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).
42 of 2004 LIT documents. Back to the full index.
| # | Title | Summary | Status |
|---|---|---|---|
| LIT-709 | Conceptualization of the Holobiont Paradigm as It Pertains to Corals | Goulet, Erill, Ascunce, Finley & Javan (2020), Frontiers in Physiology 11:566968, a review. A coral is a consortium: the animal plus the Symbiodiniaceae, bacteria, archaea, fungi and viruses in its body, mucus and skeleton, and neighbours are excluded by definition. Membership can change, so one colony may be a different holobiont at different times. Traits such as thermal tolerance belong to the host–symbiont combination: not every Durusdinium is heat tolerant, and a novel anemone–alga pairing gave higher oxygen flux under heat than both natural ones. Measuring both partners shows different routes to the same bleaching outcome. Whether the holobiont is the unit of selection is asked, not answered. | Active — read in full 2026-10-04 (NOTE-555); worth reading as a short, explicit statement of why a coral should be studied as a composite of host and microbes rather than as an animal with passengers. It is a mini-review with no data of its own (about 3,700 words), and its strongest point is conceptual: traits such as thermal tolerance belong to host–symbiont combinations, not to either partner. The physiological evidence it cites is thin and partly not from corals: its one demonstration that a combination is “not necessarily the sum of its parts” is an oxygen-flux experiment in the sea anemone Exaiptasia. It poses, and does not answer, whether the coral holobiont is a unit of selection. |
| LIT-711 | Phase Shifts, Herbivory, and the Resilience of Coral Reefs to Climate Change | Hughes et al. (2007), Current Biology 17(4):360–365. A replicated fish-exclusion experiment at Orpheus Island, Great Barrier Reef, begun in 2000 after the 1998 mass bleaching: four roofless 5 × 5 m cages, four partial cages and four open plots, over 30 months. Excluding large and medium fishes produced a phase shift to Sargassum-dominated macroalgae. Coral recovery was suppressed, through about two-thirds lower recruitment and more than double the mortality of surviving colonies. In the controls, coral cover nearly doubled to 20%, mainly by recruitment of taxa that bleaching had removed locally. Reopened cages lost their macroalgae within 30 days. | Active — read in full 2026-10-04 (NOTE-558), main text and methods; the supplement was out of reach. Worth reading as the controlled experiment behind the claim that reef recovery after bleaching depends on an ecological interaction, not only on surviving corals. On an inshore Great Barrier Reef crest after the 1998 bleaching, roofless cages kept large and medium fishes out of four 25 m² plots for 30 months. Macroalgae rose to a mean of 56% cover in the cages against 4.1% and 1.7% in partial cages and open plots. Coral cover in the cages rose only from 6.0% to 7.7%, against 19.2% and 20.2%, because recruitment was about two-thirds lower and mortality of established colonies more than double. It is one site with four replicates per treatment. The cages excluded all large and medium fishes, not herbivores alone, and the macroalgal state vanished within 30 days of reopening them. |
| LIT-712 | Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont | Boilard, Dubé, Gruet, Mercière, Hernandez-Agreda & Derome (2020), Microorganisms 8(11):1682, a review. Bleaching, the breakdown of the coral–dinoflagellate symbiosis, is redefined as a succession of three holobiont dysbiosis stages: (i) the microbiota buffers the stress and keeps essential functions; (ii) the algal partners are reorganised by shuffling or switching, with or without transient bleaching; (iii) the stress exceeds both buffers, symbionts are lost for good, opportunists invade and the coral dies, and at reef scale algae take over. The stages are a proposal, with no criteria to tell them apart, and the authors concede that microbial shifts are not shown to cause bleaching. | Active — read in full 2026-10-04 (NOTE-556); worth reading as the statement of the “adaptive dysbiosis” account of coral bleaching, which treats bleaching as three successive holobiont states: microbial buffering, reorganisation of the algal partners by shuffling or switching, and an irreversible breakdown ending in death. It is a review with no data of its own, and the account is a proposal. Its own text says that bacterial shifts during bleaching cannot yet be read as cause or consequence, so the title’s “microbial dysbiosis” claims more than the body supports. |
| LIT-720 v2 | Catastrophic shifts in ecosystems | Scheffer, Carpenter, Foley, Folke & Walker (2001), Nature 413:591–596. Lakes, coral reefs, oceans, forests and arid lands can switch abruptly to a contrasting state, and loss of resilience usually paves the way. Unread: the theory and the criteria for demonstrating alternative states are read in the authors’ 2003 review LIT-726. | Unavailable — registered 2026-10-05 from Crossref, not read: no lawful full text was found (Nature is closed; no repository or course copy was located). The authors’ 2003 review (LIT-726), read in full, restates its theory of alternative stable states and gives the criteria for showing one exists. Filed because it is the paper usually cited for catastrophic regime shifts. It stays Unavailable until a copy is supplied, not on merit. |
