Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The transition between the niche and neutral regimes in ecology.

ABSTRACT: An ongoing debate in ecology concerns the impacts of ecological drift and selection on community assembly. Here, we show that there is a transition in diverse ecological communities between a selection-dominated regime (the niche phase) and a drift-dominated regime (the neutral phase). Simulations and analytic arguments show that the niche phase is favored in communities with large population sizes and relatively constant environments, whereas the neutral phase is favored in communities with small population sizes and fluctuating environments. Our results demonstrate how apparently neutral populations may arise even in communities inhabited by species with varying traits.

SUBMITTER: Fisher CK

PROVIDER: S-EPMC4246938 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The transition between the niche and neutral regimes in ecology.

Fisher Charles K CK Mehta Pankaj P

Proceedings of the National Academy of Sciences of the United States of America 20140825 36

An ongoing debate in ecology concerns the impacts of ecological drift and selection on community assembly. Here, we show that there is a transition in diverse ecological communities between a selection-dominated regime (the niche phase) and a drift-dominated regime (the neutral phase). Simulations and analytic arguments show that the niche phase is favored in communities with large population sizes and relatively constant environments, whereas the neutral phase is favored in communities with sma ...[more]

PMID: 25157131

Similar Datasets

Phenomenology and dynamics of competitive ecosystems beyond the niche-neutral regimes.

Project description:Structure, composition, and stability of ecological populations are shaped by the inter- and intraspecies interactions within their communities. It remains to be fully understood how the interplay of these interactions with other factors, such as immigration, controls the structure, the diversity, and the long-term stability of ecological systems in the presence of noise and fluctuations. We address this problem using a minimal model of interacting multispecies ecological communities that incorporates competition, immigration, and demographic noise. We find that a complete phase diagram exhibits rich behavior with multiple regimes that go beyond the classical "niche" and "neutral" regimes, extending and modifying the "rare biosphere" or "niche-like" dichotomy. In particular, we observe regimes that cannot be characterized as either niche or neutral where a multimodal species abundance distribution is observed. We characterize the transitions between the different regimes and show how these arise from the underlying kinetics of the species turnover, extinction, and invasion. Our model serves as a minimal null model of noisy competitive ecological systems, against which more complex models that include factors such as mutations and environmental noise can be compared.

| S-EPMC9618050 | biostudies-literature

Unveiling the transition from niche to dispersal assembly in ecology.

Project description:A central goal in ecology is to understand what maintains species diversity in local communities. Classic ecological theory1,2 posits that niches dictate the maximum number of species that can coexist in a community and that the richness of observed species will be below this maximum only where immigration is very low. A new alternative theory3,4 is that niches, instead, dictate the minimum number of coexisting species and that the richness of observed species will usually be well above this because of ongoing immigration. We conducted an experimental test to discriminate between these two unified theories using a manipulative field experiment with tropical intertidal communities. We found, consistent with the new theory, that the relationship of species richness to immigration rate stabilized at a low value at low immigration rates and did not saturate at high immigration rates. Our results suggest that tropical intertidal communities have low niche diversity and are typically in a dispersal-assembled regime where immigration is high enough to overfill the niches. Observational data from other studies3,5 suggest that these conclusions may generalize to other ecological systems. Our new experimental approach can be adapted for other systems and be used as a 'niche detector' and a tool for assessing when communities are niche versus dispersal assembled.

| S-EPMC10266978 | biostudies-literature

Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging.

Project description:In this work we propose an index to estimate the gut microbiota biodiversity using a modeling approach with the aim of describing its relationship with health and aging. The gut microbiota, a complex ecosystem that links nutrition and metabolism, has a pervasive effect on all body organs and systems, undergoes profound changes with age and life-style, and substantially contributes to the pathogenesis of age-related diseases. For these reasons, the gut microbiota is a suitable candidate for assessing and quantifying healthy aging, i.e. the capability of individuals to reach an advanced age, avoiding or postponing major age-related diseases. The importance of the gut microbiota in health and aging has been proven to be related not only to its taxonomic composition, but also to its ecological properties, namely its biodiversity. Following an ecological approach, here we intended to characterize the relationship between the gut microbiota biodiversity and healthy aging through the development a parsimonious model of gut microbiota from which biodiversity can be estimated. We analysed publicly available metagenomic data relative to subjects of different ages, countries, nutritional habits and health status and we showed that a hybrid niche-neutral model well describes the observed patterns of bacterial relative abundance. Moreover, starting from such ecological modeling, we derived an estimate of the gut microbiota biodiversity that is consistent with classical indices, while having a higher statistical power. This allowed us to unveil an increase of the gut microbiota biodiversity during aging and to provide a good predictor of health status in old age, dependent on life-style and aging disorders.

| S-EPMC7599046 | biostudies-literature

Fluorescence microscopy visualization of the roughness-induced transition between lubrication regimes.

