scholarly journals Energy landscape analysis elucidates the multistability of ecological communities across environmental gradient

2019 ◽  
Author(s):  
Kenta Suzuki ◽  
Shinji Nakaoka ◽  
Shinji Fukuda ◽  
Hiroshi Masuya
Keyword(s):  
Gut Microbiota ◽  
Environmental Gradients ◽  
Empirical Studies ◽  
Energy Landscape ◽  
Population Level ◽  
Ecological Communities ◽  
Stable States ◽  
Community Function ◽  
Compositional Stability ◽  
Mouse Gut Microbiota

AbstractCompositional multistability is widely observed in multispecies ecological communities. Since differences in community composition often lead to differences in community function, understanding compositional multistability is essential to comprehend the role of biodiversity in maintaining ecosystems. In community assembly studies, it has long been recognized that the order and timing of species migration and extinction influence structure and function of communities. The study of multistability in ecology has focused on the change in dynamical stability across environmental gradients, and was developed mainly for low-dimensional systems. As a result, methodologies for studying the compositional stability of empirical multispecies communities is not well developed. Here, we show that models previously used in ecology can be analyzed from a new perspective - the energy landscape - to unveil compositional stability of multispecies communities in observational data. To show that our method can be applicable to real-world ecological communities, we simulated the assembly dynamics driven by population level processes, and show that results were mostly robust to different simulation conditions. Our method reliably captured the change of the overall compositional stability of multispecies communities over environmental change, and indicated a small fraction of community compositions that may be a channel for transition between stable states. When applied to mouse gut microbiota, our method showed the presence of two alternative states with change in age, and suggested the multiple mechanism by which aging impairs the compositional stability of the mouse gut microbiota. Our method will be a practical tool to study the compositional stability of multispecies communities in a changing world, and will facilitate empirical studies that integrate the concept of multistability developed in different fields of ecology in the past decades.

Studying Populations of Online Communities

2019 ◽  
pp. 173-193
Author(s):  
Benjamin Mako Hill ◽  
Aaron Shaw
Keyword(s):  
Online Communities ◽  
Information Diffusion ◽  
Diffusion Processes ◽  
Empirical Studies ◽  
Population Level ◽  
Study Groups ◽  
Population Based ◽  
Large Majority ◽  
Community Processes ◽  
Published Research

While the large majority of published research on online communities consists of analyses conducted entirely within individual communities, this chapter argues for a population-based approach, in which researchers study groups of similar communities. For example, although there have been thousands of papers published about Wikipedia, a population-based approach might compare all wikis on a particular topic. Using examples from published empirical studies, the chapter describes five key benefits of this approach. First, it argues that population-level research increases the generalizability of findings. Next, it describes four processes and dynamics that are only possible to study using populations: community-level variables, information diffusion processes across communities, ecological dynamics, and multilevel community processes. The chapter concludes with a discussion of a series of limitations and challenges.

scholarly journals Erratum: Corrigendum: Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome

Nature ◽  
2016 ◽  
Vol 536 (7615) ◽  
pp. 238-238 ◽  
Author(s):  
Benoit Chassaing ◽  
Omry Koren ◽  
Julia K. Goodrich ◽  
Angela C. Poole ◽  
Shanthi Srinivasan ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Gut Microbiota ◽  
Mouse Gut Microbiota

Effects of Fish Oil with a High Content of n-3 Polyunsaturated Fatty Acids on Mouse Gut Microbiota

2014 ◽  
Vol 45 (3) ◽  
pp. 195-202 ◽  
Author(s):  
Hai-Ning Yu ◽  
Jing Zhu ◽  
Wen-sheng Pan ◽  
Sheng-Rong Shen ◽  
Wei-Guang Shan ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Gut Microbiota ◽  
Polyunsaturated Fatty Acids ◽  
Fish Oil ◽  
Mouse Gut Microbiota

scholarly journals Dynamic population stage structure due to juvenile–adult asymmetry stabilizes complex ecological communities

2021 ◽  
Vol 118 (21) ◽  
pp. e2023709118
Author(s):  
André M. de Roos
Keyword(s):  
Self Regulation ◽  
Interaction Network ◽  
Population Level ◽  
Stage Structure ◽  
Current Theory ◽  
Species Interaction ◽  
Interaction Matrix ◽  
Foraging Efficiency ◽  
Ecological Communities ◽  
The Stability

Natural ecological communities are diverse, complex, and often surprisingly stable, but the mechanisms underlying their stability remain a theoretical enigma. Interactions such as competition and predation presumably structure communities, yet theory predicts that complex communities are stable only when species growth rates are mostly limited by intraspecific self-regulation rather than by interactions with resources, competitors, and predators. Current theory, however, considers only the network topology of population-level interactions between species and ignores within-population differences, such as between juvenile and adult individuals. Here, using model simulations and analysis, I show that including commonly observed differences in vulnerability to predation and foraging efficiency between juvenile and adult individuals results in up to 10 times larger, more complex communities than observed in simulations without population stage structure. These diverse communities are stable or fluctuate with limited amplitude, although in the model only a single basal species is self-regulated, and the population-level interaction network is highly connected. Analysis of the species interaction matrix predicts the simulated communities to be unstable but for the interaction with the population-structure subsystem, which completely cancels out these instabilities through dynamic changes in population stage structure. Common differences between juveniles and adults and fluctuations in their relative abundance may hence have a decisive influence on the stability of complex natural communities and their vulnerability when environmental conditions change. To explain community persistence, it may not be sufficient to consider only the network of interactions between the constituting species.

