种群与进化
This paper develops and analyzes a diffusion-advection model coupling population dynamics with toxicant transport, incorporating a boundary protection zone. For both upstream and downstream protection zone configurations, we investigate the…
Understanding the dynamics of antibody levels is crucial for characterizing the time-dependent response to immune events: either infections or vaccinations. The sequence and timing of these events significantly influence antibody level…
Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…
Bacteria and phages have been in an ongoing arms race for billions of years. To resist phages bacteria have evolved numerous defense systems, which nevertheless are still overcome by counter-defense mechanisms of specific phages. These…
The spotted lanternfly (Lycorma delicatula) has recently spread from its native range to several other countries and forecasts predict that it may become a global invasive pest. In particular, since its confirmed presence in the United…
Populations evolving in fluctuating environments face the fundamental challenge of balancing adaptation to current conditions against preparation for uncertain futures. Here, we study microbial evolution in partially predictable…
A population of individuals with the same genes can present heterogeneous traits (phenotypes). The prevalence of this heterogeneity can be explained as a bet-hedging strategy that improves the population proliferation rate (fitness) in…
The boreal forest plays a crucial role as a global carbon sink. This study uses two 250-year simulations of Canada's Taiga Plains, an area targeted by the 2 Billion Trees Program to evaluate afforestation and reforestation strategies that…
Prokaryotes have evolved various mechanisms to counter viruses, which in their turn developed numerous strategies to avoid defenses of the hosts. Dozens of such defense and counter-defense mechanisms have recently been discovered, yet the…
The true slime mold \textit{Physarum polycephalum} has the remarkable capability to perform self-organized activities such as network formation among food sources. Despite well reproducing the emergence of slime networks, existing models…
Computational multi-scale pandemic modelling remains a major and timely challenge. Here we identify specific requirements for a new class of models simulating pandemics across three scales: (1) pathogen evolution, often punctuated by the…
The release of Wolbachia-infected mosquitoes into Aedes aegypti infested areas is a promising strategy for localised eradication of dengue infection. Ae aegypti mosquitoes favour urban environments as breeding habitats, so are often found…
Background:Chronic kidney disease is one of the most prevalent non-communicable health issues globally, and high body mass index plays a significant role in the onset and progression of chronic kidney disease. Methods: Data on the disease…
This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
Measures of tree balance play an important role in many different research areas such as mathematical phylogenetics or theoretical computer science. Typically, tree balance is quantified by a single number which is assigned to the tree by a…
A new age-structured diffusive model for the mathematical modelling of epidemics is suggested. The model can be considered as a generalization of two models suggested earlier for the same purposes. The Lie symmetry classification of the…
Multi-scale systems often exhibit a combination of stochastic and deterministic dynamics. In compartmental models, low occupancy compartments tend to exhibit stochastic dynamics while high occupancy compartments tend to follow deterministic…
Phylogenetic networks are useful in representing the evolutionary history of taxa. In certain scenarios, one requires a way to compare different networks. In practice, this can be rather difficult, except within specific classes of…
Pre-exposure prophylaxis (PrEP) has been established as an effective tool for preventing HIV infection among men who have sex with men (MSM). However, there is the possibility of PrEP usage leading to increased sexual partners and increased…