| LIT-726 | Catastrophic regime shifts in ecosystems: linking theory to observation | Scheffer & Carpenter (2003), Trends in Ecology & Evolution 18:648–656. A regime shift can come from a bifurcation, not only a large shock. Field data give hints that are never conclusive. Experiments can demonstrate alternative attractors: initial states fixing end states, a temporary disturbance causing a lasting shift, or hysteresis. Positive feedbacks must be strong enough. Slow return can mimic a new state, as when a biomanipulated lake stayed clear for six years and then slipped back. | Active — read 2026-10-05 (NOTE-571): in full, from a UC Berkeley course page. Worth reading for its standard of evidence for alternative stable states. Field patterns (jumps in time series, multimodal distributions, dual relationships to a driver) are only hints. Experiments are what demonstrate: different initial states lead to different end states, a temporary disturbance causes a lasting shift, or the response to forward and backward change shows hysteresis. Positive feedback is not enough unless strong. Long return times can mimic an alternative state. |
| LIT-741 | Resilience and Stability of Ecological Systems | Holling (1973), Annual Review of Ecology and Systematics 4:1–23. Stability is how quickly and smoothly a system returns to equilibrium after a disturbance. Resilience is its ability to absorb change in state variables, drivers and parameters and still persist, a matter of the size of its domain of attraction. A system can be highly resilient and unstable, as the spruce budworm forest is. Managing for a stable maximum yield can shrink resilience until a rare event flips the system. | Active — read 2026-10-05 (NOTE-572): in full, from IIASA’s authorised reprint. Worth reading as the origin of the distinction between stability and resilience. Stability is the speed and smoothness of return to an equilibrium after a disturbance. Resilience is the capacity to absorb change and still persist, measured by the size of the domain of attraction and how near its boundary the system sits. The two can trade off: management for constancy can erode resilience. Evidence is a set of case histories (lakes, spruce budworm, salmon, fire), not tests. |
| LIT-903 | From gut microbiota to host appetite: gut microbiota-derived metabolites as key regulators | Han et al. (2021), Microbiome 9:162. A narrative review of how microbe-derived metabolites and proteins may regulate host appetite: SCFAs through FFAR2 to GLP-1 and PYY; bile acids through TGR5; indoles; ClpB as an α-MSH mimetic; and immunoglobulins against appetite peptides. Mostly rodent and in vitro evidence, by the authors’ own account. The human findings are associations, or prebiotic trials that conflict. | Active — read in full 2026-10-11 (NOTE-706) from the open-access text in Europe PMC (PMC8293578, CC BY). Worth reading as a map of the mechanisms by which gut microbes are proposed to reach host appetite (SCFAs, bile acids, tryptophan and indoles, bacterial protein mimics of host peptides such as ClpB for α-MSH), and for its own admission that the field “is mainly based on in vitro studies and rodent models”. The human evidence it cites is correlational, or comes from prebiotic and metabolite interventions that do not isolate microbes as the cause. |
| LIT-915 | One Giant Leap from Mouse to Man: The Microbiota–Gut–Brain Axis in Mood Disorders and Translational Challenges Moving towards Human Clinical Trials | Forssten, Ouwehand, Griffin & Patterson (2022), Nutrients 14(3):568. A narrative review of how gut microbes may affect mood, through the vagus, the immune system, the HPA axis and metabolites, and of why results in mice translate poorly to people. Faecal transplant from depressed humans partly transfers the phenotype to rodents. Human probiotic trials are mixed, with some reductions in subjective stress in healthy volunteers and several clean nulls. Written by employees of a probiotics manufacturer. | Active — read in full 2026-10-11 (NOTE-703) from the open-access text in Europe PMC (PMC8840472). Worth reading for the gap between mouse and human in microbiota–gut–brain research on mood: strong rodent effects, partial transfer of a depressive phenotype by faecal transplant into rodents, and repeated failures of preclinical probiotic effects to replicate in human trials. Note the source: all four authors were employed by a company that sells probiotics, and the review is narrative. |
| LIT-930 v3 | Will a Large Complex System be Stable? | May (1972), Nature 238, 413. A large system of n components with randomly signed interactions of strength s and connectance C is almost surely stable when s√(nC) < 1 and unstable when it exceeds 1, with a sharp transition: past a point, more components or more connections destabilize. It challenged the view that diversity brings stability. Not read. | Unavailable — looked for a lawful full text on 2026-10-14 and found none, so it is not read and no NOTE is filed. Unpaywall: closed, no open location. OpenAlex: two locations, doi.org and PubMed 4559589, neither open. Europe PMC: PMID 4559589, not open access, no PDF. Semantic Scholar: closed. nature.com: the article page is paywalled (“Access through your institution”), and its .pdf URL returned that HTML page. A web search on the title in quotes found no author-posted or institutional copy; May died in 2020 and has no personal page with papers. The Internet Archive could not be reached from this client (connection reset), and a 1972 Nature paper would not be public domain there. It stays Unavailable until a copy is supplied. |
