Related papers: Evolution favors protein mutational robustness in …
At any moment in time, evolution is faced with a formidable challenge: refining the already highly optimised design of biological species, a feat accomplished through all preceding generations. In such a scenario, the impact of random…
The fitness contribution of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations under selection, and can shape the…
Current-day genomes bear the mark of the evolutionary processes. One of the strongest indications is the sequence homology among families of proteins that perform similar biological functions in different species. The number of proteins in…
We study the relative importance of "top-speed" (long-term growth rate) and "acceleration" (how quickly the long-term growth rate can be reached) in the evolutionary race to increase population size. We observe that fitness alone does not…
We examine the dynamics of an age-structured population model in which the life expectancy of an offspring may be mutated with respect to that of the parent. While the total population of the system always reaches a steady state, the…
Background. Organisms use a variety of mechanisms to protect themselves against perturbations. For example, repair mechanisms fix damage, feedback loops keep homeostatic systems at their setpoints, and biochemical filters distinguish signal…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
Naturally evolving proteins gradually accumulate mutations while continuing to fold to thermodynamically stable native structures. This process of neutral protein evolution is an important mode of genetic change, and forms the basis for the…
The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of…
On rugged fitness landscapes where sign epistasis is common, adaptation can often involve either individually beneficial "uphill" mutations or more complex mutational trajectories involving fitness valleys or plateaus. The dynamics of the…
The goal of this paper is to provide mathematically rigorous tools for modelling the evolution of a community of interacting individuals. We model the population by a measure space where the measure determines the abundance of individual…
When beneficial mutations are rare, they accumulate by a series of selective sweeps. But when they are common, many beneficial mutations will occur before any can fix, so there will be many different mutant lineages in the population…
When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are…
The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…
Many life-history traits, like the age at maturity or adult longevity, are important determinants of the generation time. For instance, semelparous species whose adults reproduce once and die have shorter generation times than iteroparous…
We explore the connection between evolution and large-deviation theory. To do so, we study evolutionary dynamics in which individuals experience mutations, reproduction, and selection using variants of the Moran model. We show that, in the…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Previous evolutionary studies demonstrated how evaluating evolving agents in variable environmental conditions enable them to develop solutions that are robust to environmental variation. We demonstrate how the robustness of the agents can…