ecology.
22 of 1538 NOTE documents. Back to the full index.
| # | Title | Summary | Status |
|---|---|---|---|
| NOTE-555 | Conceptualization of the Holobiont Paradigm as It Pertains to Corals | A mini-review arguing that corals must be studied as holobionts. The holobiont is defined by location (coral plus microbiota in body, mucus and skeleton), and its membership can change. Traits belong to host–symbiont combinations: a novel anemone–alga pairing out-performed both natural ones in oxygen flux at 32–34 °C, and two octocorals lost symbionts by different routes, one per host cell and one with host cells. It asks, without answering, whether the holobiont is the unit of selection. | Read |
| NOTE-556 | Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont | A review that redefines bleaching as three holobiont dysbiosis stages: microbial buffering, Symbiodiniaceae reorganisation by shuffling or switching, and traumatic dysbiosis ending in death (Figure 3). The supporting material is cited and correlational. Vibrio rose from about 0 to 30% relative abundance in bleached corals and returned in resilient ones, but the authors say cause and consequence cannot be separated. “Dysbiosis” names both the disruption and the healthy adaptive response, and the stages have no operational boundaries. | Read |
| NOTE-558 | Phase Shifts, Herbivory, and the Resilience of Coral Reefs to Climate Change | Four roofless 25 m² cages on Orpheus Island’s reef crest kept large and medium fishes out for 30 months after the 1998 bleaching, against four partial cages and four open plots. Macroalgae averaged 56% cover in cages and 4.1% and 1.7% outside. Coral cover reached 7.7% inside against 19.2% and 20.2%. Recruitment fell to about a third (39 against 108 and 118 per 25 m²) and mortality of established colonies was 24.2% against 9.8% and 11.3%. Reopened, the cages lost their algae in 30 days. | Read |
| NOTE-571 | Catastrophic regime shifts in ecosystems: linking theory to observation | A review of how to tell whether an ecosystem has alternative stable states. Field patterns (jumps, multimodality, dual relationships) are suggestive and never conclusive, since a stepwise driver or a simple threshold produces them too. Experiments can come close to proof: initial-state dependence, lasting shifts after temporary disturbance, and hysteresis. Models show positive feedback must be strong enough. | Read |
| NOTE-572 | Resilience and Stability of Ecological Systems | Ecological theory had equated stability with behaviour near equilibrium. Holling separates stability (return to equilibrium) from resilience (the capacity to absorb change and persist, set by the domain of attraction), shows they can trade off in lakes, forests, insects and fish, and warns that managing for constant yield can erode resilience. | Read |
| NOTE-703 | Forssten et al. — One Giant Leap from Mouse to Man | A narrative review, by employees of a probiotics manufacturer, of the microbiota–gut–brain axis in mood. The routes in rodents are well documented. Faecal transplant from depressed humans partly transfers the phenotype to rodents. Human trials are mixed: some reductions in subjective stress in healthy volunteers, and several clean nulls for strains with strong preclinical records. It documents its own translational failures and ends more optimistically than they warrant. | Read |
| NOTE-706 | Han et al. — From gut microbiota to host appetite | A narrative review, not systematic, by animal-nutrition scientists, of how gut-microbe metabolites and proteins may regulate host appetite. The mechanisms are plausible and mostly shown in rodents. The human evidence is associations in eating disorders and obesity, and prebiotic or metabolite trials that conflict across populations and durations. The authors say so. The framing is mutualist: no microbe “interest” in host eating is argued. | Read |
| NOTE-1211 | Athreya, Czuppon & Gokhale — The evolution of dependence and cohesion in incipient endosymbioses | An adaptive-dynamics model in which hosts, symbionts and host–symbiont collectives are three populations. Each partner has an “obligacy” (investment in collective rather than free-living growth) and an “adhesion” (investment in synchronized, collective reproduction). The faster-growing partner, the symbiont, becomes fully obligate first. What the host’s obligacy then does depends on within-collective births and deaths: it stays, rises to full dependence, or falls to none. Obligacy rises only if the collective’s carrying capacity is high enough; collective growth rate does not matter. Early on, dependence evolves ahead of cohesion. That last result holds for the trait mapping the authors chose, and their own Table S1 reverses it under the opposite mapping. The authors say the available data can neither confirm nor refute it. | Read |
