Widespread analytical pitfalls in empirical coexistence studies and a checklist for improving their statistical robustness

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(4), P. 594 - 611

Published: Feb. 28, 2024

Abstract Modern coexistence theory (MCT) offers a conceptually straightforward approach for connecting empirical observations with an elegant theoretical framework, gaining popularity rapidly over the past decade. However, beneath this surface‐level simplicity lie various assumptions and subjective choices made during data analysis. These can lead researchers to draw qualitatively different conclusions from same set of experiments. As predictions MCT studies are often treated as outcomes, many readers reviewers may not be familiar framework's assumptions, there is particular risk ‘researcher degrees freedom’ inflating confidence in results, thereby affecting reproducibility predictive power. To tackle these concerns, we introduce checklist consisting statistical best practices promote more robust applications MCT. Our recommendations organised into four categories: presentation sharing raw data, testing model fits, managing uncertainty associated coefficients incorporating predictions. We surveyed published 15 years discovered high degree variation level rigour adherence practices. present case illustrate dependence results on seemingly innocuous among competition structure error distributions, which some cases reversed predicted outcomes. demonstrate how analytical approaches profoundly alter interpretation experimental underscoring importance carefully considering thoroughly justifying each step taken analysis pathway. serves resource authors alike, providing guidance strengthen foundation analyses. field shifts descriptive, trailblazing phase stage consolidation, emphasise need caution when building upon findings earlier studies. ensure that progress ecological based reliable evidence, it crucial subject our predictions, generalisability rigorous assessment than currently trend.

Language: Английский

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Integrating eco‐evolutionary dynamics and modern coexistence theory

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

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Accounting for demographic uncertainty increases predictions for species coexistence: A case study with annual plants

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

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Building modern coexistence theory from the ground up: The role of community assembly

Ecology Letters, Journal Year: 2023, Volume and Issue: 26(11), P. 1840 - 1861

Published: Sept. 25, 2023

Abstract Modern coexistence theory (MCT) is one of the leading methods to understand species coexistence. It uses invasion growth rates—the average, per‐capita rate a rare species—to identify when and why coexist. Despite significant advances in dissecting mechanisms occurs, MCT relies on ‘mutual invasibility’ condition designed for two‐species communities but poorly defined species‐rich communities. Here, we review well‐known issues with this component propose solution based recent mathematical advances. We clear framework expanding understanding resistance as well coexistence, especially that could not be analysed so far. Using two data‐driven community models from literature, illustrate utility our highlight opportunities bridging fields assembly

Language: Английский

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Does deterministic coexistence theory matter in a finite world?

Ecology, Journal Year: 2022, Volume and Issue: 104(1)

Published: Aug. 8, 2022

Abstract Contemporary studies of species coexistence are underpinned by deterministic models that assume competing have continuous (i.e., noninteger) densities, live in infinitely large landscapes, and coexist over infinite time horizons. By contrast, nature, composed discrete individuals subject to demographic stochasticity occur habitats finite size where extinctions time. One consequence these discrepancies is metrics species’ derived from theory may be unreliable predictors the duration nature. These include invasion growth rates niche fitness differences, which now commonly applied theoretical empirical coexistence. In this study, we tested efficacy on a world. We introduce new computational methods estimate times stochastic counterparts classic competition. Importantly, parameterized model using experimental field data for 90 pairwise combinations 18 annual plants, allowing us derive biologically informed estimates natural system. Strikingly, found expected deterministically coexist, community sizes containing only 10 had predicted more than 1000 years. also explained 60% variation intrinsic times, reinforcing their general usefulness However, integrating information both species' equilibrium population could most (>99%) explained. This integration was achieved with demographically uncoupled single‐species solely determined sizes. Moreover, because complex relationship between overlap/fitness differences sizes, increasing overlap did not always result decreasing as would predict. Nevertheless, our results tend support use understanding while highlighting need incorporate addition rates.

Language: Английский

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Exploring the impact of key performance factors on energy markets: From energy risk management perspectives

Energy Economics, Journal Year: 2024, Volume and Issue: 131, P. 107373 - 107373

Published: Feb. 15, 2024

Language: Английский

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Coexistence Theory for Microbial Ecology, and Vice Versa

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(3)

Published: March 1, 2025

ABSTRACT Classical models from theoretical ecology are seeing increasing uptake in microbial ecology, but there remains rich potential for closer cross‐pollination. Here we explore opportunities stronger integration of ecological theory into research (and vice versa) through the lens so‐called “modern” coexistence theory. Coexistence can be used to disentangle contributions different mechanisms (e.g., resource partitioning, environmental variability) make species coexistence. We begin with a short primer on fundamental concepts theory, an emphasis relevance communities. next present systematic review, which highlights paucity empirical applications systems. In light this gap, then identify and discuss ways which: (i) help answer applied questions particularly spatio‐temporally heterogeneous environments, (ii) experimental systems leveraged validate advance Finally, address several unique often surmountable challenges posed by systems, as well some conceptual limitations. Nevertheless, thoughtful presents wealth advancement both ecology.

Language: Английский

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The dynamics of coexistence and succession in a decaying ecosystem

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Elucidating the rules that govern community assembly and enable coexistence of species is central to ecology. Much current understanding revolves around composition communities at equilibrium. In contrast, transient ecological dynamics, in particular succession following an environmental disturbance, remain largely unexplored. We present Gymnogaster buphthalma beetle carcasses as a model study disequilibrium. this community, nematodes appear – with multiple feeding reproductive strategies, transience, associated dispersal creating perfect for metacommunity computationally reconstructed decaying G. beetles sampled from wild using experimentally-derived life history data, i.e. emergence times, sex ratios, fecundity measurements. Through agent-based modeling, we show nematode possible over wide range scenarios. This work provides unique experimental computational framework synthesize various approaches theories.

Language: Английский

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Inverse relationship between species competitiveness and intraspecific trait variability may enable species coexistence in experimental seedling communities

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 3, 2024

Abstract Theory suggests that intraspecific trait variability may promote species coexistence when competitively inferior have higher than their superior competitors. Here, we provide empirical evidence for this phenomenon in tree seedlings. We evaluated and plastic response of ten traits 6750 seedlings a three-year greenhouse experiment. While observed no relationship between competitiveness competition-free homogeneous environments, an inverse emerged under interspecific competition spatially heterogeneous environments. showed is driven by the species: Compared to counterparts, they exhibited greater increase variability, particularly fine-root traits, competition, environmental heterogeneity combination. Our findings contribute understanding how together structure plant communities.

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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