Related papers: Predicting evolution and visualizing high-dimensio…

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…

A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing…

Fitness consequence of dispersal depends on property of the entire landscape, which patches are available and what are the cost of moving. These are information that are not available locally when an organism make the decision to disperse.…

The purpose of this roadmap article is to draw attention to a paradigm shift in our understanding of evolution towards a perspective of ecological-evolutionary feedback, highlighted through two recent highly simplified examples of rapid…

Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish.…

Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state…

One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments which is crucial for evolvability. Recent work showed that when selective environments…

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…

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…

Sewall Wright's adaptive landscape metaphor penetrates a significant part of evolutionary thinking. Supplemented with Fisher's fundamental theorem of natural selection and Kimura's maximum principle, it provides a unifying and intuitive…

Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…

Body size or mass is one of the main factors underlying food webs structure. A large number of evolutionary models have shown that indeed, the adaptive evolution of body size (or mass) can give rise to hierarchically organised trophic…

The adaptive evolution of a population under the influence of mutation and selection is strongly influenced by the structure of the underlying fitness landscape, which encodes the interactions between mutations at different genetic loci.…

Landscape paradigm is ubiquitous in physics and other natural sciences, but it has to be supplemented with both quantitative and qualitatively meaningful tools for analyzing the topography of a given landscape. We here consider dynamic…

A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…

Predicting adaptive evolutionary trajectories is a primary goal of evolutionary biology. One can differentiate between forward and backward predictability, where forward predictability measures the likelihood of the same adaptive trajectory…

Exploring search spaces is one of the most unpredictable challenges that has attracted the interest of researchers for decades. One way to handle unpredictability is to characterise the search spaces and take actions accordingly. A…

We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic…

Machine learning and deep learning have been celebrating many successes in the application to biological problems, especially in the domain of protein folding. Another equally complex and important question has received relatively little…

Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting…