Related papers: Scaling effects in the Penna ageing model
We propose and study a class-expansion/innovation/loss model of genome evolution taking into account biological roles of genes and their constituent domains. In our model numbers of genes in different functional categories are coupled to…
Biological tools such as genetic lineage tracing, three dimensional confocal microscopy and next generation DNA sequencing are providing new ways to quantify the distribution of clones of normal and mutated cells. Population-wide clone size…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
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…
Recent studies on the phenomenology of ageing in certain many-particle systems which are at a critical point of their non-equilibrium steady-states, are reviewed. Examples include the contact process, the parity-conserving…
We present a mathematical simplification for the evolutionary dynamics of a heritable trait within a two-sex population. This trait is assumed to control the timing of sex-specific life-history events, such as the age of sexual maturity and…
This paper develops a simplified set of models describing asexual and sexual replication in unicel- lular diploid organisms. The models assume organisms whose genomes consist of two chromosomes, where each chromosome is assumed to be…
Genomic data can be used to reconstruct population size over thousands of generations, using a new class of algorithms (SMC methods). These analyses often show a recent decline in $N_e$ (effective size), which at face value implies a…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
Spatial models where growth is limited to the edge of the expansions have been instrumental to understand the population dynamics and the clone size distribution in growing cellular populations, such as microbial colonies and avascular…
It has recently been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. Thereafter the other associated phenomena can be explained as evolution tuning the amount and…
We introduce a broad class of spatial models to describe how spatially heterogeneous populations live, die, and reproduce. Individuals are represented by points of a point measure, whose birth and death rates can depend both on spatial…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
Although species longevity is subject to a diverse range of selective forces, the mortality curves of a wide variety of organisms are rather similar. We argue that aging and its universal characteristics may have evolved by means of a…
The Penna bit-string model successfully encompasses many phenomena of population evolution, including inheritance, mutation, evolution and ageing. If we consider social interactions among individuals in the Penna model, the population will…
In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly…
Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, sharing a specific functional annotation across genomes of given size.…
Sexual reproduction in Nature requires two sexes, which raises the question why the reproductive scheme did not evolve to have three or more sexes. Here we construct a constrained optimization model based on the communication theory to…
A simplified model for the growth of a population is studied in which random effects arise because reproducing individuals have a certain probability of surviving until the next breeding season and hence contributing to the next generation.…
We analyze the geometry of the species- and genotype-size distribution in evolving and adapting populations of single-stranded self-replicating genomes: here programs in the Avida world. We find that a scale-free distribution (power law)…