scholarly journals Critical energy landscape of linear soft spheres

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Silvio Franz ◽  
Antonio Sclocchi ◽  
Pierfrancesco Urbani
Keyword(s):  
Critical Exponents ◽  
Solid Phase ◽  
Energy Landscape ◽  
Amorphous Solid ◽  
Critical Energy ◽  
Contact Network ◽  
Stable States ◽  
Potential Energy Landscape ◽  
Soft Spheres ◽  
Non Linear System

We show that soft spheres interacting with a linear ramp potential when overcompressed beyond the jamming point fall in an amorphous solid phase which is critical, mechanically marginally stable and share many features with the jamming point itself. In the whole phase, the relevant local minima of the potential energy landscape display an isostatic contact network of perfectly touching spheres whose statistics is controlled by an infinite lengthscale. Excitations around such energy minima are non-linear, system spanning, and characterized by a set of non-trivial critical exponents. We perform numerical simulations to measure their values and show that, while they coincide, within numerical precision, with the critical exponents appearing at jamming, the nature of the corresponding excitations is richer. Therefore, linear soft spheres appear as a novel class of finite dimensional systems that self-organize into new, critical, marginally stable, states.

scholarly journals Modelling the influence of naturally acquired immunity from subclinical infection on outbreak dynamics and persistence of rabies in domestic dogs

2021 ◽  
Vol 15 (7) ◽  
pp. e0009581
Author(s):  
Susannah Gold ◽  
Christl A. Donnelly ◽  
Rosie Woodroffe ◽  
Pierre Nouvellet
Keyword(s):  
Control Strategies ◽  
Empirical Studies ◽  
Population Level ◽  
Domestic Dogs ◽  
Domestic Dog ◽  
Acquired Immunity ◽  
High Exposure ◽  
Common Assumption ◽  
Canine Rabies ◽  
Low Levels

A number of mathematical models have been developed for canine rabies to explore dynamics and inform control strategies. A common assumption of these models is that naturally acquired immunity plays no role in rabies dynamics. However, empirical studies have detected rabies-specific antibodies in healthy, unvaccinated domestic dogs, potentially due to immunizing, non-lethal exposure. We developed a stochastic model for canine rabies, parameterised for Laikipia County, Kenya, to explore the implications of different scenarios for naturally acquired immunity to rabies in domestic dogs. Simulating these scenarios using a non-spatial model indicated that low levels of immunity can act to limit rabies incidence and prevent depletion of the domestic dog population, increasing the probability of disease persistence. However, incorporating spatial structure and human response to high rabies incidence allowed the virus to persist in the absence of immunity. While low levels of immunity therefore had limited influence under a more realistic approximation of rabies dynamics, high rates of exposure leading to immunizing non-lethal exposure were required to produce population-level seroprevalences comparable with those reported in empirical studies. False positives and/or spatial variation may contribute to high empirical seroprevalences. However, if high seroprevalences are related to high exposure rates, these findings support the need for high vaccination coverage to effectively control this disease.

scholarly journals Relation between stability and resilience determines the performance of early warning signals under different environmental drivers

2015 ◽  
Vol 112 (32) ◽  
pp. 10056-10061 ◽  
Author(s):  
Lei Dai ◽  
Kirill S. Korolev ◽  
Jeff Gore
Keyword(s):  
Early Warning ◽  
Alternative Stable States ◽  
Basin Of Attraction ◽  
Environmental Drivers ◽  
Ecological Communities ◽  
Stable States ◽  
Warning Signals ◽  
Early Warning Signals ◽  
The Stability ◽  
Stability And Resilience

Shifting patterns of temporal fluctuations have been found to signal critical transitions in a variety of systems, from ecological communities to human physiology. However, failure of these early warning signals in some systems calls for a better understanding of their limitations. In particular, little is known about the generality of early warning signals in different deteriorating environments. In this study, we characterized how multiple environmental drivers influence the dynamics of laboratory yeast populations, which was previously shown to display alternative stable states [Dai et al., Science, 2012]. We observed that both the coefficient of variation and autocorrelation increased before population collapse in two slowly deteriorating environments, one with a rising death rate and the other one with decreasing nutrient availability. We compared the performance of early warning signals across multiple environments as “indicators for loss of resilience.” We find that the varying performance is determined by how a system responds to changes in a specific driver, which can be captured by a relation between stability (recovery rate) and resilience (size of the basin of attraction). Furthermore, we demonstrate that the positive correlation between stability and resilience, as the essential assumption of indicators based on critical slowing down, can break down in this system when multiple environmental drivers are changed simultaneously. Our results suggest that the stability–resilience relation needs to be better understood for the application of early warning signals in different scenarios.

scholarly journals Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis

Microbiome ◽  
2018 ◽  
Vol 6 (1) ◽  
Author(s):  
Yan He ◽  
Wei Wu ◽  
Shan Wu ◽  
Hui-Min Zheng ◽  
Pan Li ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Gut Microbiota ◽  
Economic Status ◽  
Population Level ◽  
Level Analysis
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