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Negligible effects of environmental fluctuations on the maintenance of coral biodiversity: A test of five storage effects

T0 review · 2 major / 5 minor · reviewed 2026-08-07 · deepseek-v4-flash

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Pith's one-line read A simulation-based test on 11 Great Barrier Reef coral species finds that the storage effect—coexistence through temporal niche partitioning—operates but is too weak to maintain coral biodiversity.

desk verdict A serious empirical test of the storage effect in corals, but the five-year window makes me wary of the covariance structure that drives the central conclusion. read the letter →

arxiv 2506.03346 v1 pith:EZRI6XEL submitted 2025-06-03 q-bio.PE

Evan C. Johnson , Sean R. Connolly This is my paper
classification q-bio.PE MSC 92D2592D40
keywords storageeffectcoralreefcoexistenceintegralprojectionmodelmoderntheoryenvironmentalfluctuationsGreatBarriertemporalnichepartitioning
verification ladder T0 review T1 audit T2 compute T3 formal

The pith

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The reading

The paper sets out to test whether the storage effect—the classic theory that species can coexist by specializing on different states of a fluctuating environment—actually maintains biodiversity in a system built for it: a community of 11 corals on the Great Barrier Reef with long-lived adults, large recruitment variability, and a competitive propagule stage. Using five years of size-structured demographic data, the authors parameterize integral projection models, simulate the community, and decompose the mechanisms of coexistence with Modern Coexistence Theory. They find that all five storage effects operate but are weak, typically about five times smaller than fluctuation-free fitness differences, and that simulated coexistence occurs mainly when species are nearly equal in the absence of fluctuations, not when temporal niches are strong. The paper concludes that environmental fluctuations contribute little to coral coexistence and that spatial processes, including microhabitat partitioning and asymmetric dispersal, are more likely to explain coral biodiversity.

What carries the argument

The argument is carried by three coupled tools. An Integral Projection Model (IPM)—a size-structured population model that tracks colony planar area through annual survival, growth, spawning, and density-dependent recruitment—generates simulated coral communities, with environmental fluctuations entering as species-specific year effects on growth and fecundity plus a wave-disturbance mortality sub-model. Bayesian hierarchical fitting propagates parameter uncertainty into every coexistence outcome. Simulation-based Modern Coexistence Theory (MCT) decomposes each species' per-capita growth rate when rare into components for mean conditions, environmental variation, competition variation, and the environment–competition interaction, and then compares invaders to residents; a fine-grained partition splits the storage effect into five sub-effects ($\Delta_{(SL)}$, $\Delta_{(SA)}$, $\Delta_{(GL)}$, $\Delta_{(GA)}$, $\Delta_{(FL)}$) indexed by which demographic process covaries with which competition axis. The load-bearing diagnostic is a two-parameter map of coexistence probability against the between-species fecundity-year-effect correlation and the scale of environmental variability, which places the fitted species in a high-correlation, low-variability region far from where the storage effect can stabilize coexistence.

What would settle it

A multi-decadal demographic time series from the same reef that reveals strongly negative correlations among species' fecundity year effects together with high interannual variance would place the community inside the coexistence regime identified in the paper's Figure 6 and undermine its central conclusion; the same measurement showing persistently high positive correlations with modest variance would corroborate the finding.

Watch

Extended reading notes

Core claim

The central discovery is that the storage effect is real but negligible: it promotes coexistence yet is nowhere near sufficient for it in this coral community. In simulations, the posterior probability that two or more of the 11 species coexist is 38%, and for three or more species only about 12%; in the exclusion cases, Goniastrea pectinata typically monopolizes the community. The Modern Coexistence Theory partition shows that fluctuation-free effects $\Delta_0$ are typically five times larger than the storage effect $\Delta_{(EC)}$, and coexistence arises when $\Delta_0$ is near zero rather than when the storage effect is unusually strong. Of the five process-based storage effects, only the fecundity-to-larvae effect $\Delta_{(FL)}$—the classic lottery-model mechanism—makes a substantive contribution; growth-based and survival-based storage effects are weak because growth fluctuations lack a positive environment–competition covariance and survival fluctuations barely move equilibrium growth rates. The decisive sensitivity result is that high-probability coexistence via the storage effect requires roughly tenfold-greater environmental variability, or roughly fivefold variability combined with strongly negative between-species correlations in fecundity year effects—conditions far outside the posterior estimates for the studied species.

