种群与进化
Over the last decade several attempts have been made to extend biodiversity studies in ways that would allow researchers to explore how biodiversity-ecosystem functioning relationships may change across different spatial and temporal…
We introduce a method for approximating posterior probabilities of phylogenetic trees and reconstructing ancestral sequences under models of sequence evolution with site-dependence, where standard phylogenetic likelihood computations…
Life demonstrates remarkable homochirality of its major building blocks: nucleic acids, amino acids, sugars, and phospholipids. We propose a mechanism that places the root of life homochirality in the formation of phospholipid bilayer…
Phylogenetic trees provide a fundamental representation of evolutionary relationships, yet the combinatorial explosion of possible tree topologies renders inference computationally challenging. Classical approaches to characterizing tree…
Tree rearrangements such as Nearest Neighbor Interchange (NNI) and Subtree Prune and Regraft (SPR) are commonly used to explore phylogenetic treespace. Computing distances based on them, however, is often intractable, so the efficiently…
A class of multiple-timescale asymptotic solutions to the equations of the susceptible-infected-recovered (SIR) model is presented for the case of high basic reproduction number, with the inverse of the latter employed as the expansion…
We introduce a new type of Mean Field Game epidemiological models, in which subpopulations have different behavioral patterns: some are viewed as "highly rational" (choosing Nash-equilibrium long-term strategies) while others follow…
Mutualistic interactions are widespread in nature, from plant communities and microbiomes to human organizations. Along with competition for resources, cooperative interactions shape biodiversity and contribute to the robustness of complex…
These notes introduce probabilistic landscape models defined on high-dimensional discrete sequence spaces. The models are motivated primarily by fitness landscapes in evolutionary biology, but links to statistical physics and computer…
Evolutionary therapy (ET) aims to steer tumor evolution by adjusting treatment timing and dosing to control rather than eradicate tumor burden. Clinical use requires reliable monitoring of tumor dynamics to inform mathematical models that…
Glioblastoma Multiforme (GBM) is a highly aggressive brain tumour with limited therapeutic options and poor prognosis. This study presents a mathematical framework to investigate the efficacy of immunotherapy strategies based on cytotoxic…
Phage therapy is an alternative treatment method for bacterial infections. It has shown particular promise in reducing bacterial load while preventing antibiotic resistance. Here, we develop a mathematical model of a bacterial infection…
Dynamic programming approaches have long been applied to fit models of univariate and multivariate trait evolution on phylogenetic trees for discrete and continuous traits, and more recently adapted to phylogenetic networks with…
In this work, we integrate theoretical modeling, molecular simulation, and empirical analysis to identify and characterize evolutionary hysteresis. We first show how epistatic interactions create bistable fitness landscapes and structural…
The origin of life on Earth via the spontaneous emergence of a protocell prior to Darwinian evolution remains a fundamental open question in physics and chemistry. Here, we develop a conceptual framework based on information theory and…
We propose and analyze a model for antibiotic resistance transfer in a bacterial biofilm and examine antibiotic dosing strategies that are effective in bacterial elimination. In particular, we consider a 1-D model of a biofilm with…
We investigate a type of lunar calendar known as lists of the 'nights of the moon', found throughout East Polynesia, including Rapa Nui (Easter Island). Using computational methods, we analyzed the lexical and structural divergence of 49…
There is extensive evidence that long-term exposure to all-source PM2.5 increases mortality. However, to date, no study has evaluated whether this effect is exacerbated in the presence of wildfire events. Here, we study 60+ million older US…
In this note we demonstrate that a number of case-heavy combinatorial proofs in the mathematical phylogenetics literature can be proven more compactly using computational support. We use these techniques to also prove several new…
During the COVID-19 pandemic, Aotearoa followed an elimination strategy followed by a mitigation strategy, which saw high success and kept health impact low. However, there were inequities in health outcomes, notably that M\=aori and…