| LIT-1219 v2 | Mechanisms of Maintenance of Species Diversity | Chesson (2000). Stable coexistence is measured by the long-term rate of recovery from low density, and coexistence mechanisms work in two ways: equalizing, by shrinking average fitness differences, and stabilizing, by making intraspecific competition stronger than interspecific; stabilizing mechanisms are necessary. | Unavailable — filed 2026-10-18 from the exchange of 2026-10-17, not read. A lawful full text was sought on 2026-10-29 and not reached. OpenAlex reports it closed with the Annual Reviews DOI as its only location; Semantic Scholar reports no open copy; Europe PMC has no record. The Annual Reviews PDF returned a 403 challenge, and it is not open access. Searches for a copy on Chesson’s pages found none: the University of Arizona experts page lists the citation only, and the old eebweb.arizona.edu faculty pages reset the connection, with no Wayback snapshot of a reprint. It stays Unavailable until a copy is supplied. Letten, Ke and Fukami (LIT-1237, read in full) restate its stabilizing and equalizing terms and the coexistence inequality ρ < f₂/f₁ < 1/ρ in Lotka–Volterra form. No NOTE is filed. |
| LIT-1225 v2 | Division of labour and the evolution of extreme specialization | Cooper & West (2018). A kin-selection model of division of labour over one cooperative trait: it needs accelerating returns to helping but is not guaranteed by them, and when it evolves one phenotype is always a pure reproductive, with a feedback driving helper and reproductive to the extremes. Relatedness does not affect whether it evolves for an essential trait and favours sterile helpers. The authors infer that it drives major transitions. | Active — read 2026-10-29 (NOTE-1369) in full, from the authors’ accepted manuscript in the Oxford University Research Archive; worth reading as the model in which division of labour, once favoured, always yields a pure reproductive and often a sterile helper, with relatedness irrelevant to whether it evolves for an essential trait. Read it knowing that the proofs and simulations are in a supplement not read, that its Table 1 and Figure 5 disagree on how efficiency affects the proportion of helpers, and that it shows dependence, not the vulnerability to losing a specialist that A46 attributed to it. |
| LIT-1230 v2 | The Minimum Environmental Perturbation Principle: A New Perspective on Niche Theory | Marsland, Cui & Mehta (2020). Generalizing MacArthur’s result that stable equilibria optimize a quadratic function, it shows that in a broad class of contemporary-niche-theory models the equilibrium minimizes the perturbation the competing species impose on their environment, subject to no species having positive net growth, and states when such a principle exists. | Active — read 2026-10-29 (NOTE-1352) in full, from arXiv 1901.09673v4; worth reading as the general form, for symmetric niche models, of the identity that uninvadable equilibria solve a constrained optimization, with the environment’s perturbation from its supply point as the objective and species abundances as KKT multipliers, and MacArthur’s principle as its dual. Read it knowing that symmetry is the hinge, that the asymmetric extension needs the answer to build its objective, and that the monotone-assembly result needs monostability. |
| LIT-1231 v2 | Constrained optimization as ecological dynamics with applications to random quadratic programming in high dimensions | Mehta, Cui, Wang & Marsland (2019). A duality between constrained optimization with inequality constraints, quadratic programming included, and consumer-resource models of ecological dynamics; with a cavity solution it gives the statistics of random high-dimensional quadratic programs, in agreement with numerics. | Active — read 2026-10-29 (NOTE-1395) in full, from arXiv 1809.04221v1; worth reading as the plain statement that inequality-constrained optimization is a consumer–resource ecology, constraints as species and multipliers as abundances, and that the Lagrangian dual of quadratic programming is a Lotka–Volterra system with α = CCᵀ. Read it knowing that the arXiv text has several algebraic slips (κ_i in the main text among them), that its “always” reduction of QP to a squared distance is not general, and that the PRE version was not compared. |
