种群与进化
Human cognitive responses, behavioral responses, and disease dynamics co-evolve over the course of any disease outbreak, and can result in complex feedbacks. We present a dynamic agent-based model that explicitly couples the spread of…
With significant population fractions in many societies who refuse vaccines, it is important to reconsider how vaccination is incorporated into compartmental epidemiology models. It is still most common to apply the vaccination rate to the…
A dramatic increase in the number of outbreaks of Dengue has recently been reported, and climate change is likely to extend the geographical spread of the disease. In this context, this paper shows how a neural network approach can…
In this paper, we develop a mean-field game model for SEIR epidemics on heterogeneous contact networks, where individuals choose state-dependent contact effort to balance infection losses against the social and economic costs of isolation.…
In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic…
Estimating the effective sample size (ESS) is fundamental in Bayesian phylogenetic inference to properly account for autocorrelation in MCMC samples. While methods for continuous parameters are well established, the discrete and…
The interplay between tumor cells and macrophages plays a central regulatory role in cancer progression. In this study, we developed a mathematical model that incorporates tumor cells, M1 type macrophages, M2 type macrophages and an M3 type…
The Reduction Principle states that, near a stable equilibrium under fixed viability selection, a selectively neutral modifier allele that reduces recombination rate among selected loci is favored, whereas one that increases recombination…
Species growing in environments that change in time and space will vary in their abundance across locations, even in the absence of persistent location preferences. Here we quantify this non-equilibrium effect by studying a minimal model of…
Replicating systems sustained by error-prone enzymatic amplification can undergo critical transitions between persistence and extinction. In RNA viruses, such transitions are classically governed by mutation rates and fitness landscapes,…
Ecological interaction networks are rarely homogeneous: species naturally form communities with distinct interaction structures, resulting in block-structured variance and correlation profiles in the interaction matrix. We study the…
One of the main goals of artificial life research is to recreate in artificial systems the trends for ever more complex and novel entities, interactions and processes that we see in Earth's biosphere, that is, to create open-ended systems.…
Understanding the mechanisms that govern species coexistence and biodiversity represents a fundamental challenge in ecology. This study extends the classic rock-paper-scissors model by introducing a context-dependent higher-order…
A colony of the queenless ant species, \emph{Pristomyrmex punctatus}, can broadly be seen as consisting of small-body sized worker ants and relatively larger body-sized cheater ants. Hence, in the presence of inter-colony migration, a set…
The ribosome is responsible for protein synthesis in all cells, and is the largest energy consumer in the cell. We propose that the ribosome originated as a mutualistic symbiont of an RNA-dependent RNA polymerase ribozyme, supplying…
In this paper we propose a Moran model that describes the population dynamics of two types: While the first type has a selective advantage during reproduction, the second type can avoid replacement during reproduction with some positive…
The introduction of stochasticity into continuous ecological models frequently relies on phenomenological, diagonal diffusion terms that lack a rigorous microscopic basis. We demonstrate that this standard practice fundamentally…
Herbivorous wild species constantly strive to optimize the trade-off between energy and nutrient intake and predation risk during foraging. This has led to the selection of several evolutionary traits -- such as diet, habitat selection, and…
Mutualistic interactions, where individuals from different species can benefit from each other, are widespread across ecosystems. This study develops a general deterministic model of mutualism involving two populations, assuming that…
Biological systems like long-lived clonal organisms, holobionts and clades challenge traditional evolutionary thinking since they adapt without populations or reproduction. This paper aims to provide an overarching theoretical framework…