种群与进化
Adaptive therapy (AT) is designed to postpone the emergence of drug resistance by exploiting evolutionary competition among tumor subclones. Most mathematical models of AT assume a binary population structure of drug-sensitive and…
We present a methodology providing a one-directional link from within-host individual heterogeneity to population-level disease transmission dynamics. The methodology works in several steps. A within-host model is investigated numerically…
Many biological processes, from cell division to viral lysis, are triggered when an internal stochastic variable reaches a threshold. Here we introduce Branching under First-Passage Resetting, a general framework in which replication events…
Multispecies ecosystems modelled by generalized Lotka-Volterra equations exhibit stationary population abundances, where large number of species often coexist. Understanding the precise conditions under which this is at all feasible and…
The replication dynamics (differential equation system) is the foundation of evolutionary game theory. When n=2, there are four possible types of replication dynamics. When n=3, there are 49 possible types of replication dynamics. However,…
Oceania and Island Southeast Asia have a rich, yet understudied, human genomic landscape. This region encompasses some of the first areas inhabited by humans following the out-of-Africa expansion, includes populations with the highest…
In this work, we introduce a Tropical Axial Attention neural reasoning architecture that replaces vanilla softmax dot-product attention with max-plus operators, inducing a piecewise-linear structure aligned with dynamic programming…
We extend the $N$ branching Brownian motions model of population invasion to higher-order asexual reproduction. Increasing reproduction order leads to qualitative changes: invasion fronts generically cease to exist beyond binary…
Phylogenetic trees are the primary framework for conveying evolutionary relationships. While many tools exist for visualizing phylogenetic trees, most are limited to static graphics, require coding expertise, or are developed for a specific…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
Biological systems perform complex multi-step processes in a reproducible way despite underlying stochasticity. The standard explanation is micromanagement by molecular machinery that recognizes and corrects specific errors. Here we study…
Individual contributions to the spread of an epidemic vary widely due to an individual's location in a social network and their intrinsic ability to spread or contract diseases. While the effect of heterogeneous population structure and…
There is little debate about the importance of the ancestral recombination graph in population genetics. An important theoretical tool, the main obstacle to its widespread usage is the computational cost required to match the…
We develop a stochastic framework for viral population dynamics at the cellular level that explicitly incorporates the replication cycle with random stage durations. The model is formulated as a structured birth-death process coupled with a…
Complex microbial habitats see the spatial competition of different clonal bacterial populations that switch between different phenotypes. Here, we determine the effect of this subpopulation structure on the invasion of one species by…
Traditional population models that include predator-prey interactions attribute demographic changes directly to predation-related effects. However, predator-induced fear in prey has increasingly been recognised as an important factor…
The origin of life is often framed primarily as a chemical problem, yet life's defining feature is evolution. Advances in geochemistry, prebiotic chemistry, and molecular biology have produced diverse scenarios for the emergence of genomes,…
In this paper, we introduce gonosomic algebras to algebraically translate the phenomenon of genetic sterility. Gonosomic algebras extend the concept of gonosomal algebras used as algebraic model of genetic phenomena related to…
Microbial adaptation to extreme stress, such as starvation, antimicrobial exposure, or freezing often reveals fundamental trade-offs between survival and proliferation. Understanding how populations navigate these trade-offs in fluctuating…
The dataset collected at the Cape Rodney-Okakari Point Marine (CR-OPM) reserve on the North Island of New Zealand is rather unique. It describes the cyclic time evolution of a rocky intertidal community, with the relative abundances of the…