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A simple model of macroevolution is proposed exhibiting both the property of punctuated equilibrium and the dynamics of potentialities for different species to evolve towards increasingly higher complexity. It is based on the phenomenon of…
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…
Cells maintain a stable size as they grow and divide. Inspired by the available experimental data, most proposed models for size homeostasis assume size control mechanisms that act on a timescale of one generation. Such mechanisms lead to…
Phenotypic evolution implies sequential fixations of new genomic sequences. The speed at which these mutations fixate depends, in part, on the relative fitness (selection coefficient) of the mutant vs. the ancestor. Using a simple…
Growth-fragmentation processes describe the evolution of systems of cells which grow continuously and fragment suddenly; they are used in models of cell division and protein polymerisation. Typically, we may expect that in the long run, the…
Weak selection, which means a phenotype is slightly advantageous over another, is an important limiting case in evolutionary biology. Recently it has been introduced into evolutionary game theory. In evolutionary game dynamics, the…
A class of models for large-scale evolution and mass extinctions is presented. These models incorporate environmental changes on all scales, from influences on a single species to global effects. This is a step towards a unified picture of…
In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly…
A fundamental problem in protobiological dynamics is to understand how chemically generated polymers can form persistent sequence distributions before the emergence of replication. We study deterministic polymer growth in which each finite…
Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the…
Frequency-dependent selection reflects the interaction between different species as they battle for limited resources in their environment. In a stochastic evolutionary game the species relative fitnesses guides the evolutionary dynamics…
We consider the effect of network structure on the evolution of a population. Models of this kind typically consider a population of fixed size and distribution. Here we consider eco-evolutionary dynamics where population size and…
Genetic interactions can strongly influence the fitness effects of individual mutations, yet the impact of these epistatic interactions on evolutionary dynamics remains poorly understood. Here we investigate the evolutionary role of…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
During bouts of evolutionary diversification, such as adaptive radiations, the emerging species cluster around different locations in phenotype space, How such multimodal patterns in phenotype space can emerge from a single ancestral…
All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments…
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,…
Even closely related prokaryotes show an astounding diversity in their ability to grow in different nutritional environments. Mechanistically, this diversity arises predominantly through horizontal gene transfer, the exchange of DNA between…
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…