A stochastic analysis of the interplay between antibiotic dose, mode of action, and bacterial competition in the evolution of antibiotic resistance

PLoS Computational Biology, Journal Year: 2023, Volume and Issue: 19(8), P. e1011364 - e1011364

Published: Aug. 14, 2023

The use of an antibiotic may lead to the emergence and spread bacterial strains resistant this antibiotic. Experimental theoretical studies have investigated drug dose that minimizes risk resistance evolution over course treatment individual, showing optimal will either be highest or lowest concentration possible administer; however, no analytical results exist help decide between these two extremes. To address gap, we develop a stochastic mathematical model dynamics under treatment. We explore various scenarios density regulation (bacterial affects cell birth death rates), modes action (biostatic biocidal). derive for survival probability subpopulation until end treatment, size at carriage time it is replaced by sensitive one after verify with simulations. find scenario mode are important determinants subpopulation. Resistant cells survive best when competition reduces biocidal antibiotics. Compared analogous deterministic model, population reached type larger slightly reduced loss cells. Moreover, obtain prediction maximizes cells, which dosage (not) administer. Our amenable experimental tests link within host scales in epidemiological models.

Language: Английский

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Graph-structured populations elucidate the role of deleterious mutations in long-term evolution

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 10, 2025

Language: Английский

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Exploring the Evolution of Altruistic Punishment with a PDE Model of Cultural Multilevel Selection

Bulletin of Mathematical Biology, Journal Year: 2025, Volume and Issue: 87(4)

Published: March 12, 2025

Language: Английский

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Understanding evolutionary and ecological dynamics using a continuum limit

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(11), P. 5857 - 5873

Published: May 1, 2021

Abstract Continuum limits in the form of stochastic differential equations are typically used theoretical population genetics to account for genetic drift or more generally, inherent randomness model. In evolutionary game theory and ecology, however, this method is less frequently study demographic stochasticity. Here, we review use continuum ecology evolution. Starting with an individual‐based model, derive a large size limit, (stochastic) equation which called limit. By example Wright–Fisher diffusion, outline how compute stationary distribution, fixation probability certain type, mean extinction time using context logistic growth equation, approximate quasi‐stationary distribution finite population.

Language: Английский

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Limits on the evolutionary rates of biological traits

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: May 17, 2024

This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These limits link variability in a population to rates. In particular, high variances fitness and quantitative trait allow for fast changes trait's average. contrast, low makes less susceptible random due The results this article generalize Fisher's fundamental theorem selection dynamics mutations drift, via trade-off relations constrain rates arbitrary traits. be used probe questions various biology ecology settings. They apply, instance, within across species bacteria strains. apply any trait, e.g., from species' weights lengths DNA strands.

Language: Английский

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Eco-evolutionary dynamics for finite populations and the noise-induced reversal of selection

The American Naturalist, Journal Year: 2024, Volume and Issue: unknown, P. 000 - 000

Published: Sept. 18, 2024

AbstractTheoretical studies from diverse areas of population biology have shown that demographic stochasticity can substantially impact evolutionary dynamics in finite populations, including scenarios where traits are disfavored by natural selection nevertheless increase frequency through the course evolution. Here, we analytically describe eco-evolutionary populations first principles. We investigate how noise-induced effects alter fate which total size may vary stochastically over time. Starting a generic birth-death process, derive set stochastic differential equations (SDEs) individuals bearing discrete traits. Our recover well-known descriptions dynamics, such as replicator-mutator equation, Price and Fisher's fundamental theorem infinite limit. For our SDEs reveal predictably bias trajectories to favor certain traits, phenomenon call "noise-induced biasing." show biasing acts two distinct mechanisms, "direct" "indirect" mechanisms. While direct mechanism be identified with classic bet-hedging theory, indirect is more subtle consequence frequency- density-dependent stochasticity. lead evolution proceeding direction opposite predicted By extending generalizing some standard genetics, thus appears alongside, interacts with, well-understood forces neutral drift determine nonconstant size.

Language: Английский

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Turnover shapes evolution of birth and death rates

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: July 12, 2022

Population turnover, a key trait shaped by the organism’s life history strategy, plays an important role in eco-evolutionary dynamics fixing timescale for individual birth and death events as well determining level of demographic stochasticity related to growth. Yet, standard theory population genetics, models heavily used data analysis, have largely ignored turnover. Here we propose reformulation genetics starting from first principles show that turnover is evolutionarily important. We derive general stochastic differential equation frequency competing birth-death processes determine appropriate corrections essential results regarding fixation, establishment, substitution mutants. Our reveal how both absolute relative rates influence evolution. further describe deterministic selection, flux, which operates small populations. Finally, analyse evolution mean it explains mechanisms underlying transitions. In conclusion, our explicitly life-history strategies, stochasticity, ecological feedback, are inseparably intertwined, thus calling unified development death.

Language: Английский

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Maintenance of long-term transposable element activity in genomes through regulation by nonautonomous elements

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 17, 2024

Abstract Transposable elements are DNA sequences that can move and replicate within genomes. Broadly speaking, two element types exist: autonomous elements, which encode the necessary enzymes for transposition, nonautonomous rely on these produced by their transposition. Nonautonomous have been proposed to regulate transposable numbers, is a possible explanation continued transposition activity over long evolutionary times. However, previous modeling studies indicate interactions between usually result in extinction of one type. Here, we study stochastic model allows stable coexistence elements. We determine conditions derive an analytical expression stationary distribution copy showing fluctuations number stationarity. find variances each be expressed as function averages covariance, enabling data comparison validation. These results suggest besides silencing or domestication regulated may alternative outcome could example explain co-evolutionary history LINE1 Alu human ancestry.

Language: Английский

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A stochastic field theory for the evolution of quantitative traits in finite populations

Theoretical Population Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 1, 2024

Infinitely many distinct trait values may arise in populations bearing quantitative traits, and modelling their population dynamics is thus a formidable task. While classical models assume fixed or infinite size, which the total size fluctuates due to demographic noise births deaths can behave qualitatively differently from constant density-dependent dynamics. In this paper, I present stochastic field theory for eco-evolutionary of finite one-dimensional traits. derive equations that describe evolution densities, frequencies, mean value any population. These recover well-known results such as replicator-mutator equation, Price gradient limit. For populations, intricate interplay between natural selection, noise-induced feedback, neutral genetic drift determining evolutionary trajectories. My methods use ideas statistical physics, calculus variations, SPDEs, providing alternative complement measure-theoretic martingale approach more common literature.

Language: Английский

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Analyzing dynamic species abundance distributions using generalized linear mixed models

Ecology, Journal Year: 2022, Volume and Issue: 103(9)

Published: May 13, 2022

Abstract Understanding the mechanisms of ecological community dynamics and how they could be affected by environmental changes is important. Population dynamic models have well known parameters that describe key characteristics species such as effect noise demographic variance on dynamics, long‐term growth rate, strength density regulation. These are also central for detecting understanding in communities species; however, incorporating vital into challenging. In this paper, we demonstrate generalized linear mixed specified intercept‐only with different random effects can used to fit abundance distributions. Each has an ecologically meaningful interpretation either describing general species‐specific responses stochasticity time or space, variation rate carrying capacity among species. We use simulations show accuracy estimation depends regulation discrete population dynamics. The covariance parameters, corresponding statistical uncertainties, demonstrated case studies fish bat communities. find heterogeneity main factor spatial temporal similarity both studies.

Language: Английский

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