种群与进化
Viruses constantly undergo mutations with genomic changes. The propagation of variants of viruses is an interesting problem. We perform numerical simulations of the microscopic epidemic model based on network theory for the spread of…
Cooperative interactions pervade in a broad range of many-body populations, such as ecological communities, social organizations, and economic webs. We investigate the dynamics of a population of two equivalent species A and B that are…
Evolutionary sparse learning (ESL) uses a supervised machine learning approach, Least Absolute Shrinkage and Selection Operator (LASSO), to build models explaining the relationship between a hypothesis and the variation across genomic…
We propose a novel epidemiological model, referred to as SEIHRDV, for the numerical simulation of the COVID-19 epidemic, which we validate using data from Italy starting in September 2020. SEIHRDV features the following compartments:…
Competition between species and genotypes is a dominant factor in a variety of ecological and evolutionary processes. Biological dynamics are typically highly stochastic, and therefore, analyzing a competitive system requires accounting for…
We obtain the exact analytical traveling wave solutions of the Kolmogorov-Petrovskii-Piskunov equation with the reaction term belonging to the class of functions, which includes that of the (generalized) Fisher equation, for the particular…
Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversity in wild…
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based)…
Phages use bacterial host resources to replicate, intrinsically linking phage and host survival. To understand phage dynamics, it is essential to understand phage-host ecology. A key step in this ecology is infection of bacterial hosts.…
We investigate the role of assortative mating in speciation using the sympatric model of Derrida and Higgs. The model explores the idea that genetic differences create incompatibilities between individuals, preventing mating if the number…
1. An understanding of how biodiversity confers ecosystem stability is crucial in managing ecosystems under major environmental changes. Multiple biodiversity drivers can stabilize ecosystem functions over time. However, we know little…
Interactions between organisms are mediated by an intricate network of physico-chemical substances and other organisms. Understanding the dynamics of mediators and how they shape the population spatial distribution is key to predict…
Life uses non-equilibrium mechanisms to create ordered structures not attainable at equilibrium; the resulting order is assumed to provide functional benefits that outweigh costs of time and energy needed by these mechanisms. Here, we show…
Altruistic punishment, where individuals incur personal costs to punish others who have harmed third parties, presents an evolutionary conundrum as it undermines individual fitness. Resolving this puzzle is crucial for understanding the…
There are various examples of phenotypic plasticity in ecosystems that serve as the basis for a wide range of inducible defences against predation. These strategies include camouflage, burrowing, mimicry, evasive actions, and even…
Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or…
The human MHC transplantation loci (HLA-A, -B, -C, -DPB1, -DQB1, -DRB1) are the most polymorphic in the human genome. It is generally accepted this polymorphism reflects a role in presenting pathogen-derived peptide to the adaptive immune…
We extend the classical Susceptible-Infected-Recovered (SIR) model to a network-based framework where the degree distribution of nodes follows a Poisson distribution. This extension incorporates an additional parameter representing the mean…
Malaria is one of the deadliest diseases in the world, every year millions of people become victims of this disease and many even lose their lives. Medical professionals and the government could take accurate measures to protect the people…
When individuals interact in groups, the evolution of cooperation is traditionally modeled using the framework of public goods games. These models often assume that the return of the public good depends linearly on the fraction of…