种群与进化
In freshwater ecosystems, aquatic insects that ontogenetically shift their habitat from aquatic to terrestrial play vital roles as prey subsidies that move nutrients and energy from aquatic to terrestrial food webs. As a result, these…
A cornerstone of the classical view of tolerance is the elimination of self-reactive T cells during negative selection in the thymus. However, high-throughput T-cell receptor sequencing data has so far failed to detect substantial…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
Dengue and Zika incidence data and the latest research have raised questions about how dengue vaccine strategies might be impacted by the emergence of Zika virus. Existing antibodies to one virus might temporarily protect or promote…
The June software package is an open-source framework for the detailed simulation of epidemics based on social interactions in a virtual population reflecting age, gender, ethnicity, and socio-economic indicators in England. In this paper,…
We investigate a tritrophic system whose cyclic dominance is modelled by the rock-paper-scissors game. We consider that organisms of one or two species are affected by movement limitations, which unbalances the cyclic spatial game.…
Population ecology theory is replete with density dependent processes. However trait-mediated or behavioral indirect interactions can both reinforce or oppose density-dependent effects. This paper presents the first two species competitive…
Wolbachia infection in Anopheles albimanus mosquitoes can render mosquitoes less capable of spreading malaria. We develop and analyze an ordinary differential equation model to evaluate the effectiveness of Wolbachia-based vector control…
In the analysis of complex ecosystems it is common to use random interaction coefficients, often assumed to be such that all species are statistically equivalent. In this work we relax this assumption by choosing interactions according to…
Feedback loops are essential for regulating cell proliferation and maintaining the delicate balance between cell division and cell death. Thanks to the exact solution of a few simple models of cell growth it is by now clear that stochastic…
Ecosystems are commonly organized into trophic levels -- organisms that occupy the same level in a food chain (e.g., plants, herbivores, carnivores). A fundamental question in theoretical ecology is how the interplay between trophic…
If the origin of life is rare and sensitive to the local conditions at the site of its emergence, then, using the principle of mediocrity within a multiverse framework, we may expect to find ourselves in a universe that is better than usual…
The transmission dynamics of infectious diseases in animal production are driven by several propagation routes. Contaminated vehicles traveling between farms have been associated with indirect disease transmission. In this study, we used…
This paper conducts a numerical study of a geometrical structure called $\epsilon$-school for predator-avoidance fish schools, based on our previous mathematical model. Our results show that during a predator attack, the number of…
Environmental heterogeneity can drive genetic heterogeneity in expanding populations; mutant strains may emerge that trade overall growth rate for an improved ability to survive in patches that are hostile to the wild type. This…
Genome-wide association study (GWAS) tests single nucleotide polymorphism (SNP) markers across the genome to localize the underlying causal variant of a trait. Because causal variants are seldom observed directly, a surrogate model based on…
Conjugation is a central characteristic of plasmid biology and an important mechanism of horizontal gene transfer in bacteria. However, there is little consensus on how to accurately estimate and report plasmid conjugation rates, in part…
Antibiotics resistance has caused much complication in the treatment of diseases, where the pathogen is no longer susceptible to specific antibiotics and the use of such antibiotics are no longer effective for treatment. A recent study that…
The Voter model is a well-studied stochastic process that models the invasion of a novel trait $A$ (e.g., a new opinion, social meme, genetic mutation, magnetic spin) in a network of individuals (agents, people, genes, particles) carrying…
This work presents a population genetic model of evolution, which includes haploid selection, mutation, recombination, and drift. The mutation-selection equilibrium can be expressed exactly in closed form for arbitrary fitness functions…