种群与进化
In SIR-type epidemic models time derivative of prevalence $I$ can always be cast into the form $\dot{I}=(X-1)I$, where $X$ is the replacement number and recovery rate is normalized to one. Assuming $\dot{X}=f(X,I)$ for some smooth function…
The role of memory and cognition in the movement of individuals (e.g. animals) within a population, is thought to play an important role in population dispersal. In response, there has been increasing interest in incorporating spatial…
Quantifying interaction strengths between state variables in dynamical systems is essential for understanding ecological networks. Within the empirical dynamic modeling approach, multivariate S-map infers the interaction Jacobian from time…
We consider the problem of identifying jointly the ancestral sequence, the phylogeny and the parameters in models of DNA sequence evolution with insertion and deletion (indel). Under the classical TKF91 model of sequence evolution, we…
Evolutionary competition often occurs simultaneously at multiple levels of organization, in which traits or behaviors that are costly for an individual can provide collective benefits to groups to which the individual belongs. Building off…
By the end of 2021, COVID-19 had spread to over 230 countries, with over 5.4 million deaths. To contain its spread, many countries implemented non-pharmaceutical interventions, notably contact tracing and self-quarantine policies. However,…
We address the question of how to connect predictions by hydrodynamic models of how sea lice move in water to observable measures that count the number of lice on each fish in a cage in the water. This question is important for management…
I present a replication and, to some extent, a refutation of key results published by Zhong, Zhang, Li, Dai, & Yang in their 2022 paper "Species coexistence in spatial cyclic game of five species" (Chaos, Solitons and Fractals, 156:…
SARS-CoV-2 usually evolves at a relatively constant rate over time. Occasionally, however, lineages arise with higher-than-expected numbers of mutations given the date of sampling. Such lineages can arise for a variety of reasons, including…
Human papillomavirus (HPV) infection is the most common sexually transmitted infection in the world. Persistent oncogenic Human papillomavirus infection has been a leading threat to global health and can lead to serious complications such…
Understanding how viral mutant spectra organize and explore genotype space is essential for unraveling the mechanisms driving evolution at the finest scale. Here we use deep-sequencing data of an amplicon in the A2 protein of the RNA…
We consider a recently introduced model of mosquito dynamics that includes mating and progression through breeding, questing and egg-laying stages of mosquitoes using human and other vertebrate sources for blood meals. By exploiting a…
Genetic diversity is central to the process of evolution. Both natural selection and random genetic drift are influenced by the level of genetic diversity of a population; selection acts on diversity while drift samples from it. At a given…
The main goal of Multiland is to generate neutral landscapes made of several types of regions, with an exact control of the proportions occupied by each type of region. An important feature of the software is that it allows a control of the…
This study aimed to investigate the evolutionary dynamics of a three-strategy game that combines snowdrift and stag hunt games. This game is motivated by an experimental study, which found that individual solution lowers cooperation levels.…
In many real life applications, a continuous culture bioreactor may cease to function properly due to bioclogging which is typically caused by the microbial overgrowth. This is a problem that has been largely overlooked in the chemostat…
Modeling and simulation approaches for infectious disease dynamics have proven to be essential tools for effective control of the spread of epidemics in the population. Among these approaches, it is obvious that compartmental mathematical…
We show that the epidemiological Renormalization Group (eRG) framework is a useful and minimal tool to effectively describe the temporal evolution of the Dengue multi-wave pandemics. We test the framework on the Dengue history of several…
People often engage in costly cooperation, especially in repeated interactions. When deciding whether to cooperate, individuals typically take into account how others have acted in the past. For instance, when one person is deciding whether…
The paper describes and compares three approaches to modeling an epidemic spread. The first approach is a well-known system of SIR ordinary differential equations. The second is a mean-field model, in which an isolation strategy for each…