种群与进化
As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
The Allee effect describes a decline in population fitness at low densities, potentially leading to extinction. In predator-prey systems, an emergent Allee effect can arise due to interactions such as density-dependent maturation rates and…
There are many positive and negative factors present in the predator-prey interaction which affect the net growth of the species. Fear of predation is one such factor that creates psychological stress in a prey species, which causes a…
Genetic variation in a population can sometimes arise so fast as to modify ecosystem dynamics. Such phenomena have been observed in natural predator-prey systems, and characterized in the laboratory as showing unusual phase relationships in…
Examining the dissemination dynamics of foot-and-mouth disease (FMD) is critical for revising national response plans. We developed a stochastic SEIR metapopulation model to simulate FMD outbreaks in Bolivia and explore how the national…
Maize production in sub-Saharan Africa faces significant challenges due to the maize stalk borer (Busseola fusca), a major pest that causes substantial yield losses. Chemical control methods have raised concerns about environmental impact…
Single-cell experiments revealed substantial variability in generation times, growth rates but also in birth and division sizes between genetically identical cells. Understanding how these fluctuations determine the fitness of the…
We propose a novel multi-scale modeling framework for infectious disease spreading, borrowing ideas and modeling tools from the so-called Refractory Density (RD) approach. We introduce a microscopic model that describes the probability of…
Nearly neutral theory predicts that evolutionary processes will differ in small populations compared to large populations, a key point of concern for endangered species. The nearly-neutral threshold, the span of neutral variation, and the…
The study was conducted during 2013 in Bouchebka, located in the central west of Tunisia.Such territory has a typical landscape of the transfrontier region. The series of the forest in Bouchebka is a part of the great mass of Aleppo pine.…
Disordered systems theory provides powerful tools to analyze the generic behaviors of highdimensional systems, such as species-rich ecological communities or neural networks. By assuming randomness in their interactions, universality…
We study the effect of speciation, i.e. the introduction of new species through evolution into communities, in the setting of predator-prey systems. Predator-prey dynamics is classically well modeled by Lotka-Volterra equations, also when…
In this work, we introduce a quantum-inspired epidemic model to study the dynamics of an infectious disease in a population divided into compartments. By treating the healthy population as a large reservoir, we construct a framework based…
We consider the impact of network connectivity on the dynamics of a population in a stream environment. The population is modeled using a graph theoretical framework, with habitats represented by isolated patches. We introduce a change in…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
Bayesian phylogenetics typically estimates a posterior distribution, or aspects thereof, using Markov chain Monte Carlo methods. These methods integrate over tree space by applying local rearrangements to move a tree through its space as a…
Statistical models are often structurally unidentifiable, because different sets of parameters can lead to equal model outcomes. To be useful for prediction and parameter inference from data, stochastic population models need to be…
The Price equation provides a formal account of selection building on a right-total mapping between two classes of individuals, that is usually interpreted as a parent-offspring relation. This paper presents a new formulation of the Price…
Species' interactions are shaped by their traits. Thus, we expect traits -- in particular, trait (dis)similarity -- to play a central role in determining whether a particular set of species coexists. Traits are, in turn, the outcome of an…