Related papers: Evolution as fitness landscape navigation: Concept…

Macroevolution is considered as a problem of stochastic dynamics in a system with many competing agents. Evolutionary events (speciations and extinctions) are triggered by fitness records found by random exploration of the agents' fitness…

We explore the connection between migration patterns and emergent behaviors of evolving populations in spatially heterogeneous environments. Despite extensive studies in ecologically and medically important systems, a unifying framework…

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…

The relationship between genotype and phenotype plays a crucial role in determining the function and robustness of biological systems. Here the evolution progresses through the change in genotype, whereas the selection is based on the…

We study how correlations in the random fitness assignment may affect the structure of fitness landscapes. We consider three classes of fitness models. The first is a continuous phenotype space in which individuals are characterized by a…

Movement is fundamental to life, shaping population dynamics, biodiversity patterns, and ecosystem structure. Recent advances in tracking technology have enabled fundamental questions about movement to be tackled, leading to the development…

Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…

Predicting fitness of biologically-active populations, communities or systems in fluctuating environments is a long-standing challenge. Phenotypic plasticity and bet-hedging strategy, two key evolutionary traits living systems harness to…

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…

Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…

Current GP frameworks are highly effective on a range of real and simulated benchmarks. However, due to the high dimensionality of the genotypes for GP, the task of visualising the fitness landscape for GP search can be difficult. This…

In epistatic fitness landscapes, the fitness effect of a mutation depends on the genetic background and may even switch between deleterious and beneficial depending on the presence of another mutation. Epistatic interactions may cause both…

We develop a generally covariant description of evolutionary dynamics that operates consistently in both genotype and phenotype spaces. We show that the maximum entropy principle yields a fundamental identification between the inverse…

Machine learning models increasingly map biological sequence-fitness landscapes to predict mutational effects. Effective evaluation of these models requires benchmarks curated from empirical data. Despite their impressive scales, existing…

The nature of epistasis has important consequences for the evolutionary significance of sex and recombination. Recent efforts to find negative epistasis as source of negative linkage disequilibrium and associated long-term sex advantage…

We discuss fitness landscapes and how they can be modified to account for co-evolution. We are interested in using the landscape as a way to model rational decision making in a toy economic system. We develop a model very similar to the…

Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is essential for…

We study the evolution of large but finite asexual populations evolving in fitness landscapes in which all mutations are either neutral or strongly deleterious. We demonstrate that despite the absence of higher fitness genotypes, adaptation…

Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…

The characterization of plasticity, robustness, and evolvability, an important issue in biology, is studied in terms of phenotypic fluctuations. By numerically evolving gene regulatory networks, the proportionality between the phenotypic…