| LIT-1233 v2 | Permanence via invasion graphs: incorporating community assembly into modern coexistence theory | Hofbauer & Schreiber (2022). For ecological ODEs whose invasion growth rates have nonzero, well-defined signs on each subcommunity, it defines the invasion graph of communities and invasions and proves that when the graph is acyclic, robust permanence holds if each species has a positive invasion growth rate at every −i community (a community without it that no other missing species can invade), and, for smooth models, only if. With cycles, signs are not enough. | Active — read 2026-10-29 (NOTE-1379) in full, from arXiv 2204.03773v2; worth reading as the theorem that says when signs of invasion growth rates decide coexistence: with an acyclic invasion graph, robust permanence holds exactly when each species can invade each of its −i communities. Read it knowing that it is deterministic, that its sign-parity assumption excludes common non-Lotka–Volterra cases, that cycles are left open, and that its switching-predator example swaps the labels of two invasion conditions. |
| LIT-1234 v2 | Ecological communities with Lotka-Volterra dynamics | Bunin (2017). For a community assembled by migration from a pool of S species with random Lotka–Volterra interactions (mean μ/S, variance σ²/S, symmetry γ), the cavity method gives exact large-S results where a unique uninvadable fixed point exists: abundances are a Gaussian truncated at zero, and that phase ends at σ = √2/(1 + γ) for equal carrying capacities, independent of μ. Beyond lies a multiple-attractor phase in which, by simulation, the community reached depends on history. | Active — read 2026-10-29 (NOTE-1397) in full, from the published PDF on the author’s Technion page; worth reading as the clean cavity solution of the random generalized Lotka–Volterra community assembled from a species pool: a truncated-Gaussian abundance distribution, the surviving fraction, and a loss of the unique fixed point at σ = √2/(1 + γ) for equal carrying capacities, whatever the mean interaction. Read it knowing that the multiple-attractor phase beyond that line is located, not solved, and that its history dependence is shown by repeated simulation only. |
| LIT-1235 v2 | What can ecosystems learn? Expanding evolutionary ecology with learning theory | Power et al. (2015). In a competitive Lotka–Volterra community, individual selection lowers species i’s sensitivity to species j at a rate proportional to x_i x_j, which with a normalising trade-off on each species’ total competition is Hebbian learning. Simulated with symmetric interactions, the community comes to hold attractors for two past forcing patterns, completes them from fragments and switches with hysteresis; in the long run the memory degrades. | Active — read 2026-10-29 (NOTE-1368) in full, from the publisher’s version in PubMed Central (PMC4672551) with its erratum; worth reading as the model in which individual selection on competitive interactions acts like Hebbian learning, so that a community with no community-level selection comes to hold and recall several past compositions. Read it knowing that the memory needs an imposed trade-off that fixes each species’ total competition, that simulations keep interactions symmetric, that the two-memory state collapses in the long run, and that its printed equations (1) and (10)–(11) are wrong as printed. |
| LIT-1236 v2 | Phase Transition to Chaos in Complex Ecosystems with Nonreciprocal Species-Resource Interactions | Blumenthal, Rocks & Mehta (2024). In MacArthur’s consumer–resource model with species’ benefits from and impacts on resources correlated by ρ, the cavity method’s steady state loses stability when ρ falls below ρ*, with ρ*² = (surviving species)/(non-depleted resources) at the boundary; below it simulations show chaotic dynamics with positive Lyapunov exponents. With ρ = 1 competitive exclusion keeps the ratio at most 1 and the transition never occurs. | Active — read 2026-10-29 (NOTE-1366) in full, from arXiv v2 (the letter and its supplement); worth reading as the result that in MacArthur’s consumer–resource model with benefits and impacts correlated by ρ the cavity fixed point loses stability at ρ*² = surviving species over non-depleted resources, a boundary the symmetric model never reaches (THEORY-1162). Read it knowing that the boundary rests on a replica-symmetric ansatz, that the chaos beyond it is shown by simulation at a few parameter points, and that the letter’s fast-resource formula carries a stray R_α. |
| LIT-1237 v2 | Linking modern coexistence theory and contemporary niche theory | Letten, Ke & Fukami (2017). Translating Tilman’s two-consumer, two-resource model into Chesson’s niche overlap and fitness ratio, at equilibrium and without alternative stable states: varying the resource supply ratio is equalizing (for essential resources, at extreme ratios niche overlap jumps to 1), varying impact-niche overlap is stabilizing, and varying requirement-niche overlap is both but leaves coexistence unchanged. | Active — read 2026-10-29 (NOTE-1377) in full, from the published PDF on Fukami’s Stanford page; worth reading as the worked translation of Tilman’s two-consumer, two-resource model into Chesson’s niche overlap and fitness ratio: supply ratios mostly equalize, impacts stabilize, requirements do both. Read it knowing that the results are for two species and two resources at a stable equilibrium, drawn from worked cases with the general derivations in online appendices not read here, and that Chesson’s overlap is pairwise. |
