Related papers: Adaptation through stochastic switching into trans…
Biological actuators -- from myosin motors to muscles -- follow Hill's model where a dimensionless parameter $\alpha$ captures the nonlinear coupling between contraction rate and force generation. Our prior work identified a characteristic…
We propose a model to characterize how a diffusing population adapts under a time periodic selection, while its environment undergoes shifts and size changes, leading to significant differences with classical results on fixed domains. After…
Living systems adapt to various environmental conditions by changing their internal states. Inspired by gene expression and epigenetic modification dynamics, we herein propose a generic mechanism for adaptation by combining fast oscillatory…
The study of adaptive dynamics, involving many degrees of freedom on two separated timescales, one for fast changes of state variables and another for the slow adaptation of parameters controlling the former's dynamics is crucial for…
The evolutionary process has been modelled in many ways using both stochastic and deterministic models. We develop an algebraic model of evolution in a population of asexually reproducing organisms in which we represent a stochastic walk in…
We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The…
We consider the adaptation dynamics of an asexual population that walks uphill on a rugged fitness landscape which is endowed with large number of local fitness peaks. We work in a parameter regime where only those mutants that are single…
Genetic inactivation of essential genes creates an evolutionary scenario distinct from escape from drug inhibition, but the mechanisms of microbe adaptations in such cases remain unknown. Here we inactivate E. coli dihydrofolate reductase…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
In large asexual populations, beneficial mutations have to compete with each other for fixation. Here, I derive explicit analytic expressions for the rate of substitution and the mean beneficial effect of fixed mutations, under the…
We study a general setting of neutral evolution in which the population is of finite, constant size and can have spatial structure. Mutation leads to different genetic types ("traits"), which can be discrete or continuous. Under minimal…
It is likely that the strength of selection acting upon a mutation varies through time due to changes in the environment. However, most population genetic theory assumes that the strength of selection remains constant. Here we investigate…
We study the evolution of asexual microorganisms with small mutation rate in fluctuating environments, and develop techniques that allow us to expand the formal solution of the evolution equations to first order in the mutation rate. Our…
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…
A new approach to understanding evolution [Val09], namely viewing it through the lens of computation, has already started yielding new insights, e.g., natural selection under sexual reproduction can be interpreted as the Multiplicative…
We show that the Tangled Nature model can be interpreted as a general formulation of the quasi-species model by Eigen et al. in a frequency dependent fitness landscape. We present a detailed theoretical derivation of the mutation threshold,…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
We consider a stationary continuous model of random size population with non-neutral mutations using a continuous state branching process with non-homogeneous immigration. We assume the type (or mutation) of the immigrants is random given…
Molecular evolution is often conceptualised as adaptive walks on rugged fitness landscapes, driven by mutations and constrained by incremental fitness selection. It is well known that epistasis shapes the ruggedness of the landscape's…