种群与进化
The maintenance of diversity, the `commonness of rarity', and compositional turnover are ubiquitous features of species-rich communities. Through a minimal model, we consider how these features reflect the interplay between environmental…
We consider the following question: how close to the ancestral root of a phylogenetic tree is the most recent common ancestor of $k$ species randomly sampled from the tips of the tree? For trees having shapes predicted by the Yule-Harding…
Large animal groups -- bird flocks, fish schools, insect swarms -- are often assumed to form by gradual aggregation of sparsely distributed individuals. Using a mathematically precise framework based on time-varying directed interaction…
Building upon the eco-evolutionary game dynamics framework established by Tilman et al., we investigate stochastic fluctuations in a two-strategy system incorporating environmental feedback mechanisms, where the payoff matrix exhibits…
The genetic evolution of SARS-CoV-2 has caused recurring epidemic waves, understanding its global dispersal patterns is critical for effective surveillance. We developed the Site-based mutation dynamics - Equal Power Sampling (S-EPS)…
Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we systematically assess the impact of various fixed-topology…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Mechanistic models are essential tools across ecology, epidemiology, and the life sciences, but parameter inference remains challenging when likelihood functions are intractable. Approximate Bayesian Computation with Sequential Monte Carlo…
We considered a model for an infectious disease outbreak, when the depletion of susceptible individuals is negligible, and assumed that individuals adapt their behavior according to the information they receive about new cases. In line with…
Clemmesen's hook refers to a commonly observed slowdown and rebound in breast cancer incidence around the age at menopause. It suggests a shift in the underlying carcinogenic dynamics, but the mechanistic basis remains poorly understood.…
We look at the interaction of dispersal and environmental stochasticity in $n$-patch models. We are able to prove persistence and extinction results even in the setting when the dispersal rates are stochastic. As applications we look at…
The epidemiological dynamics of Mycoplasma pneumoniae is characterized by poorly understood complex multiannual cycles. The origins of these cycles have long been debated, and multiple explanations of varying complexity have been suggested.…
Evolutionarily stable strategy (ESS) is the defining concept of evolutionary game theory. It has a fairly unanimously accepted definition for the case of symmetric games which are played in a homogeneous population where all individuals are…
Collective vigilance describes how animals in groups benefit from the predator detection efforts of others. Empirical observations typically find either a many-eyes strategy with all (or many) group members maintaining a low level of…
Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a…
Understanding how cooperation emerges and persists is a central challenge in evolutionary game theory. Existing models often rely on restricted, hand-picked strategy sets, which can overlook critical behavioural pathways. A recent…
Consider a population of organisms that harvest free energy from their environment to reproduce. This paper shows that if the organisms' reproductive rates are proportional to the amount of physical free energy that they can convert into…
Benthic habitat is challenging due to the environmental complexity of the seafloor, technological limitations, and elevated operational costs, especially in under-explored regions. This generates knowledge gaps for the sustainable…
A pipeline to evaluate the evolution of viral dynamics based on a new model-driven approach has been developed in the present study. The proposed methods exploit real data and the multiscale structure of the infection dynamics to provide…
There are complex interactions between antibody levels and epidemic propagation, the antibody level of an individual influences the probability of infection, and the spread of the virus influences the antibody level of each individual.…