| LIT-1557 v3 | Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora | Nowack & Grossman (2012). In the amoeba Paulinella chromatophora, whose photosynthetic chromatophores arose about 60 million years ago, three photosystem I subunits encoded by genes transferred to the nucleus are made in the cytoplasm, traffic into the chromatophores, apparently via the Golgi, and assemble there with chromatophore-encoded subunits. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC3325729) and the publisher’s free PDF is at pnas.org/content/pnas/109/14/5340.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1559 v3 | Extreme genome reduction in symbiotic bacteria | McCutcheon & Moran (2011 online; 2012 issue). Review of bacterial symbionts with extraordinarily small genomes, from independent lineages: gene sets rivalling some organelles, lacking genes thought essential elsewhere, with fast protein evolution and abundant chaperones. The authors read these as highly degenerate genomes retaining only the most essential functions, many serving the host. | Unavailable — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1560 v3 | Protein import into bacterial endosymbionts and evolving organelles | Sørensen, Stiller, Kröninger & Nowack (2024 online; 2025 issue). Review of the evidence for protein import from host into bacterial endosymbionts, long taken to mark an organelle off from an endosymbiont. Import of hundreds of proteins is established in two systems, the Paulinella chromatophore and the nitroplast, where the imported proteins come mostly from the host’s own genes or from other bacteria, so gene transfer from the endosymbiont is not required. Elsewhere there are one to seven targeted proteins per system. Each system uses its own targeting signal, and the mechanisms are largely unknown. | Active — read in full 2026-10-27 (NOTE-1241) from the PubMed Central copy of the version of record (PMC12176269, open access); worth reading as the system-by-system statement of what is known about host proteins entering bacterial endosymbionts, import at scale in the Paulinella chromatophore and the nitroplast and single proteins elsewhere, for its point that gene transfer from the endosymbiont is not needed for an organelle (THEORY-1100), and for its ordered scenario of effectors, dependence and general import (THEORY-1107). Read it knowing that it is a review whose import-at-scale evidence is two proteomic studies, that most single-protein cases rest on antibody localization, that the scenario is offered as plausible on limited data, and that import mechanisms are almost entirely unknown. |
| LIT-1562 v3 | Nitrogen-fixing organelle in a marine alga | Coale et al. (2024). UCYN-A, a streamlined nitrogen-fixing cyanobacterium known as an endosymbiont of a marine alga, is integrated into the alga’s cell architecture and organellar division and imports proteins encoded by the algal genome, so the authors call it an early-stage nitrogen-fixing organelle, the “nitroplast”. | Unavailable — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1563 v3 | Sympatric Speciation in a Bacterial Endosymbiont Results in Two Genomes with the Functionality of One | Van Leuven, Meister, Simon & McCutcheon (2014). In some cicadas of the genus Tettigades, the endosymbiont Hodgkinia has split into two cytologically distinct, metabolically interdependent lineages whose gene loss and retention are almost perfectly complementary, so a three-member symbiosis became four. The authors suggest nonadaptive forces can build organismal complexity. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S009286741401037X/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1565 v3 | An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs | McCutcheon & von Dohlen (2011). In the mealybug Planococcus citri, the gammaproteobacterium Moranella lives inside the betaproteobacterium Tremblaya. Their complete genomes show little overlap in nutrient-production genes, and several essential amino-acid pathways need a patchwork of gene products from Tremblaya, Moranella and possibly the insect. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC3169327) and the publisher’s free PDF is at cell.com/article/S096098221100724X/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1568 v3 | The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss | Morris, Lenski & Zinser (2012). In free-living bacteria such as Prochlorococcus and Pelagibacter, loss of a costly, leaky function whose products are public goods is favoured at the individual level, and proceeds until production just suffices for the community, leaving the losers dependent on co-occurring helpers. Selection, not drift, makes the dependency. The one worked case is Prochlorococcus’s loss of catalase-peroxidase (katG). | Active — read in full 2026-10-27 (NOTE-1212) from the PubMed Central copy of the version of record (PMC3315703, CC BY-NC-SA); worth reading as the selection route to microbial dependency, in which losing a costly, leaky function is favoured until helpers just supply the community (THEORY-1048). Read it knowing that it is an opinion piece with one worked case (katG in Prochlorococcus) whose benefit is computed, not measured; that it is stated for free-living microbes and credits drift for endosymbiont reduction; that its equations assume linear responses; and that its other examples and the “shooting the moon” acceleration are suggestions. |
