Ecological networks are theoretical abstractions that represent ecological communities. These networks are usually defined as static entities, in which the occurrence of a particular interaction between species is considered fixed despite the intrinsic dynamics of ecological systems. However, empirical analysis of the temporal variation of trophic interactions is constrained by the lack of data with high spatial, temporal, and taxonomic resolution. Here, we evaluate the spatiotemporal variability of multiple consumer-resource interactions of large marine networks. The tropic interactions of all of the analyzed networks had low temporal persistence, which was well described by a common exponential decay in the rank-frequency relationship of consumer-resource interactions. This common pattern of low temporal persistence was evident despite the dissimilarities of environmental conditions among sites. Between-site rank correlations of frequency of occurrence of interactions ranged from 0.59 to 0.73. After removing the interactions with <50% frequency, the between-site correlations decreased to values between 0.60 and 0.28, indicating that low-frequency interactions accounted for the apparent similarities between sites. Our results showed that the communities studied were characterized by few persistent interactions and a large number of transient trophic interactions. We suggest that consumer-resource temporal asynchrony in addition to varying local environmental conditions and opportunistic foraging could be among the mechanisms generating the observed rank-frequency relationship of trophic interactions. Therefore, our results question the analysis of ecological communities as static and persistent natural entities and stress the need for strengthening the analysis of temporal variability in ecological networks and long-term studies.
High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloging of functional characteristics of microbial community members as well as their taxonomic identity. Such studies have found that a community's composition in terms of ecologically relevant functional traits or guilds can be conserved more strictly across varying settings than taxonomic composition is. I use a standard ecological resource-consumer model to examine the dynamics of traits relevant to resource consumption, and analyze determinants of functional composition. This model demon…
Consumer foraging behaviors are dynamic, changing in response to prey availability, seasonality, competition, and even the consumer's physiological state. The isotopic composition of a consumer is a product of these factors as well as the isotopic 'landscape' of its prey, i.e. the isotopic mixing space. Here we build a mechanistic framework that links the ecological and physiological processes of an individual consumer to the isotopic distribution that describes its diet, and ultimately to the isotopic composition of its own tissues, defined as its 'isotopic niche'. By coupling these processes…
The consumption rate is a process critically important for the stability of consumer-resource systems and the persistence, sustainability and biodiversity of complex food webs. Its mathematical description in the form of functional response equations is a key problem for describing all trophic interactions. Because some of the functional response models used in this study presented redundancy between its parameters two methods were used to check for parameter redundancy: the Hessian matrix calculation using automatic differentiation (AD) which calculates derivatives numerically, but does not u…
In 1972, Robert May triggered a worldwide research program studying ecological communities using random matrix theory. Yet, it remains unclear if and when we can treat real communities as random ecosystems. Here, we draw on recent progress in random matrix theory and statistical physics to extend May's approach to generalized consumer-resource models. We show that in diverse ecosystems adding even modest amounts of noise to consumer preferences results in a transition to "typicality" where macroscopic ecological properties of communities are indistinguishable from those of random ecosystems, e…
Separate artificial neural network (ANN) models were developed from data in two geographical regions and years apart for a marsh-nesting bird, the red-winged blackbird Agelaius phoeniceus. Each model was independently tested on the spatially and temporally distinct data from the other region to determine how generalizable it was. The first model was developed to predict occurrence of nests in two wetlands on Lake Erie, Ohio in 1995 and 1996. The second model was developed to predict breeding success in two marshes in Connecticut, USA in 1969 and 1970. Independent variables were vegetation dura…
Ecological systems show a variety of characteristic patterns of biodiversity in space and time. It is a challenge for theory to find models that can reproduce and explain the observed patterns. Since the advent of island biogeography these models revolve around speciation, dispersal, and extinction, but they usually neglect trophic structure. Here, we propose and study a spatially extended evolutionary food web model that allows us to study large spatial systems with several trophic layers. Our computer simulations show that the model gives rise simultaneously to several biodiversity patterns …
Quadratic programming (QP) is a common and important constrained optimization problem. Here, we derive a surprising duality between constrained optimization with inequality constraints -- of which QP is a special case -- and consumer resource models describing ecological dynamics. Combining this duality with a recent `cavity solution', we analyze high-dimensional, random QP where the optimization function and constraints are drawn randomly. Our theory shows remarkable agreement with numerics and points to a deep connection between optimization, dynamical systems, and ecology.