Load-bearing premise

The load-bearing premise is that the between-species correlations in year-to-year vital rates computed from five years of data represent true long-term environmental responses; the study window included a cyclone and thermal stress, and if those events inflated the correlations, the storage effect's strength could be substantially underestimated.

Editorial extensions

If this is right

  • If the storage effect is this weak in a coral community possessing all its theoretical prerequisites, fluctuation-driven coexistence mechanisms are likely minor in most ecosystems, and fluctuating environments should not be treated as a default explanation for biodiversity.
  • Coral coexistence research should shift toward spatial mechanisms—microhabitat settlement preferences, spatial fitness-density covariance, and asymmetric larval dispersal—which the paper identifies as the most plausible alternative supports.
  • Among storage-effect pathways, fecundity fluctuations coupled to larval competition dominate, so empirical effort on temporal coexistence should concentrate on propagule production and settlement rather than on growth- or survival-driven mechanisms.
  • Coexistence in this system, when it happens, reflects near-equal mean fitnesses rather than strong stabilization, so demographic equalizing processes deserve as much attention as stabilizing mechanisms.

Reading between the lines

Editorial extensions of the paper, not claims the author makes directly.

  • If the cyclone- and heat-stress years inflated the estimated between-species correlations, a multi-decadal demographic record could shift the fitted community toward the negative-correlation, high-variability regime where the storage effect stabilizes coexistence—my inference, not a claim the paper makes.
  • Because the model is deliberately aspatial, it does not rule out a spatial storage effect; a spatially explicit version with microhabitat patches and larval dispersal could test whether space substitutes for time in maintaining the same coral diversity.
  • The simulated dominance of Goniastrea pectinata, which contradicts its field abundance, implies an omitted process such as species-specific thermal sensitivity or microhabitat segregation; quantifying that omission would show how much real-world coexistence the single-habitat, fluctuation-only model misses.
  • Recruitment-density parameters were tuned to produce realistic coral cover rather than estimated from data, so direct species-level recruit measurements would sharpen the fluctuation-free fitness differences and could confirm or revise the reported fivefold gap.
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Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, and a circularity audit.

Referee Report

2 major / 5 minor

Summary. The paper parameterizes integral projection models for 11 coral species at Lizard Island using five years of demographic data, simulates community dynamics, and applies simulation-based Modern Coexistence Theory to quantify five storage effects arising from survival, growth, and fecundity fluctuations interacting with larval and space competition. The central claim is that storage effects operate but are weak: they are generally smaller than fluctuation-free fitness differences, coexistence is uncommon in simulations, and coexistence becomes probable only under greatly exaggerated environmental variability or strongly negative interspecific correlations. The authors support this with extensive robustness checks, posterior uncertainty propagation, and comparisons of fecundity fluctuations to literature values.

Significance. If the central claim holds, this is a valuable empirical test of a prominent coexistence mechanism in a system thought to favor strong storage effects, and it would reinforce a growing literature suggesting that temporal storage effects are generally weak. The study's strengths include explicit propagation of parameter uncertainty into coexistence outcomes, quantification of five distinct storage-effect pathways, and a broad set of alternative-model and parameter-sensitivity analyses. The concern raised below about the low-rank covariance structure of simulated year effects is load-bearing for the weak-storage-effect conclusion, because the simulated environmental responses are generated from covariance matrices that cannot represent the full dimensionality of species-specific environmental responses and may thereby bias the storage-effect estimates downward.