| LIT-1569 v3 | Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis | Husnik et al. (2013). Tremblaya’s extreme genomic degeneracy likely followed its acquiring Moranella; at least 22 expressed genes transferred to the mealybug genome from diverse bacteria complement missing symbiont genes, none of them from Tremblaya. The three-way symbiosis depends on genes from at least six lineages, a path to intimate endosymbiosis distinct from the organelles’. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S0092867413006466/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1570 v3 | The Evolution of Dependence and Cohesion in Incipient Endosymbioses | Athreya, Czuppon & Gokhale (2025). An adaptive-dynamics model characterizes endosymbiosis by two collective properties, mutual dependence (survival as a collective) and reproductive cohesion (synchronized reproduction). The faster-growing partner becomes fully obligate first, and the other’s dependence then stays, rises or falls with births and deaths inside the collective. Dependence evolves at all only if the collective’s carrying capacity is high enough. Early on, dependence outruns cohesion, but only under the authors’ chosen trait mapping, which their own appendix shows decides the result. | Active — read in full 2026-10-27 (NOTE-1211) from the bioRxiv preprint, version 2 of 2025-05-31 (CC BY-NC 4.0), not the version of record, which was not reached; worth reading as the first model to separate mutual dependence from reproductive cohesion in an incipient endosymbiosis, with logistic growth for host, symbiont and collective, and for its results that the faster-evolving partner becomes obligate first and that the other’s fate turns on births and deaths inside the collective (THEORY-1051). Read it knowing that its headline result, dependence evolving ahead of cohesion, is fixed by the authors’ choice of how traits enter free growth and dissociation and reverses under the opposite choice in their own appendix (THEORY-1050); that nothing is tested against data, as the authors say; and that obligacy is a phenomenological trade-off, not gene loss. |
| LIT-1571 v3 | How do bacterial endosymbionts work with so few genes? | McCutcheon, Garber, Spencer & Warren (2024). An “Unsolved Mystery” essay on how radically reduced, compositionally biased endosymbiont gene sets function and interact with the host cell. Below about 400 kb endosymbionts lose the ability to build their own envelope, and below about 200 kb, the “tipping point”, translation-related genes erode. Host supply of membranes, transport and translation components is proposed, not shown. | Active — read in full 2026-10-27 (NOTE-1213) from the PubMed Central copy of the version of record (PMC11020763, CC BY); worth reading as the current statement of what endosymbionts with the smallest genomes lack, envelope biogenesis below about 400 kb and parts of translation below about 200 kb, and of the host’s presumed role in supplying them (THEORY-1049). Read it knowing that the thresholds come from a hand-picked matrix with draft genomes, that the composition analysis is called preliminary, and that every mechanism of host supply it names is a hypothesis. |
| LIT-1572 v3 | Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis | Husnik & McCutcheon (2016). Host and symbiont genomes from five mealybug species show Tremblaya from a single ancestral infection but the gammaproteobacterial symbionts inside it from multiple replacements by related lineages, while horizontally transferred genes on the host genome stay stable through the turnover. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC5027413), the bioRxiv preprint is at biorxiv.org/content/10.1101/042267v1, and the publisher’s PDF is at pnas.org/content/pnas/113/37/E5416.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1573 v3 | Accelerated evolution and Muller’s rachet in endosymbiotic bacteria | Moran (1996). Endosymbiont lineages, with small populations and no recombination, should accumulate mildly deleterious mutations. 16S rDNA of five independent endosymbiont clades evolves faster than in free-living relatives, and Buchnera coding genes show elevated nonsynonymous change and A+T-rich substitutions: Muller’s ratchet with mutational bias. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds the scanned article (PMC39726), and Europe PMC’s REST service lists its PDF at europepmc.org/articles/PMC39726?pdf=render. This client could not fetch it: both PMC and Europe PMC answered with a Cloudflare challenge page, and Europe PMC has no full-text XML for the scan. |
