Related papers: Selection Against Demographic Stochasticity in Age…
This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These \emph{rate limits} link the…
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…
How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a…
Heterozygote disadvantage is potentially a potent driver of population genetic divergence. Also referred to as underdominance, this phenomena describes a situation where a genetic heterozygote has a lower overall fitness than either…
Understanding the temporal spread of gene drive alleles -- alleles that bias their own transmission -- through modeling is essential before any field experiments. In this paper, we present a deterministic reaction-diffusion model describing…
We study the adaptation dynamics of an initially maladapted asexual population with genotypes represented by binary sequences of length $L$. The population evolves in a maximally rugged fitness landscape with a large number of local optima.…
Biochemical and regulatory interactions central to biological networks are expected to cause extensive genetic interactions or epistasis affecting the heritability of complex traits and the distribution of genotypes in populations. However,…
We consider a stochastic individual-based model for the evolution of a haploid, asexually reproducing population. The space of possible traits is given by the vertices of a (possibly directed) finite graph $G=(V,E)$. The evolution of the…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But…
The biological theory of adaptive dynamics proposes a description of the long-term evolution of a structured asexual population. It is based on the assumptions of large population, rare mutations and small mutation steps, that lead to a…
We study the stationary state of a population evolving under the action of random genetic drift, selection and recombination in which both deleterious and reverse beneficial mutations can occur. We find that the equilibrium fraction of…
This study elaborates some examples of a simple evolutionary stochastic rate process where the population rate of change depends on the distribution of properties--so different cohorts change at different rates. We investigate the effect on…
In evolutionary algorithms, the fitness of a population increases with time by mutating and recombining individuals and by a biased selection of more fit individuals. The right selection pressure is critical in ensuring sufficient…
Populations are made up of an integer number of individuals and are subject to stochastic birth-death processes whose rates may vary in time. Useful quantities, like the chance of ultimate fixation, satisfy an appropriate difference…
We show how concepts from statistical physics, such as order parameter, thermodynamic limit, and quantum phase transition, translate into biological concepts in mutation-selection models for sequence evolution and can be used there. The…
Compared to a neutral model, purifying selection distorts the structure of genealogies and hence alters the patterns of sampled genetic variation. Although these distortions may be common in nature, our understanding of how we expect…
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…
Geographic structure can affect patterns of genetic differentiation and speciation rates. In this article, we investigate the dynamics of genetic distances in a geographically structured metapopulation. We model the metapopulation as a…
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…