Related papers: Predicting evolution and visualizing high-dimensio…
Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to…
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…
Background: Recent experimental and theoretical studies have shown that small asexual populations evolving on complex fitness landscapes may achieve a higher fitness than large ones due to the increased heterogeneity of adaptive…
We study biological evolution in a high-dimensional genotype space in the regime of rare mutations and strong selection. The population performs an uphill walk which terminates at local fitness maxima. Assigning fitness randomly to…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
We consider the optimal dynamics in the infinite population evolution models with general symmetric fitness landscape. The search of optimal evolution trajectories are complicated due to sharp transitions (like shock waves) in evolution…
Expression level is known to be a strong determinant of a protein's rate of evolution. But the converse can also be true: evolutionary dynamics can affect expression levels of proteins. Having implications in both directions fosters the…
Evolution is the process of optimal adaptation of biological populations to their living environments. This is expressed via the concept of fitness, defined as relative reproductive success. However, it has been pointed out that this…
A model for the evolution of a finite population in a rugged fitness landscape is introduced and solved. The population is trapped in an evolutionary loop, alternating periods of stasis to periods in which it performs adaptive walks. The…
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-…
We study self-replicating molecules under externally varying conditions. Changing conditions such as temperature variations and/or alterations in the environment's resource composition lead to both non-constant replication and decay rates…
Energy landscapes play a crucial role in shaping dynamics of many real-world complex systems. System evolution is often modeled as particles moving on a landscape under the combined effect of energy-driven drift and noise-induced diffusion,…
Deep neural networks proved to be a very useful and powerful tool with many practical applications. They especially excel at learning from large data sets with labeled samples. However, in order to achieve good learning results, the network…
We consider an asexual population under strong selection-weak mutation conditions evolving on rugged fitness landscapes with many local fitness peaks. Unlike the previous studies in which the initial fitness of the population is assumed to…
We study the adaptation dynamics of an initially maladapted population evolving via the elementary processes of mutation and selection. The evolution occurs on rugged fitness landscapes which are defined on the multi-dimensional genotypic…
Much of our understanding of ecological and evolutionary mechanisms derives from analysis of low-dimensional models: with few interacting species, or few axes defining "fitness". It is not always clear to what extent the intuition derived…
One essential ingredient of evolutionary theory is the concept of fitness as a measure for a species' success in its living conditions. Here, we quantify the effect of environmental fluctuations onto fitness by analytical calculations on a…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But…
Natural selection drives populations towards higher fitness, but crossing fitness valleys or plateaus may facilitate progress up a rugged fitness landscape involving epistasis. We investigate quantitatively the effect of subdividing an…
We consider the adaptation dynamics of an asexual population that walks uphill on a rugged fitness landscape which is endowed with large number of local fitness peaks. We work in a parameter regime where only those mutants that are single…