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The evolution of complex molecular traits such as disulphide bridges often requires multiple mutations. The intermediate steps in such evolutionary trajectories are likely to be selectively neutral or deleterious. Therefore, large…
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…
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…
Organisms result from adaptive processes interacting across different time scales. One such interaction is that between development and evolution. Models have shown that development sweeps over several traits in a single agent, sometimes…
Robot multimodal locomotion encompasses the ability to transition between walking and flying, representing a significant challenge in robotics. This work presents an approach that enables automatic smooth transitions between legged and…
In theoretical ecology, models describing the spatial dispersal and the temporal evolution of species having non-overlapping generations are often based on integrodifference equations. For various such applications the environment has an…
Evolutionary adaptation is often likened to climbing a hill or peak. While this process is simple for fitness landscapes where mutations are independent, the interaction between mutations (epistasis) as well as mutations at loci that affect…
Computer experiments that mirror the evolutionary dynamics of sexual and asexual organisms as they occur in nature, tested features proposed to explain the evolution of sexual recombination. Results show that this evolution is better…
The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard…
Microscopic mechanisms of natural processes are frequently understood in terms of random walk models by analyzing local particle transitions. This is because these models properly account for dynamic processes at the molecular level and…
We have generalized our ``unified'' model of evolutionary ecology by taking into account the possible movements of the organisms from one ``patch'' to another within the same eco-system. We model the spatial extension of the eco-system…
We consider an asexually reproducing population on a finite type space whose evolution is driven by exponential birth, death and competition rates, as well as the possibility of mutation at a birth event. On the individual-based level this…
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…
Classical discrete-time adaptive controllers provide asymptotic stabilization and tracking; neither exponential stabilization nor a bounded noise gain is typically proven. In recent work it has been shown, in both the pole placement…
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 use fitness graphs, or directed cube graphs, for analyzing evolutionary reversibility. The main application is antimicrobial drug resistance. Reversible drug resistance has been observed both clinically and experimentally. If drug…
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes,…
The fitness landscape - the mapping between genotypes and fitness - determines properties of the process of adaptation. Several small genetic fitness landscapes have recently been built by selecting a handful of beneficial mutations and…
The co-evolution of structure and dynamics, known as adaptivity, is a fundamental property in various systems and drives diverse emergent behaviors. However, the adaptivity in previous works is primarily stemmed from pairwise situations,…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…