The need to harmonise apparently irreconcilable arrangements in an ecosystem --nestedness and segregation-- has triggered so far different strategies. Methodological refinements, or the inclusion of behavioural preferences to the network dynamics offer a limited approach to the problem, since one remains constrained within a 2-dimensional view of an ecosystem, i.e. a presence-absence matrix. Here we question this partial-view paradigm, and show that nestedness and segregation may coexist across a varied range of scenarios. To do so, we rely on an upscaled representation of an ecological commun…
Consumers face numerous risks that can be minimized by incorporating different life-history strategies. How much and when a consumer adds to its energetic reserves or invests in reproduction are key behavioral and physiological adaptations that structure much of how organisms interact. Here we develop a theoretical framework that explicitly accounts for stochastic fluctuations of an individual consumer's energetic reserves while foraging and reproducing on a landscape with resources that range from uniformly distributed to highly clustered. First, we show that optimal life-history strategies v…
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-f…
We show how highly-diverse ecological communities may display persistent abundance fluctuations, when interacting through resource competition and subjected to migration from a species pool. This turns out to be closely related to the ratio of realized species diversity to the number of resources. This ratio is set by competition, through the balance between species being pushed out and invading. When this ratio is smaller than one, dynamics will reach stable equilibria. When this ratio is larger than one, fixed-points are either unstable or marginally stable, as expected by the competitive ex…
When evaluating the ecological value of land use within a landscape, investigators typically rely on measures of habitat selection and habitat quality. Traditional measures of habitat selection and habitat quality require data from resource intensive study designs (e.g., telemetry or mark-recapture). Often, managers must evaluate ecological value despite only having data from less resource intensive study designs. In this paper, we use occupancy data to measure habitat quality and habitat selection response for the Puerto Rican Vireo, an endemic songbird whose population growth is depressed by…
Understanding the spread of any disease is a highly complex and interdisciplinary exercise as biological, social, geographic, economic, and medical factors may shape the way a disease moves through a population and options for its eventual control or eradication. Disease spread poses a serious threat in animal and plant health and has implications for ecosystem functioning and species extinctions as well as implications in society through food security and potential disease spread in humans. Space-time epidemiology is based on the concept that various characteristics of the pathogenic agents a…
Ecosystems are commonly organized into trophic levels -- organisms that occupy the same level in a food chain (e.g., plants, herbivores, carnivores). A fundamental question in theoretical ecology is how the interplay between trophic structure, diversity, and competition shapes the properties of ecosystems. To address this problem, we analyze a generalized Consumer Resource Model with three trophic levels using the zero-temperature cavity method and numerical simulations. We find that intra-trophic diversity gives rise to ``emergent competition'' between species within a trophic level due to fe…
Scaling laws in ecology, intended both as functional relationships among ecologically-relevant quantities and the probability distributions that characterize their occurrence, have long attracted the interest of empiricists and theoreticians. Empirical evidence exists of power laws associated with the number of species inhabiting an ecosystem, their abundances and traits. Although their functional form appears to be ubiquitous, empirical scaling exponents vary with ecosystem type and resource supply rate. The idea that ecological scaling laws are linked had been entertained before, but the ful…
A central question in ecology is to understand the ecological processes that shape community structure. Niche-based theories have emphasized the important role played by competition for maintaining species diversity. Many of these insights have been derived using MacArthur's consumer resource model (MCRM) or its generalizations. Most theoretical work on the MCRM has focused on small ecosystems with a few species and resources. However theoretical insights derived from small ecosystems many not scale up large ecosystems with many resources and species because large systems with many interacting…
Fused Lasso Improves Accuracy of Co-occurrence Network Inference in Grouped Samples
School of Informatics, Computing, and Cyber Systems, Northern Arizona University（信息学、计算与网络系统学院，北亚利桑那大学）；Department of Plant and Microbial Biology, University of Minnesota（植物与微生物生物学系，明尼苏达大学）；Department of Biological Sciences, Northern Arizona University（生物科学系，北亚利桑那大学）；Département d’informatique, Université de Sherbrooke（计算机系，Sherbrooke大学）
Chaos and stability in the marine trophic network: the importance of interactions over complexity
OGS-National Institute of Oceanography and Applied Geophysics（意大利海洋地球物理国家研究所）；NBFC-National Biodiversity Future Center（国家生物多样性未来中心）；MARBEC, Univ Montpellier, CNRS, Ifremer, IRD（蒙彼利埃大学/法国国家科学研究中心/法国海洋开发研究院/法国国家科研信息中心）；Department of Biology, McGill University（麦吉尔大学生物系）
Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities without losing generality remains a challenge. Here we propose to model cross-feeding interactions at an intermediate level between genome-scale metabolic models of individual species and consumer-resource models of ecosystems, which is suitable to empirical data. We applied our method to three published examples of multi-strain Escherichia coli communities with i…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from…
