Related papers: Evolution of molecular phenotypes under stabilizin…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…
The concept of fitness is introduced, and a simple derivation of the Fundamental Theorem of Natural Selection (which states that the average fitness of a population increases if its variance is nonzero) is given. After a short discussion of…
This paper introduces a variational formulation of natural selection, paying special attention to the nature of "things" and the way that different "kinds" of "things" are individuated from - and influence - each other. We use the Bayesian…
The basic mechanics of evolution have been understood since Darwin. But debate continues over whether macroevolutionary phenomena are driven primary by the fitness structure of genotype space or by ecological interaction. In this paper we…
Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from…
In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…
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…
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and…
We propose a stochastic model for evolution. Births and deaths of species occur with constant probabilities. Each new species is associated with a fitness sampled from the uniform distribution on [0,1]. Every time there is a death event…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
We study the evolution of artificial learning systems by means of selection. Genetic programming is used to generate a sequence of populations of algorithms which can be used by neural networks for supervised learning of a rule that…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
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…
Biological evolution is realised through the same mechanisms of birth and death that underlie change in population density. The deep interdependence between ecology and evolution is well-established, and recent models focus on integrating…
Since protein mutations are the main driving force of evolution at the molecular level, a proper analysis of them (and the factors controlling them) will enable us to find a response to several crucial queries in evolutionary biology. Among…
How does the interplay between selection, mutation and horizontal gene transfer modify the phenotypic distribution of a bacterial or cell population? While horizontal gene transfer, which corresponds to the exchange of genetic material…
We present an individual-based model of phenotypic trait evolution in two-sex populations, which includes semi-random mating of individuals of the opposite sex, natural death and intra-specific competition. By passing the number of…
This is an introductory review of deterministic mutation-selection models for asexual populations (i.e., quasispecies theory) and related topics. First, the basic concepts of fitness, mutations, and sequence space are introduced. Different…