| NOTE-1212 | Morris, Lenski & Zinser — The Black Queen Hypothesis | Proposes that in free-living microbes, losing a costly function whose product leaks to neighbours is favoured by ordinary individual selection, and the loss runs until the remaining producers (“helpers”) just supply the community, leaving most cells (“beneficiaries”) dependent on a rare few. No relatedness, cooperation or collective is needed, only leakiness and frequency dependence. The one worked case is the loss of catalase-peroxidase (katG) in Prochlorococcus, which cannot survive the hydrogen peroxide that its community removes. The other cases are suggestions. | Read |
| NOTE-1213 | McCutcheon, Garber, Spencer & Warren — How do bacterial endosymbionts work with so few genes? | An essay on the endosymbionts with genomes under about 200 kb, which the authors call “tipping-point endosymbionts”. Below about 400 kb, symbionts almost always lose the genes to build their own envelope and to move proteins across it. Below about 200 kb, even translation erodes: ribosomal proteins, tRNAs and aminoacyl-tRNA synthetases go. Their proteomes are among the most compositionally biased in bacteria. The paper asks four questions it cannot answer: where their membranes, transporters, missing translation parts and protein stability come from. Its best guess is from the host, as in organelles. The thresholds come from a hand-picked set of genomes, and the composition analysis is called preliminary. | Read |
| NOTE-1235 | Campbell et al. — Changes in endosymbiont complexity drive host-level compensatory adaptations in cicadas | In cicadas whose endosymbiont Hodgkinia has split into many lineages, each essential, the mother must put every lineage into every egg. A simulation shows that random transmission would need far more cells as lineages multiply and grow uneven. Counts in eggs of four species find Sulcia numbers roughly constant, and Hodgkinia numbers up to about six times higher in Magicicada septendecim than in a single-lineage species. Amplicon sequencing found every tracked Hodgkinia genotype in every egg sampled. The transmission route looks the same under the light microscope. Only M. septendecim differs significantly; the six-lineage species does not. So the compensation rests on one species. The authors call the raised titre a cost of fragmentation, and speculate that it could feed further splitting. | Read |
| NOTE-1236 | Shigenobu, Watanabe, Hattori, Sakaki & Ishikawa — Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS | The first complete genome of an obligate insect endosymbiont. Buchnera APS, from the pea aphid, has a 640,681-bp chromosome with 583 ORFs and two small plasmids. It is a subset of the E. coli gene set, produced by loss from a larger common ancestor. It keeps the pathways for the amino acids its host cannot make, lacks almost all of those the host can, and draws some precursors from the host, so the two partners’ pathways interlock. It also lacks phospholipid and lipopolysaccharide synthesis, almost all transcriptional regulators, and recA and uvrABC. The authors infer that it can live only in the bacteriocyte and compare it to an organelle. Everything here is read from gene content; no experiment on the symbiont is reported, and the host’s dependence is asserted from the literature, not shown. | Read |
| NOTE-1241 | Sørensen, Stiller, Kröninger & Nowack — Protein import into bacterial endosymbionts and evolving organelles | A review of the evidence that hosts import their own proteins into bacterial endosymbionts, which has long been taken to mark an organelle off from an endosymbiont. Import of hundreds of nucleus-encoded proteins is established, by proteomics of isolated endosymbionts, in two systems only: the chromatophore of Paulinella and the nitroplast of Braarudosphaera. In both, the imported proteins come mostly from the host’s own genes and from bacteria other than the endosymbiont, and the authors say that gene transfer from the endosymbiont “is not a precondition” for genetic integration. Elsewhere, in a trypanosomatid, a diatom and four insects, there are one to seven imported or targeted proteins per system, each found by antibodies or proteomics. The authors propose an order, effector proteins first and dependence on an imported redundant protein second, which they call plausible on limited data. The import mechanisms are almost entirely unknown. | Read |
| NOTE-1352 | Marsland, Cui and Mehta — The minimum environmental perturbation principle | In niche models whose environmentally mediated interactions are symmetric, which it characterizes as impact vectors of the form q_iα = −a_i b_α ∂g_i/∂R_α, the uninvadable equilibrium minimizes a perturbation d(R0, R) of the environment from its supply point subject to no species having positive growth, with the species’ scaled abundances as KKT multipliers. MacArthur’s minimization principle is its Lagrange dual. d rises with every successful invasion. | Read |
