Foraging adaptation and the relationship between food-web complexity and stability

Simple biophysical model of tumor evasion from immune system control

The competitive nonlinear interplay between a tumor and the host's immune system is not only very complex but is also time-changing. A fundamental aspect of this issue is the ability of the tumor to slowly carry out processes that gradually allow it to become less harmed and less susceptible to recognition by the immune system effectors. Here we propose a simple epigenetic escape mechanism that adaptively depends on the interactions per time unit between cells of the two systems. From a biological point of view, our model is based on the concept that a tumor cell that has survived an encounter with a cytotoxic T-lymphocyte (CTL) has an information gain that it transmits to the other cells of the neoplasm. The consequence of this information increase is a decrease in both the probabilities of being killed and of being recognized by a CTL. We show that the mathematical model of this mechanism is formally equal to an evolutionary imitation game dynamics. Numerical simulations of transitory phases complement the theoretical analysis. Implications of the interplay between the above mechanisms and the delivery of immunotherapies are also illustrated.

Genetic variation, predator-prey interactions and food web structure

Food webs are networks of species that feed on each other. The role that within-population phenotypic and genetic variation plays in food web structure is largely unknown. Here, I show via simulation how variation in two key traits, growth rates and phenology, by influencing the variability of body sizes present through time, can potentially affect several structural parameters in the direction of enhancing food web persistence: increased connectance, decreased interaction strengths, increased variation among interaction strengths and increased degree of omnivory. I discuss other relevant traits whose variation could affect the structure of food webs, such as morphological and additional life-history traits, as well as animal personalities. Furthermore, trait variation could also contribute to the stability of food web modules through metacommunity dynamics. I propose future research to help establish a link between within-population variation and food web structure. If appropriately established, such a link could have important consequences for biological conservation, as it would imply that preserving (functional) genetic variation within populations could ensure the preservation of entire communities.

Persistence increases with diversity and connectance in trophic metacommunities

BACKGROUND

We are interested in understanding if metacommunity dynamics contribute to the persistence of complex spatial food webs subject to colonization-extinction dynamics. We study persistence as a measure of stability of communities within discrete patches, and ask how do species diversity, connectance, and topology influence it in spatially structured food webs.

METHODOLOGY/PRINCIPAL FINDINGS

We answer this question first by identifying two general mechanisms linking topology of simple food web modules and persistence at the regional scale. We then assess the robustness of these mechanisms to more complex food webs with simulations based on randomly created and empirical webs found in the literature. We find that linkage proximity to primary producers and food web diversity generate a positive relationship between complexity and persistence in spatial food webs. The comparison between empirical and randomly created food webs reveal that the most important element for food web persistence under spatial colonization-extinction dynamics is the degree distribution: the number of prey species per consumer is more important than their identity.

CONCLUSIONS/SIGNIFICANCE

With a simple set of rules governing patch colonization and extinction, we have predicted that diversity and connectance promote persistence at the regional scale. The strength of our approach is that it reconciles the effect of complexity on stability at the local and the regional scale. Even if complex food webs are locally prone to extinction, we have shown their complexity could also promote their persistence through regional dynamics. The framework we presented here offers a novel and simple approach to understand the complexity of spatial food webs.

Modifying modifiers: what happens when interspecific interactions interact?

1. The strength of the trophic link between any given pair of species in a food web is likely to depend on the presence and/or densities of other species in the community. How these trophic interaction modifications (TIMs) interact with one another to produce a net modifying effect is an important but under-explored issue. 2. We review several specific types of TIMs that are well understood to address whether the magnitude of the net modification changes with the number of modifiers, and whether modifiers usually increase or decrease each other's effects. 3. Modifications of interactions are generally not independent. It is likely that TIMs interact antagonistically in the majority of cases; the magnitudes of TIMs decrease as more modifiers are added, or new TIMs reduce the magnitudes of modifications that are already present. 4. Individual modifications are likely to have a smaller effect in many-species systems than expected from independent combination of modifications measured in systems with relatively few species. Thus, models that lack explicit TIMs may in some cases yield adequate predictions for species-level perturbations, provided that the net effects of TIMs are implicitly included in measured interaction strengths. 5. Many types of TIMs share structural similarities. Nevertheless, a complete understanding of their effects may require theory that distinguishes different 'functional groups' of modifiers and addresses how these are structured according to trophic relationships.