major comments (2)
  1. [Section 2.3 and Appendix A.3/A.4, Eqs. (A.15)-(A.16) and (A.22)-(A.25)] The 11x11 empirical correlation matrices RG, RF1, and RF2 are computed from only 5-6 annual species-specific year-effect estimates, so for any posterior draw each matrix has rank at most 4 (growth) or 5 (fecundity). The covariance matrices constructed in Eqs. (A.15), (A.22), and (A.23) are therefore singular, and the MVN draws in Eqs. (A.16), (A.24), and (A.25) confine all 11 species' environmental responses to a 4-5 dimensional linear subspace. This rank constraint mechanically limits the diversity of species-specific responses, which is the first ingredient of the storage effect, and it imposes a lower bound on average squared pairwise correlations among the 11 simulated response vectors; this is a distinct pathway by which the five-year window can bias Delta(EC) and coexistence probabilities downward, independent of whether the mean correlations are themselves biased. The diffuse-correlation robustness check in Appendix B.5 uses a full-rank compound-symmetry matrix with a single shared rho and therefore does not test the low-rank constraint. Please add a robustness analysis that breaks the low-rank constraint, for example by using an LKJ or factor-model prior on the full covariance matrix, or by adding species-specific independent noise to the simulated year effects, and report the resulting coexistence probabilities and Delta(EC) values. If the weak-storage-effect conclusion persists under that alternative, it would substantially strengthen the paper.
  2. [Section 3 and Fig. 4] The model predicts that Goniastrea pectinata dominates in 88-91% of no-coexistence simulations, yet this species is neither the most abundant nor the most abundant within its morphological group in the observed community. The text offers two plausible explanations, but the possibility that the five-year demographic rates are unrepresentative is also directly relevant to the storage-effect estimates: the study period ended with Tropical Cyclone Nathan and included thermal stress that disproportionately affected Acropora, so the estimated year effects and their between-species correlations may be dominated by a common disturbance response. Because the central claim concerns the strength of environmental covariance, please test how the estimated year-effect covariance structure and the MCT storage-effect estimates change when the cyclone-affected year is excluded or when year effects are estimated under a longer-term disturbance regime, and report whether the qualitative conclusion remains.
minor comments (5)
  1. [Results, Section 3] The phrase 'the probability of three or more species coexisting was only than 12%' appears to contain a typo; it should likely read 'only 12%'.
  2. [Appendix A.2] The phrase 'Combining this with wave-disturbance morality (sub-model A.1)' should read 'mortality' rather than 'morality'.
  3. [Appendix C] The paragraph beginning 'The early life history of corals involves two critical transitions...' is duplicated verbatim; one copy should be removed.
  4. [Appendix B.5 and Table B.1] The diffuse-correlation robustness model is described qualitatively but its quantitative results are not reported in Table B.1 or elsewhere; please add the coexistence probabilities for this scenario so that readers can compare it with the baseline and other alternatives.
  5. [Section 5 / References] The reference list contains entries cited in the text that appear with inconsistent formatting (e.g., some entries have missing journal names or incomplete page ranges); a careful copyedit of the reference list is recommended.

Circularity Check

0 steps flagged · score 2.0 of 10

No significant circularity: storage-effect magnitudes are emergent simulation outputs, not fitted values; the fitted environmental covariance does not force them by construction, and the self-cited MCT tools have independent anchors.

full rationale

The paper's central claim—that five storage effects are weak contributors to coral coexistence—is a measured simulation output, not a fitted parameter or a self-referential prediction. The inputs fitted to data (year-effect means, variances, and empirical between-species correlations for growth and fecundity; survival and wave-disturbance parameters) do not by construction determine the MCT storage-effect terms Delta(EC) or the sub-storage effects Delta(SL), Delta(SA), Delta(GL), Delta(GA), Delta(FL): those quantities emerge from full size-structured simulations with density-dependent recruitment and invader-resident comparisons (Eqs. D.1-D.5), including competition feedbacks not imposed by the fitted covariance. The only tuned parameter, beta_j,R, is matched to observed coral-cover ranges (Section 2.2, Appendix A.5) rather than to storage-effect magnitude, and Appendix B shows coexistence probabilities are insensitive or less favorable under alternative recruitment, growth, survival, and correlation structures. Figure 6 and G.1 further show that the fitted (rho, sigma) location does not force weak storage effects by definition: coexistence becomes probable only under roughly 10x larger fluctuations or strongly negative correlations, far from the posterior—an empirical mapping, not an identity. The paper self-cites Johnson and Hastings (2022a,b,c; 2023) for the ingredient-list definition, the simple-comparison method, and the storage-effect approximation (Eq. E.1); these are methodological or explanatory citations with independent anchors (Chesson 1994; Ellner et al. 2016b, 2019), and the main result does not rest on any single self-cited theorem—the simple-versus-scaled comparison is checked directly in Fig. D.1. The acknowledged five-year window (Section 2.3) may bias estimated correlation matrices, and those covariance matrices can be low-rank; this is a genuine data-limitation and bias risk (a correctness concern), not a circularity, because the storage effect is not defined as the fitted covariance and the diffuse-correlation robustness check (Appendix B.5) tests an alternative full-rank correlation structure with qualitatively identical outcomes. Accordingly, no circular step satisfies the evidence standard, and the score of 2 reflects only the presence of minor, non-load-bearing self-citations.