| NOTE-1366 | Blumenthal, Rocks and Mehta — Phase transition to chaos with nonreciprocal species-resource interactions | In MacArthur’s consumer–resource model with species’ benefits c and impacts e on resources correlated by ρ, the cavity method’s replica-symmetric fixed point loses stability at ρ² = (surviving species)/(non-depleted resources); below ρ simulations do not settle, their largest Lyapunov exponents are positive and the probability of reaching a steady state falls with system size. With ρ = 1 the model has an optimization principle and competitive exclusion keeps the ratio ≤ 1, so the transition never occurs. | Read |
| NOTE-1368 | Power et al. — What can ecosystems learn? | In a competitive Lotka–Volterra community where individual selection lowers the competitive effect ω_ij of species j on species i at a rate proportional to x_i x_j, and a normalising trade-off holds each row and column sum of ω fixed, interactions change as Hebbian learning does. In simulation (400 species, symmetric ω) the community comes to hold attractors for two past forcing patterns, completes them from fragments and switches with hysteresis. The memory needs the imposed trade-off, and in the long run it degrades. | Read |
| NOTE-1369 | Cooper and West — Division of labour and the evolution of extreme specialization | A kin-selection model of one cooperative trait with two phenotypes that invest q1 and q2 in helping. Division of labour needs accelerating returns to helping (α > 1) but is not guaranteed by it; when it evolves one phenotype is always a pure reproductive (q2 = 0), so a feedback between helper and reproductive specialization drives the extremes. Relatedness does not affect whether division evolves for an essential trait, and favours sterile helpers. The authors infer that division of labour drives major transitions; the model contains no transition. | Read |
| NOTE-1377 | Letten, Ke and Fukami — Linking modern coexistence theory and contemporary niche theory | Translating Tilman’s two-consumer, two-resource model into Lotka–Volterra coefficients and then into Chesson’s niche overlap ρ and fitness ratio, the authors find, by worked cases at equilibrium, that shifting the resource supply ratio changes only the fitness ratio (equalizing) except at extremes where essential-resource competitors become limited by the same resource and ρ jumps to 1; that impact-niche overlap moves ρ (stabilizing); and that requirement-niche overlap moves both, without changing whether the species coexist. | Read |
| NOTE-1379 | Hofbauer and Schreiber — Permanence via invasion graphs | For ecological ODEs whose invasion growth rates have well-defined, nonzero signs on each subcommunity, it defines the invasion graph (edges S → T when every species in T but not S can invade S and every species lost cannot invade T) and proves that when the graph is acyclic, robust permanence holds if, and essentially only if, each species i has a positive invasion growth rate at every −i community. With cycles, signs are not enough. | Read |
| NOTE-1395 | Mehta, Cui, Wang and Marsland — Constrained optimization as ecological dynamics | Any minimization of f(R) over R ≥ 0 under constraints g_i(R) ≤ 0 has the KKT points of a consumer–resource dynamics as its steady states: variables are resources, each constraint is a species whose abundance is its Lagrange multiplier, and binding constraints are the surviving species. For quadratic programs the dynamics is MacArthur’s model, and the Lagrangian dual is a generalized Lotka–Volterra system. A cavity solution then gives the statistics of random quadratic programs, in agreement with numerics at M = 100. | Read |
| NOTE-1397 | Bunin — Ecological communities with Lotka-Volterra dynamics | For generalized Lotka–Volterra dynamics of a community assembled from a pool of S species with random interactions of mean μ/S, variance σ²/S and symmetry γ, the cavity method gives exact large-S results in the phase with a unique uninvadable fixed point: a Gaussian truncated at zero for abundances, the fraction of surviving species, and a loss of stability at σ = √2/(1 + γ) for equal carrying capacities, independent of μ. Beyond it lies a multiple-attractor phase in which the outcome depends on history; that phase is located, not solved, and its history dependence is shown numerically. | Read |
| NOTE-1422 | Serván and Allesina — Tractable models of ecological assembly | For competitive Lotka–Volterra communities with A = D(v)BD(w), B symmetric with positive entries, assembled by rare, low-density, well-separated invasions, MacArthur’s Lyapunov function V orders the feasible sub-communities, so the assembly graph is acyclic and every feasible sub-community can be assembled without extinctions; with the paper’s Theorem 1 this makes sequential and all-at-once assembly reach the same end-points. One end-point when B is positive definite, several when it is not. | Read |