Related papers: Polytopes, graphs and fitness landscapes
The theory of life history evolution provides a powerful framework to understand the evolutionary dynamics of pathogens in both epidemic and endemic situations. This framework, however, relies on the assumption that pathogen populations are…
Mutational neighbourhoods in genotype-phenotype (GP) maps are widely believed to be more likely to share characteristics than expected from random chance. Such genetic correlations should, as John Maynard Smith famously pointed out,…
We adapt a fitness function from evolutionary game theory as a mechanism for aggregation and dispersal in a partial differential equation (PDE) model of two interacting populations, described by density functions $u$ and $v$. We consider a…
All living things exhibit adaptations that enable them to survive and reproduce in the natural environment that they inhabit. From a biological standpoint, it has long been understood that adaptation comes from natural selection, whereby…
Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…
We analytically study the dynamics of evolving populations that exhibit metastability on the level of phenotype or fitness. In constant selective environments, such metastable behavior is caused by two qualitatively different mechanisms.…
Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is…
Population structure can have a significant effect on evolution. For some systems with sufficient symmetry, analytic results can be derived within the mathematical framework of evolutionary graph theory which relate to the outcome of the…
This Letter studies the quasispecies dynamics of a population capable of genetic repair evolving on a time-dependent fitness landscape. We develop a model that considers an asexual population of single-stranded, conservatively replicating…
Evolution is the theory that plants and animals today have come from kinds that have existed in the past. Scientists such as Charles Darwin and Alfred Wallace dedicate their life to observe how species interact with their environment, grow,…
We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not…
Identifying and quantifying the benefits of sex and recombination is a long standing problem in evolutionary theory. In particular, contradictory claims have been made about the existence of a benefit of recombination on high dimensional…
The alignment of shapes has been a crucial step in statistical shape analysis, for example, in calculating mean shape, detecting locational differences between two shape populations, and classification. Procrustes alignment is the most…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
Species do not merely evolve, they also coevolve with other organisms. Coevolution is a major force driving interacting species to continuously evolve ex- ploring their fitness landscapes. Coevolution involves the coupling of species fit-…
Preferential attachment models form a popular class of growing networks, where incoming vertices are preferably connected to vertices with high degree. We consider a variant of this process, where vertices are equipped with a random initial…
Evolutionary game theory has been successfully used to investigate the dynamics of systems, in which many entities have competitive interactions. From a physics point of view, it is interesting to study conditions under which a coordination…
A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the…
We study biological evolution on a random fitness landscape where correlations are introduced through a linear fitness gradient of strength $c$. When selection is strong and mutations rare the dynamics is a directed uphill walk that…
A quasispecies evolving on a fitness landscape with a single peak of fluctuating height is studied. In the approximation that back mutations can be ignored, the rate equations can be solved analytically. It is shown that the error threshold…