protein coding sequences have shown a specific role of genetic code in minimizing the effect of nucleotide substitutions on the amino acid composition of proteins. The results of simulations were compared with the results of analyses of genomic and proteomic data bases. This chapter is considered as an introduction to further chapters where chromosomes with genes represented by nucleotide sequences were replaced by bitstrings with single bits representing genes., Comment: 32 pages, 19 figures

We have used the Monte Carlo based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to critical crossover rate, where genomes may switch between the Darwinian purifying selection or complementation of haplotypes, the distribution of recombination events and the force of selection exerted on genes affect the structure of chromosomes. The order of expression of gene s and their location on chromosome may decide about the extinction or survival of competing populations., Comment: 13 pages, 7 figures, publication

We have modified the sexual Penna model by introducing the fluctuating environment and fluctuations representing physiological functions of individuals. Additionally, we have introduced the mother care corresponding to the protection against the deleterious influence of the environment, the learning capacity of individuals corresponding to their immunity and adaptation to the environment fluctuations and the other risk factors appearing at puberty. Each of the above mentioned elements influences mainly the survival of newborns and young individuals while genetic defects accumulated in the genomes increase the noise of individuals and were responsible for higher mortality of older individuals. All these modifications enable precise fitting the age structure of the simulated populations to the age distributions of human populations., Comment: 10 pages, 8 figures, presented on MARF2

We have used the Penna ageing model to analyze how the differences in evolution of sex chromosomes depend on the strategy of reproduction. In panmictic populations, when females (XX) can freely choose the male partner (XY) for reproduction from the whole population, the Y chromosome accumulates defects and eventually the only information it brings is a male sex determination. As a result of shrinking Y chromosome the males become hemizygous in respect to the X chromosome content and are characterized by higher mortality, observed also in the human populations. If it is assumed in the model that the presence of the male is indispensable at least during the pregnancy of his female partner and he cannot be seduced by another female at least during the one reproduction cycle - the Y chromosome preserves its content, does not shrink and the lifespan of females and males is the same. Thus, Y chromosome shrinks not because of existing in one copy, without the possibility of recombination, but because it stays under weaker selection pressure; in panmictic populations without the necessity of being faithful, a considerable fraction of males is dispensable and they can be eliminated from the population without reducing its reproduction potential., Comment: 8 pages, 5 figures

Using Monte Carlo model of biological evolution we have discovered that populations can switch between two different strategies of their genomes' evolution; Darwinian purifying selection and complementing the haplotypes. The first one is exploited in the large panmictic populations while the second one in the small highly inbred populations. The choice depends on the crossover frequency. There is a power law relation between the critical value of crossover frequency and the size of panmictic population. Under the constant inbreeding this critical value of crossover does not depend on the population size and has a character of phase transition. Close to this value sympatric speciation is observed., Comment: 13 pages, 8 figures

We have used the sexual Penna ageing model to show that the relation between dominance and recessiveness could be a force which optimizes the genome size. While the possibility of complementation of the damaged allele by its functional counterparts (recessiveness) leads to the redundancy of genetic information, the dominant effect of defective genes tends to diminish the number of alleles fulfilling the same function. Playing with the fraction of dominant loci in the genome it is possible to obtain the condition where the diploid state of the genome is optimal. If the status of each bit position as dominant or recessive mutations is changed for each individual randomly and rarely, then after a long time a stationary equilibrium of many recessive and few dominant loci is established in the sexual Penna model. This effect vanishes if the same changing distribution of dominant loci applies to all individuals., Comment: 11 pages including 10 figures, in prep. for Theoy in Biosci

Biological genomes are divided into coding and non-coding regions. Introns are non-coding parts within genes, while the remaining non-coding parts are intergenic sequences. To study the evolutionary significance of recombination inside introns we have used two models based on the Monte Carlo method. In our computer simulations we have implemented the internal structure of genes by declaring the probability of recombination between exons. One situation when inside-intron recombination is advantageous is recovering functional genes by combining proper exons dispersed in the genetic pool of the population after a long period without selection for the function of the gene. Populations have to pass through the bottleneck, then. These events are rather rare and we have expected that there should be other phenomena giving profits from the inside-intron recombination. In fact we have found that inside-intron recombination is advantageous only in the case when after recombination, besides the recombinant forms, parental haplotypes are available and selection is set already on gametes., Comment: 12 pages inc. 5 Figs., for Int. J. Mod. Phys. C 17, issue 4 (2006)

As cell proliferation is limited due to the loss of telomere repeats in DNA of normal somatic cells during division, telomere attrition can possibly play an important role in determining the maximum life span of organisms as well as contribute to the process of biological ageing. With computer simulations of cell culture development in organisms, which consist of tissues of normal somatic cells with finite growth, we otain an increase of life span and life expectancy for longer telomeric DNA in the zygote. By additionally considering a two-mutation model for carcinogenesis and indefinite proliferation by the activation of telomerase, we demonstrate that the risk of dying due to cancer can outweigh the positive effect of longer telomeres on the longevity., Comment: 9 pages including 5 figures

The Penna ageing model is based on mutation accumulation theory. We show that it also allows for self-organization of antagonistic pleiotropy which helps at young age at the expense of old age. This can be interpreted as emergence of altruism., Comment: 4 pages including 2 figures

Using Monte Carlo methods, we simulated the effects of bias in generation and elimination of paralogs on the size distribution of paralog groups. It was found that the function describing the decay of the number of paralog groups with their size depends on the ratio between the probability of duplications of genes and their deletions, which corresponds to different selection pressures on the genome size. Slightly different slopes of curves describing the decay of the number of paralog groups with their size were also observed when the threshold of homology between paralogous sequences was changed., Comment: 10 pages including figs, for ICCS 2004 Cracow