| LIT-1586 v2 | Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas | Łukasik et al. (2018). A single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over four million years, giving complexes of two to six lineages per host. The lineages differ in abundance, size and gene content, and their losses imply extensive sharing of gene products. Together they encode nearly the ancestral gene set. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC5777040) and the publisher’s PDF is at pnas.org/content/pnas/115/2/E226.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1590 v2 | Changes in Endosymbiont Complexity Drive Host-Level Compensatory Adaptations in Cicadas | Campbell et al. (2018). Where Hodgkinia has split into essential lineages of very uneven abundance, rare lineages risk loss at the transmission bottleneck from mother to egg, and a simulation shows the cells needed per egg rising steeply with complexity. Counts in eggs of four cicada species find Sulcia roughly constant and Hodgkinia up to about six times higher in Magicicada septendecim than in a single-lineage species, though only that species differs significantly. Every sampled egg carried every tracked lineage, and the transmission route looks unchanged. The authors read the raised titre as host compensation and a cost of fragmentation, and speculate that it could feed further splitting. | Active — read in full 2026-10-27 (NOTE-1235) from the PubMed Central copy of the version of record (PMC6234865, CC BY 4.0); worth reading as the record’s one documented case of a host compensating for its symbiont’s changes at transmission: cicadas whose Hodgkinia has split into many lineages send more Hodgkinia cells to each egg, not more Sulcia, and every sampled egg carried every tracked lineage (THEORY-1106). Read it knowing that the rise in titre is significant for one species, Magicicada septendecim, of four compared, with five or six eggs each and no phylogenetic control; that the six-lineage species does not differ significantly from single-lineage ones; that lineage presence was tracked by one or two marker genes; and that the order of cause, splitting before titre, is inferred. |
| LIT-1596 v2 | Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS | Shigenobu et al. (2000). The first complete genome of an obligate insect endosymbiont: Buchnera sp. APS, maternally transmitted in aphid bacteriocytes, has a 640,681-bp chromosome with 583 ORFs and two small plasmids, a subset of E. coli’s gene set reached by loss. It keeps the genes for the amino acids essential to the host and lacks almost all of those for non-essential ones, and uses host-made glutamate and aspartate as precursors, so the two partners’ pathways interlock. It also lacks phospholipid and lipopolysaccharide synthesis, nearly all transcriptional regulators, and recA and uvrABC. The authors infer that it can live only in the bacteriocyte, with membrane lipids perhaps from the host, and compare it to an organelle. All of this is read from gene content. | Active — read in full 2026-10-27 (NOTE-1236) from the publisher’s free PDF of the version of record; worth reading as the first complete genome of an obligate insect endosymbiont, and for its gene-by-gene account of a symbiont that keeps the amino-acid pathways its host lacks, draws precursors from the host, and has lost phospholipid synthesis and nearly all its own regulators (THEORY-1103). Read it knowing that every functional statement is inferred from gene content in one strain, that the host’s dependence is cited from earlier work and maternal transmission stated, neither shown here, and that it names no mechanism of genome reduction: drift and Muller’s ratchet are not in it. |
| LIT-1602 v2 | Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas | Campbell, Łukasik, Simon & McCutcheon (2017). Every Magicicada species harbours Hodgkinia populations of at least twenty genomic circles, 256 in all, with little synteny except between the closest species. Most splitting happened within Magicicada and gives highly variable gene dosages, so Hodgkinia’s degradation has followed different paths in different hosts. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC8879801), the bioRxiv preprint is at biorxiv.org/content/10.1101/199760v1, and the publisher’s free PDF is at cell.com/article/S0960982217313118/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1603 v2 | The Evolution of Cooperation | Sachs, Mueller, Wilcox & Bull (2004). A tripartite framework for how cooperation within and between species evolves and is maintained: directed reciprocation, shared genes (kin selection) and byproduct benefits, each subdivided. Plant–rhizobium and squid–Vibrio symbioses are fitted to it, and natural systems often combine models. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1605 v2 | Host Control of Symbiont Transmission: The Separation of Symbionts Into Germ and Soma | Frank (1996b). A model of hosts that control which symbionts are transmitted, sequestering a germ line of symbionts apart from the somatic ones that serve the host, so as to limit competition among symbiont lineages. No abstract was seen: PubMed’s DOI search returned an unrelated record. The summary is drawn from the title and from what the paper is standardly cited for, and a reading should check it. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1608 v2 | Branching Processes: Variation, Growth, and Extinction of Populations | Haccou, Jagers & Vatutin (2005). A monograph on branching processes as models of populations, written for biologists: growth and extinction probabilities, single- and multi-type processes, and their use in establishing mutants and invading types. No abstract was seen. The summary is what the book is standardly cited for. