Related papers: Accessibility percolation in random fitness landsc…
The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic…
An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability relies on the existence of sufficiently large genotype networks, that is ensembles of sequences with the same phenotype that…
We consider a fixed size population that undergoes an evolutionary adaptation in the weak mutuation rate limit, which we model as a biased Langevin process in the genotype space. We show analytically and numerically that, if the fitness…
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…
We consider populations evolving according to natural selection, mutation, and recombination, and assume that the genomes of all or a representative selection of individuals are known. We pose the problem if it is possible to infer fitness…
When biological populations expand into new territory, the evolutionary outcomes can be strongly influenced by genetic drift, the random fluctuations in allele frequencies. Meanwhile, spatial variability in the environment can also…
Understanding how genes influence phenotype across species is a fundamental challenge in genetic engineering, which will facilitate advances in various fields such as crop breeding, conservation biology, and personalized medicine. However,…
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…
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and…
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…
The adaptation rate in theoretical models of biological evolution increases with the mutation rate but only to a point when mutations into lethal states cause extinction. One would expect that removing such states should be beneficial for…
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…
Environmental heterogeneity can drive genetic heterogeneity in expanding populations; mutant strains may emerge that trade overall growth rate for an improved ability to survive in patches that are hostile to the wild type. This…
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…
Much of the current theory of adaptation is based on Gillespie's mutational landscape model (MLM), which assumes that the fitness values of genotypes linked by single mutational steps are independent random variables. On the other hand, a…
The concept of fitness as a measure for a species's success in natural selection is central to the theory of evolution. We here investigate how reproduction rates which are not constant but vary in response to environmental fluctuations,…
A microscopic agent dynamical model for diploid age-structured populations is used to study evolution of polymorphism and sympatric speciation. The underlying ecology is represented by a unimodal distribution of resources of some width.…
Adaptive dynamics is a widely used framework for modeling long-term evolution of continuous phenotypes. It is based on invasion fitness functions, which determine selection gradients and the canonical equation of adaptive dynamics. Even…
Percolation is a model for random damage to a network. It is one of the simplest models that displays a phase transition: when the network is severely damaged, it falls apart in many small connected components, while if the damage is light,…
In this paper, we explore the theory and expand upon the practice of fitness landscape analysis for optimization problems over the space of permutations. Many of the computational and analytical tools for fitness landscape analysis, such as…