种群与进化
Tipping points are one of the hot topics in modern physics of complex systems. But what is a tipping point? A generic definition declares it as ``a state of the system where a small change in its parameters can lead to a significant change…
Theoretical ecology has traditionally equated persistence with the stability of a fixed equilibrium point. Here we argue that the primary threat to ecosystem persistence need not be the loss of stability, but instead the escape of the…
Evolutionary analyses of large populations commonly incorporate stochasticity through temporal variation in selection while treating genetic transmission as fixed. Much less attention has been given to stochasticity in transmission itself.…
Fish migration is a dynamic phenomenon observed in many surface water bodies on the earth, while its understanding is still insufficient. Particularly, the biological mechanism behind fish migration is not fully understood. Moreover, its…
Population size is a key metric for management and conservation. This is especially true for large carnivore populations for which management decisions are often based on population size estimates. In France, gray wolves (Canis lupus) have…
Infectious disease outbreaks have precipitated a profusion of mathematical models. Epidemic curves predicted by these models are typically qualitatively similar, despite distinct model assumptions, but there is no theoretical explanation…
Background: Human behavior shapes infectious disease dynamics, yet its integration into transmission models remains fragmented. Recent epidemics, particularly COVID-19, highlight the need for models capturing adaptation to perceived risk,…
Diversity-Generating Retroelements (DGRs) create rapid, targeted variation within specific genomic regions in phages and bacteria. They operate through stochastic retro-transcription of a template region (TR) into a variable region (VR),…
Natural birth and death are fundamental mechanisms of population dynamics in ecosystems and have played pivotal roles in shaping population dynamics. Nevertheless, in studies of cyclic competition systems governed by the rock-paper-scissors…
The loss of biodiversity due to the likely widespread extinction of species in the near future is a focus of current concern in conservation biology. One approach to measure the impact of this extinction is based on the predicted loss of…
Complex change is often described as "evolutionary" in economics, policy, and technology, yet most system dynamics models remain constrained to fixed state spaces and equilibrium-seeking behavior. This paper argues that evolutionary…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
Household size impacts the spread of respiratory infectious diseases: Larger households tend to boost transmission by acquiring external infections more frequently and subsequently transmitting them back into the community. Furthermore,…
We investigate the spatial organization of dengue cases in the city of Recife, Brazil, from 2015 to 2024, using tools from statistical physics and topological data analysis. Reported cases are modeled as point clouds in a metric space, and…
Antimicrobial protocols - using substances such as antibiotics or disinfectants - remain the preferred option for preventing the spread of pathogenic bacteria. However, bacteria can develop mechanisms to reduce their antimicrobial…
In the context of multistability driven diseases, like cancer, spatiotemporal plasticity plays a significant role to achieve a spectrum of phenotypic variations. The interplay between gene regulatory networks and environmental factors, such…
Classical ecological models predict that large, diverse communities should be unstable, presenting a central challenge to explaining the stable biodiversity seen in nature. We revisit this long-standing problem by extending the generalized…
Dryland vegetation can survive water stress by forming spatial patterns but is often subjected to herbivory as an additional stress that puts it at risk of desertification. Understanding the mutual relationships between vegetation…
Summary: A bioinformatics tool is presented for estimating recent effective population size by using a neural network to automatically compute linkage disequilibrium-related features as a function of genomic distance between polymorphisms.…
Motivation: mtDNA distance matrices are standard inputs for distance-based phylogeny, but computing all pairwise alignments is costly. Missing entries can degrade inferred topology and branch lengths, and generic matrix-completion methods…