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1612 v2 | Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia | Campbell et al. (2015). In the long-lived periodical cicada Magicicada tredecim, the Hodgkinia genome has fragmented into many chromosomes or genomes, some in discrete cells, together about 1.1 Mb, nearly ten times the hypothetical single ancestor. The authors tested whether long host life cycles enable the splitting, and compare the result with organelle genome fragmentation. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC4547289), and the publisher’s version is at pnas.org/doi/pdf/10.1073/pnas.1421386112. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1617 v2 | Host–symbiont conflict over the mixing of symbiotic lineages | Frank (1996a). Symbionts favour dispersal to escape competition with relatives; mixing of symbiont lineages breeds competition and virulence; hosts are favoured to restrict mixing. But a host modifier that reduces mixing spreads only when it is directly associated with reduced virulence, a condition taken from Hoekstra’s work on uniparental inheritance and extended across symbiont life histories. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1824 v2 | Tractable models of ecological assembly | Serván & Allesina (2021), Ecology Letters 24: 1029–1037. Represents assembly by rare, low-density, well-separated invasions as a directed graph on feasible sub-communities, and proves that sequential (bottom-up) and all-at-once (top-down) assembly reach the same end-points when the graph is acyclic and attractors are exactly the uninvadable sub-communities. For competitive Lotka–Volterra with A = D(v)BD(w), B symmetric with positive entries, MacArthur’s Lyapunov function orders the sub-communities, so both hold: with B positive definite there is one end-point, the sub-community of greatest total biomass when r = v, reachable by invasions without extinctions; with B indefinite there are several, and order of arrival matters. A consumer–resource model whose consumers can exclude resources can have cycles. | Active — read 2026-10-29 (NOTE-1422) in full, from its first author’s dissertation in the University of Chicago’s repository (chapter 3, appendix included); worth reading as the result that, for symmetric competitive Lotka–Volterra communities, MacArthur’s Lyapunov function orders every sub-community, so the assembly graph is acyclic, every feasible sub-community can be built by invasions without extinctions, and sequential and all-at-once assembly reach the same end-points. Read it knowing that the copy read is the dissertation chapter of August 2020, not the Ecology Letters version, which was not compared; that order-independence (a single end-point) needs the interaction matrix positive definite, and an indefinite one still has priority effects; and that the step from the Lyapunov function to acyclicity is asserted, not written out. |
| LIT-1826 | MacArthur’s consumer-resource model | Chesson (1990), Theoretical Population Biology 37: 26–38. By the abstract: reviews MacArthur’s consumer-resource model and develops statistical measures of association between species’ utilization functions that express its coexistence conditions without strong symmetry assumptions. Not read. | Unfetched — filed 2026-10-29 from the triage of the day, not read. A lawful free copy is located: the author’s own reprint on his University of Arizona faculty pages, at http://www.eebweb.arizona.edu/Faculty/chesson/Peter/Reprints/1990_MacArthur’s%20consumer-resource%20model.pdf (given by Semantic Scholar as the paper’s open copy). On 2026-10-29 the host returned 503 over http and reset the connection over https, to curl and to WebFetch, and web.archive.org reset every connection, so no Wayback capture could be checked. An academia.edu upload (https://www.academia.edu/113408254/MacArthurs_consumer_resource_model, uploader not seen) returned a Cloudflare 403 challenge. OpenAlex reports the Elsevier copy closed. No NOTE is filed. |
| LIT-1827 | Multispecies Competition in Variable Environments | Chesson (1994), Theoretical Population Biology 45: 227–276. By the abstract: a general model of several species competing in a fluctuating environment, analysed by one method that sorts mechanisms of coexistence and exclusion into three categories: those that do not need fluctuations, the storage effect, and fluctuating competition with species-specific nonlinear responses to it; illustrated with a Lotka–Volterra model, nonlinear resource consumption and two recruitment models. Not read. | Unavailable — filed 2026-10-29 from the triage of the day, not read. A lawful full text was sought on 2026-10-29 and not reached. OpenAlex reports it closed with the Elsevier DOI as its only location, and Semantic Scholar reports no open copy. The author’s other reprints are on his old University of Arizona faculty pages (www.eebweb.arizona.edu/Faculty/chesson/Peter/Reprints/), but that host returned 503 or reset the connection on 2026-10-29, its publication list could not be opened, and no address for this paper’s reprint was found by search; the lab’s current pages (eeb.arizona.edu/chesson-lab, /chesson-publications) list it without a link. web.archive.org reset every connection, so no capture of a reprint could be checked. It stays Unavailable until a copy is supplied or the faculty pages answer. No NOTE is filed. |