Antibiotics in microbial communities: an ecological frame of resistance DOI Creative Commons
Andrew D. Letten, Alex R. Hall, Jonathan M. Levine

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2020, Volume and Issue: unknown

Published: May 11, 2020

Abstract There is growing awareness that our ability to tackle antibiotic resistance limited by a lack of mechanistic understanding the communities in which resistant microbes are embedded. The widespread coexistence and sensitive bacteria microbial systems presents an especially frustrating paradox. Recent advances ecological theory offer powerful framework probe mechanisms regulating intra- inter-specific coexistence, but significance this body problem antimicrobial has been largely overlooked. In Perspectives article, we draw on emerging illustrate how changes both competitive niche overlap critical for costs persistence pathogens systems. We then show trade-offs resource acquisition strategies can have counter-intuitive consequences susceptible genotypes variable environments. These insights highlight numerous opportunities innovative experimental theoretical research into microbiome.

Language: Английский

Using ecological coexistence theory to understand antibiotic resistance and microbial competition DOI
Andrew D. Letten, Alex R. Hall, Jonathan M. Levine

et al.

Nature Ecology & Evolution, Journal Year: 2021, Volume and Issue: 5(4), P. 431 - 441

Published: Feb. 1, 2021

Language: Английский

Citations

83
Integrating eco‐evolutionary dynamics and modern coexistence theory DOI Creative Commons
Masato Yamamichi, Theo Gibbs, Jonathan M. Levine

et al.

Ecology Letters, Journal Year: 2022, Volume and Issue: 25(10), P. 2091 - 2106

Published: Aug. 12, 2022

Community ecology typically assumes that competitive exclusion and species coexistence are unaffected by evolution on the time scale of ecological dynamics. However, recent studies suggest rapid operating concurrently with competition may enable coexistence. Such findings necessitate general theory incorporates contributions eco-evolutionary processes in parallel purely mechanisms provides metrics for quantifying role shaping outcomes both modelling empirical contexts. To foster development such theory, here we extend interpretation two principal modern theory-niche ability differences-to systems where competitors evolve. We define versions these considering how invading resident adapt to conspecific heterospecific competitors. show niche differences sums evolutionary processes, they accurately predict potential stable previous theoretical Finally, this frames assessments effects coexistence, work dynamics can be further integrated.

Language: Английский

Citations

34
Accounting for demographic uncertainty increases predictions for species coexistence: A case study with annual plants DOI
Catherine Bowler, Christopher Weiss‐Lehman, Isaac R. Towers

et al.

Ecology Letters, Journal Year: 2022, Volume and Issue: 25(7), P. 1618 - 1628

Published: May 28, 2022

Abstract Natural systems contain more complexity than is accounted for in models of modern coexistence theory. Coexistence modelling often disregards variation arising from stochasticity biological processes, heterogeneity among individuals and plasticity trait values. However, these unaccounted‐for sources uncertainty are likely to be ecologically important have the potential impact estimates coexistence. We applied a Bayesian framework data an annual plant community Western Australia propagate outcomes using invasion criterion ratio niche fitness differences. found accounting this altered predictions versus competitive exclusion 3 out 14 species pairs yielded probability priority effects additional pair. The propagation improves our ability predict accurately natural systems.

Language: Английский

Citations

28
Technical Comment on Pande et al. (2020): Why invasion analysis is important for understanding coexistence DOI
Stephen P. Ellner, Robin E. Snyder, Peter B. Adler

et al.

Ecology Letters, Journal Year: 2020, Volume and Issue: 23(11), P. 1721 - 1724

Published: Aug. 26, 2020

Abstract Pande et al . (2020) point out that persistence time can decrease even as invader growth rates (IGRs) increase, which potentially undermines modern coexistence theory. However, because increases rapidly with system size only when IGR > 0, to understand how any real community persists, we should first identify the mechanisms producing positive IGR.

