种群与进化
In mathematical phylogenetics, labeled histories describe the sequences by which sets of labeled lineages coalesce to a shared ancestral lineage. We study labeled histories for at-most-$r$-furcating trees. Consider a rooted leaf-labeled…
Bacteria evolve in volatile environments and complex spatial structures. Migration, fluctuations and environmental variability therefore have a significant impact on the evolution of microbial populations. Here, we consider a class of…
There is mounting evidence that species interactions often involve long-term memory, with highly-varying waiting times between successive events and long-range temporal correlations. Accounting for memory undermines the common Markovian…
An age structured mathematical model with time dependent parameters is developed to investigate the dynamics of dengue transmission. Its properties are thoroughly analyzed in the first part of this work, as for example its disease free…
In this work, we study the finite-population behaviour of the Reed-Frost epidemic model. Our analysis relies on the exact expression for the final epidemic size, replaced by Monte Carlo simulations in cases where the exact formula becomes…
Understanding how age-specific social contact patterns and susceptibility influence infectious disease transmission is crucial for accurate epidemic modeling. This study presents an eigenvector-based sensitivity analysis framework to…
Density dependence occurs at the individual level and thus is greatly influenced by spatial local heterogeneity in habitat conditions. However, density dependence is often evaluated at the population level, leading to difficulties or even…
Antigenic escape constitutes the main mechanism allowing rapidly evolving viruses to achieve endemicity. Beyond granting immune escape, empirical evidence also suggests that mutations of viruses might increase their inter-host…
Ecological processes depend on the flow and balance of essential elements such as carbon (C) and phosphorus (P), and changes in these elements can cause adverse effects to ecosystems. The theory of Ecological Stoichiometry offers a…
In this article we prove that the distance $d_{\mathrm{MP}}(T_1,T_2) = k$ between two unrooted binary phylogenetic trees $T_1, T_2$ on the same set of taxa can be defined by a character that is convex on one of $T_1, T_2$ and which has at…
We investigate stochastic predator-prey dynamics and their spatial phase synchronization using the Rosenzweig-MacArthur model coupled across multiple patches. Combining stochastic simulations based on the Gillespie algorithm with analytical…
This paper considers large-scale vaccination campaigns, a major platform for vaccine access in a lot of the world, as a recapture estimate of the target population marked by routine immunization. Framing the campaign as a measurement, we…
Antimicrobial resistance (AMR) poses a mounting global health crisis, requiring rapid and reliable prediction frameworks that capture its complex evolutionary dynamics. Traditional antimicrobial susceptibility testing (AST), while accurate,…
A correlation between karyotype diversity and species richness was first observed in mammals in 1980, and subsequently confirmed after controlling for phylogenetic signal. The correlation was attributed to submicroscopic factors, presumably…
A social norm defines what is good and what is bad in social contexts, as well as what to do based on such assessments. A stable social norm should be maintained against errors committed by its players. In addition, individuals may have…
Secondary forests now dominate tropical landscapes and play a crucial role in achieving COP15 conservation objectives. This study develops a replicable national approach to identifying and characterising forest ecosystems, with a focus on…
Stochastic chemical reaction or population dynamics in finite systems often terminates in an absorbing state. Yet in large spatially extended systems, the time to reach species extinction (or fixation) becomes exceedingly long. Tuning…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
Given an evolutionary model, such as Wright--Fisher (WF) or Moran, the n-coalescent problem consists of going backward in time to find for example the time to the most recent common ancestor (MRCA) and the topology of the tree. In the…
Rabies continues to pose a significant zoonotic threat, particularly in areas with high populations of domestic dogs that serve as viral reservoirs. This study conducts a comparative analysis of Stochastic Continuous-Time Markov Chain…