Project description:We investigate the transition between different regimes of lubrication and directly observe the thickness of nanometric lubrication films with a sensitivity of a single molecular layer at a multi-asperity interface through fluorescence microscopy. We redefine specific film thickness as the ratio of the lubricant film thickness and the surface roughness measured only at those regions of the interface where the gap is "minimal." This novel definition of specific film thickness successfully captures the transition from full elastohydrodynamic lubrication to mixed and boundary lubrication. The transition can be triggered by increasing the surface roughness and is accurately predicted by using the new film thickness definition. We find that when the liquid carries part of the load, its apparent viscosity is greatly increased by confinement, and show how the transition between different lubrication regimes is well described by the viscosity increase and subsequent glass transition in the film.

| S-EPMC6897541 | biostudies-literature

Transition between two regimes describing internal fluctuation of DNA in a nanochannel.

Project description:We measure the thermal fluctuation of the internal segments of a piece of DNA confined in a nanochannel about 50-100 nm wide. This local thermodynamic property is key to accurate measurement of distances in genomic analysis. For DNA in ~100 nm channels, we observe a critical length scale ~10 m for the mean extension of internal segments, below which the de Gennes' theory describes the fluctuations with no fitting parameters, and above which the fluctuation data falls into Odijk's deflection theory regime. By analyzing the probability distributions of the extensions of the internal segments, we infer that folded structures of length 150-250 nm, separated by ~10 m exist in the confined DNA during the transition between the two regimes. For ~50 nm channels we find that the fluctuation is significantly reduced since the Odijk regime appears earlier. This is critical for genomic analysis. We further propose a more detailed theory based on small fluctuations and incorporating the effects of confinement to explicitly calculate the statistical properties of the internal fluctuations. Our theory is applicable to polymers with heterogeneous mechanical properties confined in non-uniform channels. We show that existing theories for the end-to-end extension/fluctuation of polymers can be used to study the internal fluctuations only when the contour length of the polymer is many times larger than its persistence length. Finally, our results suggest that introducing nicks in the DNA will not change its fluctuation behavior when the nick density is below 1 nick per kbp DNA.

| S-EPMC3057976 | biostudies-literature

Transition between Functional Regimes in an Integrate-And-Fire Network Model of the Thalamus.

Project description:The thalamus is a key brain element in the processing of sensory information. During the sleep and awake states, this brain area is characterized by the presence of two distinct dynamical regimes: in the sleep state activity is dominated by spindle oscillations (7 - 15 Hz) weakly affected by external stimuli, while in the awake state the activity is primarily driven by external stimuli. Here we develop a simple and computationally efficient model of the thalamus that exhibits two dynamical regimes with different information-processing capabilities, and study the transition between them. The network model includes glutamatergic thalamocortical (TC) relay neurons and GABAergic reticular (RE) neurons described by adaptive integrate-and-fire models in which spikes are induced by either depolarization or hyperpolarization rebound. We found a range of connectivity conditions under which the thalamic network composed by these neurons displays the two aforementioned dynamical regimes. Our results show that TC-RE loops generate spindle-like oscillations and that a minimum level of clustering (i.e. local connectivity density) in the RE-RE connections is necessary for the coexistence of the two regimes. We also observe that the transition between the two regimes occurs when the external excitatory input on TC neurons (mimicking sensory stimulation) is large enough to cause a significant fraction of them to switch from hyperpolarization-rebound-driven firing to depolarization-driven firing. Overall, our model gives a novel and clear description of the role that the two types of neurons and their connectivity play in the dynamical regimes observed in the thalamus, and in the transition between them. These results pave the way for the development of efficient models of the transmission of sensory information from periphery to cortex.

| S-EPMC5012668 | biostudies-literature

Cross-scale neutral ecology and the maintenance of biodiversity.

