种群与进化
The COVID-19 pandemic is spreading rapidly around the world, causing countries to impose lockdowns and efforts to develop vaccines on a global scale. However, human-to-animal and animal-to-human transmission cannot be ignored, as severe…
Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the…
Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian fitness and $N_e$ and…
Based on the SIRD-model a new model including time-delay is proposed for a description of the outbreak of the novel coronavirus Sars-CoV-2 pandemic. All data were analysed by representing all quantities as a function of the susceptible…
Stochastic diffusion is the noisy and uncertain process through which dynamics like epidemics, or agents like animal species, disperse over a larger area. Understanding these processes is becoming increasingly important as we attempt to…
Social contact studies, investigating social contact patterns in a population sample, have been an important contribution for epidemic models to better fit real life epidemics. A contact matrix $M$, having the \emph{mean} number of contacts…
This paper describes a recently developed software called ``TGL-Lambda'' enables quantifying lure attractiveness under a variety of field capture scenarios including mixed lure/trap combinations. TGL-Lambda delivers a flexible approach to…
Master equations provide researchers with the ability to track the distribution over possible states of a system. From these equations, we can summarize the temporal dynamics through a method of moments. These distributions and their…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
Even in large systems, the effect of noise arising from when populations are initially small can persist to be measurable on the macroscale. A deterministic approximation to a stochastic model will fail to capture this effect, but it can be…
Carnivores interact with herbivores to indirectly impact plant populations, creating trophic cascades within plant-herbivore-carnivore systems. We developed and analyzed a food chain model to gain a mechanistic understanding of the critical…
Introduction. Here we reported the virological, entomological and epidemiological characteristics of the large autochthonous outbreak of dengue (DENV) occurred in a small village of the Lombardy region (Northern Italy) during summer 2023.…
We present a version of the classical Moran model, in which mutations are taken into account; the possibility of mutations was introduced by Moran in his seminal paper, but it is more often overlooked in discussing the Moran model. For this…
In this study, we couple a population dynamics model with a model for optimal foraging to study the interdependence between individual-level cost-benefits and population-scale dynamics. Specifically, we study the logistic growth model,…
Arboviruses represent a significant threat to human, animal, and plant health worldwide. To elucidate transmission, anticipate their spread and efficiently control them, mechanistic modelling has proven its usefulness. However, most models…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
We expand the calculation of the upper bound on epidemic overshoot in SIR models to account for nonlinear incidence. We lay out the general procedure and restrictions to perform the calculation analytically for nonlinear functions in the…
It has been recently shown that the exponential growth rate of a population of bacterial cells starting from a single cell shows transient oscillations due to early synchronized bursts of division. These oscillations are enhanced by cell…
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of…
To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside…