Topics — What a work is about. Nucleation holds whatever reading the owner files here, whether or not an Anthology of the SOTA topic could also hold it; instruction for ML practice belongs to the anthology (ADR-048). The words are seeded from the clusters the reading-time triage of 2026-09-25 found, and grow by decision.
Ecology — how organisms interact with each other and their environment — symbiosis and host–microbe partnerships, competition, herbivory and trophic interactions, community structure, resilience and regime shifts in ecosystems (ADR-028). How a partner comes to live inside another and depend on it is endosymbiosis (ADR-055).
12 of 1352 THEORY documents. Back to the full index.
| # | Title | Summary | Status |
|---|---|---|---|
| THEORY-128 | After mass bleaching, coral recovery on a reef crest depends on large herbivorous fishes keeping macroalgae down, because recovery runs through recruitment and survival that macroalgae suppress, not through the persistence of surviving colonies alone | Hughes et al. (2007), LIT-711. On the reef crest at Orpheus Island after the 1998 bleaching, four roofless cages kept large and medium fishes out of 25 m² plots for 30 months. Macroalgae averaged 56% cover inside against 4.1% and 1.7% in controls. Coral cover reached 7.7% inside against 19.2% and 20.2%, with recruitment about two-thirds lower and mortality of established colonies more than double. Control recovery came mainly from recruits of taxa bleaching had removed. Proposed: one site, four replicates, plot scale, and fish exclusion standing in for herbivore exclusion. The algal state vanished within 30 days of reopening. | Proposed |
| THEORY-130 | Coral bleaching is the breakdown of a regulated host–symbiont exchange, reached by more than one route, not a single mechanism of symbiont loss | Two reviews, with no data of their own. Boilard et al. (2020), LIT-712, collect the regulators of the coral–dinoflagellate exchange: the host controls symbiont density, bacteria shift the nitrogen supply, and heat leads either to host rejection of symbionts (apoptosis, autophagy, exocytosis, detachment, necrosis) or to pigment loss under oxidative stress. Goulet et al. (2020), LIT-709, report two octocorals whose similar symbiont losses at +3 °C came by different routes, one by fewer symbionts per host cell and one by loss of host cells. Proposed. The claim that the wider microbiome drives bleaching is declined: its own source says it cannot yet be tested. | Proposed |
| THEORY-132 | Stability, a system’s speed of return to equilibrium after disturbance, and resilience, its capacity to absorb change and persist within its domain of attraction, are distinct properties that can trade off, so a system can be highly unstable and highly resilient, and managing it for constancy can erode its resilience | Holling (1973), LIT-741. Stability is return to equilibrium. Resilience is persistence under change, set by the extent of the domain of attraction and the system’s distance from its edge. Budworm forests and insect populations in harsh climates are unstable and resilient; homogeneous lakes are stable and fragile. Active for the distinction, which has become standard. The claim that management for constancy erodes resilience rests on suggestive cases. | Active |
| THEORY-136 v3 | A persistent or abrupt change is not evidence that a system has alternative stable states: field patterns such as jumps, multimodality and dual relationships also arise from a stepwise driver or a simple threshold, and only hysteresis, initial-state dependence or a lasting shift after a temporary disturbance, with slow return excluded, comes close to showing one | Scheffer & Carpenter (2003), LIT-726. Alternative attractors predict sudden shifts, multimodal states and dual responses to a driver, and so do discontinuous drivers and threshold responses. Discriminating evidence is experimental: different starting states reaching different end states, temporary disturbances causing lasting shifts, or hysteresis. Slow recovery can mimic all three. Positive feedback must be strong to produce alternative states. Active as a methodological standard. | Active |
| THEORY-469 | Because persistence (mean absolute fitness at least 1) and selection (fitness differences) are logically independent, niche construction theory’s evolutionary niche, read externally as the factors producing fitness differences in a population, differs in extension from the realized population ecological niche even after unit and modality are matched, so it is not a simple translation of Hutchinson’s niche | Trappes (2021), LIT-169, read in NOTE-155. The non-identity follows from a conceptual argument the reading grades strong. The three kinds of case that populate the gap are weaker: habitat degradation rests on a projected persistence failure, commensalism on one field study after the author’s first candidate failed, and non-limiting resources on a “possible example”. The result is scoped to Odling-Smee, Laland & Feldman’s 2003 niche concept and to the externalist reading of selection pressure. It does not say the two niches differ much; they “still coincide to a large extent”. | Active |
| THEORY-473 | Scaled down to one organism, Hutchinson’s niche, defined as the conditions that give that individual an expected lifetime reproductive success of at least one, is observed only as a point; the rest of it is counterfactual, reached by translocation in only a few dimensions and otherwise inferred from other individuals, so in practice it is the niche of a phenotype class, and its authors call it mostly metaphorical | Takola & Schielzeth (2022), LIT-127, read in full in NOTE-170. The working definition (p. 5) gives the individualized niche an absolute-fitness boundary, expected LRS ≥ 1, and splits it into realized, potential, time-slice, prospective and trajectory-based niches. That the realized niche is a point and the potential niche unobservable follows from the definitions. The paper concedes there is “no empirical solution” at the individual level (p. 15), and its fix, marginalizing fitness functions across individuals, is schematic. It is a framework for structuring research, by its authors’ own account, not a measurement. | Active |
| THEORY-548 v2 | In generalised Lotka–Volterra dynamics with every interaction delayed by τ, a feasible equilibrium that is stable without delay loses stability at τ_c = min over the community eigenvalues j of arctan(|Re j|/|Im j|)/|j|, where a pair of roots crosses the imaginary axis transversally (a Hopf point), so the critical delay is set by the community spectrum; in Saeedian et al.’s strongly self-regulated setting the oscillating regime’s community-level variability falls with diversity (S = 10–70) while species-level variability rises, and the fall matches what summing independently oscillating species gives | Saeedian et al. (2021), LIT-057, a preprint, read in NOTE-061. The critical delay is the linear delay result on the community matrix, re-derived on promotion (2026-10-20), and matched simulation at one strongly self-regulated setting. The variability result was re-run on promotion against an averaging null and matches it: the fall of community-level variability with diversity is what summing independent oscillators gives, not an ecological stabilisation. | Active |
| THEORY-560 | In rodents, gut microbes can drive stress and affect-related behaviour through vagal, immune, endocrine and metabolite routes, and faecal transplant from depressed people partly transfers the phenotype; in people, probiotics have so far shown at most small reductions in subjective stress in healthy volunteers, and strains with strong preclinical records have failed in controlled trials | Forssten et al. (2022), LIT-915, read in NOTE-703. A narrative review with no search method, by employees of a probiotics manufacturer, which documents its own translational failures: L. rhamnosus JB-1 had no effect on any outcome against placebo after “comprehensive preclinical evidence”. The rodent half is well documented; the human half rests on one meta-analysis of healthy volunteers and trials with nulls. Proposed because the source is a narrative industry review; the gap it describes runs against its authors’ interest. | Proposed |
| THEORY-1048 v2 | On the Black Queen Hypothesis of Morris, Lenski and Zinser, losing a costly function whose product leaks to neighbours is favoured by ordinary individual selection in large free-living microbial populations, and the loss proceeds until the remaining producers just supply the community, so that most cells come to depend on a rare few with no relatedness, cooperation or collective required | Morris, Lenski & Zinser (2012), LIT-1568, read in NOTE-1212. A loss-of-function mutant invades when its resource saving B = (Q_A − Q_M)/Q_A exceeds its cost C, which falls as other cells’ leaky activity protects it. Because protection falls as producers become rare, the loss is frequency dependent and stops short of community-wide loss. The evidence is Prochlorococcus’s loss of katG and its dependence on a peroxide-removing community. The dependence it produces is one-way, from beneficiaries to helpers, and involves no collective. | Active |
| THEORY-1162 | In a consumer-resource model whose species-resource benefits and impacts have correlation rho, the replica-symmetric cavity fixed point loses stability where rho squared equals surviving species over non-depleted resources | Blumenthal, Rocks and Mehta (2024), LIT-1236: in MacArthur’s consumer–resource model with benefits c and impacts e correlated by ρ, the replica-symmetric steady state is unstable when ρ < ρ*, ρ² = S/M* at the boundary. With ρ = 1 competitive exclusion keeps S*/M* ≤ 1, so the symmetric model never crosses it. What this does not say: that non-reciprocity by itself breaks the optimization picture; it does so only past a boundary set by species packing, and that the other side is chaotic is shown numerically, not derived. | Active |
| THEORY-1168 | In a Lotka–Volterra community with a symmetric interaction matrix, the growth-weighted biomass rᵀx strictly increases along every edge of the invasion graph, so the invasion graph has no cycles | Re-derived from Serván and Allesina (2021), LIT-1824, read in NOTE-1422, and applied to Hofbauer and Schreiber’s invasion graph (LIT-1233). At an equilibrium V = 2rᵀx − xᵀAx equals rᵀx, and for two equilibria the difference is a sum of invasion growth rates weighted by abundances, which an edge of the invasion graph makes positive. It needs symmetry and one equilibrium per vertex, not positive definiteness. It does not say assembly is order-independent: an indefinite symmetric matrix has several sinks. | Active |
| THEORY-1235 | Losing a costly function whose product leaks to neighbours is favoured by ordinary individual selection in large free-living microbial populations, and the loss proceeds until the remaining producers just supply the community, so that most cells come to depend on a rare few with no relatedness, cooperation or collective required | The Black Queen Hypothesis itself, filed beside THEORY-1048 by the twenty-fourth status review (ADR-065 §3; ADR-047 kind 1). THEORY-1048, Active, holds what the hypothesis says; whether it is true is this entry’s question, with THEORY-1048’s old condition word for word. | Proposed |