Language: Английский

Citations

21
Understanding evolutionary and ecological dynamics using a continuum limit DOI Creative Commons
Peter Czuppon, Arne Traulsen

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

Citations

20
Exclusion of the fittest predicts microbial community diversity in fluctuating environments DOI Open Access
Shota Shibasaki, Mauro Mobilia, Sara Mitri

et al.

Journal of The Royal Society Interface, Journal Year: 2021, Volume and Issue: 18(183)

Published: Oct. 1, 2021

Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities their diversity, but we still lack an intuition on how. Here, build a mathematical model describing two species living environment where substrate supplies randomly switch abundant scarce. We then vary of switching as well different properties interacting species, measure probability weaker driving stronger one extinct. find this increases with strength demographic noise under peaks either low, high, or intermediate rates depending both species' ability to withstand environment. This complex relationship shows why finding patterns environmental diversity has historically been difficult. In parameter ranges fittest was most likely be excluded, however, beta larger also peaked. sum, how affect interactions few pairs predicts effect whole community.

Language: Английский

Citations

15
An approximation scheme for quasi-stationary distributions of killed diffusions DOI Creative Commons
Andi Q. Wang,

Gareth O. Roberts,

David Steinsaltz

et al.

Stochastic Processes and their Applications, Journal Year: 2019, Volume and Issue: 130(5), P. 3193 - 3219

Published: Sept. 23, 2019

In this paper we study the asymptotic behavior of normalized weighted empirical occupation measures a diffusion process on compact manifold which is killed at smooth rate and then regenerated random location, distributed according to measure. We show that almost surely comprise an pseudo-trajectory for certain deterministic measure-valued semiflow, after suitably rescaling time, with probability one they converge quasi-stationary distribution diffusion. These results provide theoretical justification scalable Monte Carlo method sampling from Bayesian posterior distributions.

Language: Английский

Citations

12
Building modern coexistence theory from the ground up: the role of community assembly DOI Creative Commons
Jürg W. Spaak, Sebastian J. Schreiber

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 16, 2023

Abstract Modern coexistence theory (MCT) is one of the leading methods to understand species coexistence. It uses invasion growth rates – average, per-capita rate a rare identify when and why coexist. Despite significant advances in dissecting mechanisms occurs, MCT relies on “mutual invasibility” condition designed for two communities, but poorly defined rich communities. Here, we review well-known issues with this component propose solution based recent mathematical advances. We clear framework expanding communities understanding resistance as well coexistence, especially which could not be analyzed so far. Using data-driven community models from literature, illustrate utility our highlight opportunities bridging fields assembly Statement authorship : Studied conceived jointly by JWS SJS. SJS wrote manuscript together. python code R code. Data accessibility All computer used will made publicly available figshare. Niche fitness differences | Storage effect Coexistence

Language: Английский

Citations

3
Exclusion of the fittest predicts microbial community diversity in fluctuating environments DOI Creative Commons
Shota Shibasaki, Mauro Mobilia, Sara Mitri

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2020, Volume and Issue: unknown

Published: July 24, 2020

Abstract Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities their diversity, but we still lack an intuition on how. Here, build a mathematical model describing two species living environment where substrate supplies randomly switch abundant scarce. We then vary of switching as well different properties interacting species, measure probability weaker driving stronger one extinct. find this increases with strength demographic noise under peaks either low, high, or intermediate rates depending both species’ ability to withstand environment. This complex relationship shows why finding patterns environmental diversity has historically been difficult. In parameter ranges fittest was most likely be excluded, however, beta larger also peaked. sum, how affect interactions few pairs predicts effect whole community.

Language: Английский

Citations

5
Extinction scenarios in evolutionary processes: a multinomial Wright–Fisher approach DOI
Alexander Roitershtein, Reza Rastegar, Robert S. Chapkin

et al.

Journal of Mathematical Biology, Journal Year: 2023, Volume and Issue: 87(4)

Published: Sept. 26, 2023

Language: Английский

Citations

0