种群与进化
We develop a framework for non-Markovian, well-mixed SIR and SIS models beyond mean field, utilizing the continuous-time random walk formalism. Using a gamma distribution for the infection and recovery inter-event times as a test case, we…
Complex spatial structure, with partially isolated subpopulations, and environment heterogeneity, such as gradients in nutrients, oxygen, and drugs, both shape the evolution of natural populations. We investigate the impact of environment…
Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the convergent evolution of synonymous codon…
Several theoretical models predict that spatial patterning increases ecosystem resilience. However, these predictions rely on simplifying assumptions, such as assuming isotropic and infinitely large ecosystems, and empirical evidence…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Foraging is a central decision-making behavior performed by all animals, essential to garnishing enough energy for an organism to survive. Similarly, mating is crucial for evolutionary continuity and offspring production. Mate choice is one…
We present a unified theoretical model relating stochastic microscopic epidemic dynamics with macroscopic non-linear population behavior. Utilizing the Doi-Peliti formalism, we model the pathogen as a gauge mediator field coupled to…
In this paper, we introduce a gauge-mediated Epidemiological Model inspired by Quantum Electrodynamics (QED). In this model, the ``direct contact'' paradigm of classical SIR models is replaced by a gauge-mediated interaction where the…
The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…
Anthropogenic activity threatens biodiversity through climate change, habitat fragmentation, and increasing frequency and scale of disturbance. Various theoretical studies have sought to shed light on how these factors could promote or…
Evolutionary graph theory (EGT) studies the effect of population structure on evolutionary dynamics. The vertices of the graph represent the $N$ individuals. The edges denote interactions for competitive replacement. Two standard update…
We consider a population constituted by two types of individuals; each of them can produce offspring in two different islands (as a particular case the islands can be interpreted as active or dormant individuals). We model the evolution of…
Although many phenotypic traits are determined by a large number of genetic variants, the behavior of allele frequencies in a polygenic trait is not completely understood. The problem is especially challenging when the quantitative trait of…
We consider the SEIRS epidemiology model with such features of the COVID-19 outbreak as: abundance of unidentified infected individuals, limited time of immunity and a possibility of vaccination. The control of the pandemic dynamics is…
The transmission dynamics of the common enteric pathogen Lawsonia intracellularis are not fully understood. To evaluate the transmission parameters of this pathogen, one and two conventional weaned pigs, were inoculated with a pure culture…
We report the emergence of Log-normal Superstatistics in the collective motion of ants confined in a quasi-2D arena and exposed to a panic-inducing stimulus. A data-driven superstatistical Langevin model accurately reproduces the transition…
Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…
Short tandem repeats (STRs) are low-entropy regions in the genome, consisting of a short (1-6 bp) unit that is consecutively repeated multiple times. They are known for high mutational instability, due to so-called stutter-mutations, in…
What substrate features allow life? We exhaustively classify all 262,144 outer-totalistic binary cellular automata rules with Moore neighbourhood for self-replication and produce phase diagrams in the $(\lambda, F)$ plane, where $\lambda$…
One of the fundamental questions in population dynamics is how biological populations respond to environmental perturbations. In population dynamics, the mean fitness and the fraction of a trait in the steady state are important because…