Assumptions & free parameters 1 free parameters · 4 assumptions · 0 invented entities

No new physical entities are introduced. The five storage effects are measurement decompositions, not new hypothetical objects.

free parameters (1)
  • beta_j,R (maximum recruit density per species) = Species-specific values, chosen by simulation to produce single-species coral cover between 0.1 and 0.5; interquartile…
    Cannot be estimated directly from data. A simulation-based calibration interpolates beta that yields target cover for each posterior draw. This tuning can influence the strength of density dependence and thus coexistence outcomes, though Appendix B robustness checks (equal beta, low settlement) give qualitatively identical results.
assumptions (4)
  • domain assumption An aspatial integral projection model adequately approximates coral community dynamics despite local colony interactions (overgrowth, digestion, competition for light).
    Section 2.2 states that competitive interactions between colonies minimally impact growth and survival, and larvae rarely settle near parents, justifying the aspatial approach. If spatial processes are important, the competition term (total egg production relative to open space) may be misspecified.
  • ad hoc to paper Recruitment is density-dependent in all years, at the asymptotic maximum of the settlement-recruitment curve, so the quotient L_j / sum(L_k) fully determines species recruit shares.
    Section 2.2 and Eq. 2. The authors state this maximizes the potential for storage effects, strengthening the conclusion if storage effects are weak. The assumption is relaxed in Appendix B (low settlement probability, variable settlement) with similar results.
  • domain assumption The empirical correlation matrix of species-specific year effects, computed from 5 years of data, is representative of long-term interspecific environmental covariance.
    Section 2.3. Year effects are estimated independently per species and then their Pearson correlations are used to build the multivariate normal covariance for simulations. With only 5 time points, these correlations carry large uncertainty; Figure 6 shows the conclusion depends on them being not strongly negative.
  • standard math Simulation-based Modern Coexistence Theory, with the shuffling approach to remove environment-competition covariance, correctly separates the storage effect from higher-order interactions.
    Appendix D.2-D.4. The method follows Ellner et al. 2016/2019 and Johnson & Hastings 2023. The paper notes the correspondence to classic MCT storage effect is not exact, but shuffling preserves within-environment correlations.

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Pith. "Pith review of Negligible effects of environmental fluctuations on the maintenance of coral biodiversity: A test of five storage effects." pith.science (2026). https://pith.science/paper/EZRI6XEL

@misc{pith2026250603346,
  author       = {Pith},
  title        = {Pith review of: Negligible effects of environmental fluctuations on the maintenance of coral biodiversity: A test of five storage effects},
  year         = {2026},
  howpublished = {\url{https://pith.science/paper/EZRI6XEL}},
  note         = {Machine review of arXiv:2506.03346}
}
read the original abstract

The storage effect is a general explanation for ecological coexistence, wherein different species specialize on different states of a fluctuating environment, e.g., hot vs. cold years. Despite the storage effect's prominence in theoretical ecology, we lack evidence on whether it maintains biodiversity in nature. Here, we examine five storage effects in a community of 11 coral species from the Great Barrier Reef, using detailed size-structured demographic data collected over five years. We parameterize integral projection models, simulate coral communities, and quantify coexistence mechanisms through Modern Coexistence Theory. Results show that storage effects promote coexistence but are weak compared to fitness differences. Despite coral communities exhibiting theoretical prerequisites for strong temporal niche partitioning, the storage effect plays only a minor role in maintaining coral biodiversity. This aligns with growing evidence that storage effects are weak across ecosystems. Coral coexistence likely depends more on spatial processes, including microhabitat partitioning and asymmetric dispersal.

Figures

Figures reproduced from arXiv: 2506.03346 by the authors.

Figure 1
Figure 1. Illustration of the 5 storage effects (SE). [PITH_FULL_IMAGE:figures/full_fig_p007_1.png] view at source ↗
Figure 2
Figure 2. Visual summary of coral size-structured dynamics. Panel A) Background survival is [PITH_FULL_IMAGE:figures/full_fig_p009_2.png] view at source ↗
Figure 3
Figure 3. Example communities with simulated time series and corresponding Modern Coexis [PITH_FULL_IMAGE:figures/full_fig_p013_3.png] view at source ↗
Figures from the paper (3 more)
Figure 4
Figure 4. Figure 4: The posterior probability of coexistence is low, both in the full community and across [PITH_FULL_IMAGE:figures/full_fig_p014_4.png]
Figure 5
Figure 5. Figure 5: The Modern Coexistence Theory partition reveals two key findings about the storage [PITH_FULL_IMAGE:figures/full_fig_p016_5.png]
Figure 6
Figure 6. Figure 6: Coexistence via the storage effect occurs when species have strong environmental [PITH_FULL_IMAGE:figures/full_fig_p017_6.png]

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Pith tools

Reviewed August 7, 2026 · model on record in the stance chip above.