Project description:One of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances changes with spatial scale, and this gap has hampered attempts to use observed species abundances as a way to quantify what non-neutral processes are needed to fully explain observed patterns. To address this, we introduce a new formulation of spatial neutral biodiversity theory and derive analytical predictions for the way abundance distributions change with scale. For tropical forest data where neutrality has been extensively tested before now, we apply this approach and identify an incompatibility between neutral fits at regional and local scales. We use this approach derive a sharp quantification of what remains to be explained by non-neutral processes at the local scale, setting a quantitative target for more general models for the maintenance of biodiversity.

| S-EPMC6033888 | biostudies-literature

Plasma functionalization for cyclic transition between neutral and charged excitons in monolayer MoS2.

Project description:Monolayer MoS2 (1L-MoS2) has photoluminescence (PL) properties that can greatly vary via transition between neutral and charged exciton PLs depending on carrier density. Here, for the first time, we present a chemical doping method for reversible transition between neutral and charged excitons of 1L-MoS2 using chlorine-hydrogen-based plasma functionalization. The PL of 1L-MoS2 is drastically increased by p-type chlorine plasma doping in which its intensity is easily tuned by controlling the plasma treatment duration. We find that despite their strong adhesion, a post hydrogen plasma treatment can very effectively dedope chlorine adatoms in a controllable way while maintaining robust structural integrity, which enables well-defined reversible PL control of 1L-MoS2. After exhaustive chlorine dedoping, the hydrogen plasma process induces n-type doping of 1L-MoS2, degrading the PL further, which can also be recovered by subsequent chlorine plasma treatment, extending the range of tunable PL into a bidirectional regime. This cyclically-tunable carrier doping method can be usefully employed in fabricating highly-tunable n- and p-type domains in monolayer transition-metal dichalcogenides suitable for two-dimensional electro-optic modulators, on-chip lasers, and spin- and valley-polarized light-emitting diodes.

| S-EPMC4761959 | biostudies-literature

Role of Adhesion Stress in Controlling Transition between Plastic, Grinding and Breakaway Regimes of Adhesive Wear.

Project description:A discrete-element based model of elastic-plastic materials with non-ideal plasticity and with an account of both cohesive and adhesive interactions inside the material is developed and verified. Based on this model, a detailed study of factors controlling the modes of adhesive wear is performed. Depending on the material and loading parameters, we observed three main modes of wear: slipping, plastic grinding, cleavage, and breakaway. We find that occurrence of a particular mode is determined by the combination of two dimensionless material parameters: (1) the ratio of the adhesive stress to the pure shear strength of the material, and (2) sensitivity parameter of material shear strength to local pressure. The case study map of asperity wear modes in the space of these parameters has been constructed. Results of this study further develop the findings of the widely discussed studies by the groups of J.-F. Molinari and L. Pastewka.

| S-EPMC6994689 | biostudies-literature

Baboon feeding ecology informs the dietary niche of Paranthropus boisei.

Project description:Hominins are generally considered eclectic omnivores like baboons, but recent isotope studies call into question the generalist status of some hominins. Paranthropus boisei and Australopithecus bahrelghazali derived 75%-80% of their tissues' δ(13)C from C4 sources, i.e. mainly low-quality foods like grasses and sedges. Here I consider the energetics of P. boisei and the nutritional value of C4 foods, taking into account scaling issues between the volume of food consumed and body mass, and P. boisei's food preference as inferred from dento-cranial morphology. Underlying the models are empirical data for Papio cynocephalus dietary ecology. Paranthropus boisei only needed to spend some 37%-42% of its daily feeding time (conservative estimate) on C4 sources to meet 80% of its daily requirements of calories, and all its requirements for protein. The energetic requirements of 2-4 times the basal metabolic rate (BMR) common to mammals could therefore have been met within a 6-hour feeding/foraging day. The findings highlight the high nutritional yield of many C4 foods eaten by baboons (and presumably hominins), explain the evolutionary success of P. boisei, and indicate that P. boisei was probably a generalist like other hominins. The diet proposed is consistent with the species' derived morphology and unique microwear textures. Finally, the results highlight the importance of baboon/hominin hand in food acquisition and preparation.

| S-EPMC3885648 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data