种群与进化
Using as a narrative theme the example of Darwin's finches, a microscopic agent-based model is introduces to study sympatric speciation as a result of competition for resources in the same ecological niche. Varying competition among…
Species-rich ecosystems often exhibit multiple stable states with distinct species compositions. Yet, the factors determining the likelihood of each state's occurrence remain poorly understood. Here, we characterize and explain the…
A novel mathematical framework is proposed to describe the ecological and evolutionary consequences of consumer--resource interactions. Both the consumer and resource are assumed to consist of several (sub)species, which interact between…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
RNA-based vaccination has been broadly applied in the COVID pandemic. A characteristic of the immunization was fast waning immunity. However, the time scale of this process varied considerable for virus subtypes and among individuals.…
We extend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall \& D'Souza, 2025). That work showed that time itself is multifractal -- not a universal background dimension, but an…
Basic and instantaneous reproduction numbers, "R" _"0" and "R" _"t" , are important metrics to assess progress of an epidemic and effectiveness of preventative interventions undertaken, and also to estimate coverage needed for vaccination.…
Dengue continues to pose a major global threat, infecting nearly 390 million people annually. Recognizing the pivotal role of vector competence (vc), recent research focuses on mosquito parameters to inform transmission modeling and vector…
Habitat fragmentation, often driven by human activities, alters ecological landscapes by disrupting connectivity and reshaping species interactions. In such fragmented environments, habitats can be modeled as networks, where individuals…
Social contact patterns are a key input to many infectious disease models. Contact surveys, where participants are asked to provide information on their recent close and casual contacts with others, are one of the standard methods to…
A major challenge for community ecology is using spatio-temporal data to infer parameters of dynamical models without conducting laborious experiments. We present a novel framework from statistical physics -- Maximum Caliber -- to…
Estimating species and gene trees from sequence data is challenging. Gene tree estimation is often hampered by low phylogenetic signal in alignments, leading to inaccurate trees. Species tree estimation is complicated by incomplete lineage…
Bacteria develop resistance to antibiotics through various mechanisms, with the specific mechanism depending on the drug-bacteria pair. It remains unclear, however, which resistance mechanism best supports favorable treatment outcomes,…
Island endemism is shaped by complex interactions among environmental, ecological, and evolutionary factors, yet the relative contributions of topography, climate, and land cover remain incompletely quantified. We investigated the drivers…
Reliable short term forecasting can provide potentially lifesaving insights into logistical planning, and in particular, into the optimal allocation of resources such as hospital staff and equipment. By reinterpreting COVID-19 daily cases…
Growing literatures on epidemic and rumor dynamics show that infection and information coevolve. We present a unified framework for modeling the spread of infection and information: a general class of interaction-driven fluid-limit models…
Zika fever, a mosquito-borne viral disease with potential severe neurological complications and birth defects, remains a significant public health concern. The epidemiological models often oversimplify the dynamics of Zika transmission by…
We analyse a series of bacterial growth models with in-built inter-individual variation in rates of cell division. We show that this variation leads to reduced population growth in favorable regimes and reduced population killing in…
In this paper we use Species Distribution Models (SDMs) to forecast the future diversity and distribution of orchids in Great Britain and Ireland under scenarios of climate and land-use change. The study analyzes occurrence data for native…
Aquaculture is pivotal for global food security but faces significant challenges from infectious diseases, particularly those caused by Streptococcus species such as Streptococcus iniae and Streptococcus agalactiae. These pathogens induce…