Fast food in ant communities: how competing species find resources

An understanding of foraging behavior is crucial to understanding higher level community dynamics; in particular, there is a lack of information about how different species discover food resources. We examined the effect of forager number and forager discovery capacity on food discovery in two disparate temperate ant communities, located in Texas and Arizona. We defined forager discovery capacity as the per capita rate of resource discovery, or how quickly individual ants arrived at resources. In general, resources were discovered more quickly when more foragers were present; this was true both within communities, where species identity was ignored, as well as within species. This pattern suggests that resource discovery is a matter of random processes, with ants essentially bumping into resources at a rate mediated by their abundance. In contrast, species that were better discoverers, as defined by the proportion of resources discovered first, did not have higher numbers of mean foragers. Instead, both mean forager number and mean forager discovery capacity determined discovery success. The Texas species used both forager number and capacity, whereas the Arizona species used only forager capacity. There was a negative correlation between a species' prevalence in the environment and the discovery capacity of its foragers, suggesting that a given species cannot exploit both high numbers and high discovery capacity as a strategy. These results highlight that while forager number is crucial to determining time to discovery at the community level and within species, individual forager characteristics influence the outcome of exploitative competition in ant communities.

Robust estimation for ordinary differential equation models

Applied scientists often like to use ordinary differential equations (ODEs) to model complex dynamic processes that arise in biology, engineering, medicine, and many other areas. It is interesting but challenging to estimate ODE parameters from noisy data, especially when the data have some outliers. We propose a robust method to address this problem. The dynamic process is represented with a nonparametric function, which is a linear combination of basis functions. The nonparametric function is estimated by a robust penalized smoothing method. The penalty term is defined with the parametric ODE model, which controls the roughness of the nonparametric function and maintains the fidelity of the nonparametric function to the ODE model. The basis coefficients and ODE parameters are estimated in two nested levels of optimization. The coefficient estimates are treated as an implicit function of ODE parameters, which enables one to derive the analytic gradients for optimization using the implicit function theorem. Simulation studies show that the robust method gives satisfactory estimates for the ODE parameters from noisy data with outliers. The robust method is demonstrated by estimating a predator-prey ODE model from real ecological data.

Universal power-law diet partitioning by marine fish and squid with surprising stability-diversity implications

A central question in community ecology is how the number of trophic links relates to community species richness. For simple dynamical food-web models, link density (the ratio of links to species) is bounded from above as the number of species increases; but empirical data suggest that it increases without bounds. We found a new empirical upper bound on link density in large marine communities with emphasis on fish and squid, using novel methods that avoid known sources of bias in traditional approaches. Bounds are expressed in terms of the diet-partitioning function (DPF): the average number of resources contributing more than a fraction f to a consumer's diet, as a function of f. All observed DPF follow a functional form closely related to a power law, with power-law exponents independent of species richness at the measurement accuracy. Results imply universal upper bounds on link density across the oceans. However, the inherently scale-free nature of power-law diet partitioning suggests that the DPF itself is a better defined characterization of network structure than link density.

Influence of evolution on the stability of ecological communities

In randomly assembled communities, diversity is known to have a destabilizing effect. Evolution may affect this result, but our theoretical knowledge of its role is mostly limited to models of small food webs. In the present article, I introduce evolution in a two-species Lotka-Volterra model in which I vary the interaction type and the cost constraining evolution. Regardless of the cost type, evolution tends to stabilize the dynamics more often in trophic interactions than for mutualism or competition. I then use simulations to study the effect of evolution in larger communities that contain all interaction types. Results suggest that evolution usually stabilizes the dynamics. This stabilizing effect is stronger when evolution affects trophic interactions, but happens for all interaction types. Stabilization decreases with diversity and evolution becomes destabilizing in very diverse communities. This suggests that evolution may not counteract the destabilizing effect of diversity observed in random communities.

Consequences of adaptive behaviour for the structure and dynamics of food webs

Species coexistence within ecosystems and the stability of patterns of temporal changes in population sizes are central topics in ecological theory. In the last decade, adaptive behaviour has been proposed as a mechanism of population stabilization. In particular, widely distributed adaptive trophic behaviour (ATB), the fitness-enhancing changes in individuals' feeding-related traits due to variation in their trophic environment, may play a key role in modulating the dynamics of feeding relationships within natural communities. In this article, we review and synthesize models and results from theoretical research dealing with the consequences of ATB on the structure and dynamics of complex food webs. We discuss current approaches, point out limitations, and consider questions ripe for future research. In spite of some differences in the modelling and analytic approaches, there are points of convergence: (1) ATB promotes the complex structure of ecological networks, (2) ATB increases the stability of their dynamics, (3) ATB reverses May's negative complexity-stability relationship, and (4) ATB provides resilience and resistance of networks against perturbations. Current knowledge supports ATB as an essential ingredient for models of community dynamics, and future research that incorporates ATB will be well positioned to address questions important for basic ecological research and its applications.

Ecological release from interspecific competition leads to decoupled changes in population and individual niche width

A species's niche width reflects a balance between the diversifying effects of intraspecific competition and the constraining effects of interspecific competition. This balance shifts when a species from a competitive environment invades a depauperate habitat where interspecific competition is reduced. The resulting ecological release permits population niche expansion, via increased individual niche widths and/or increased among-individual variation. We report an experimental test of the theory of ecological release in three-spine stickleback (Gasterosteus aculeatus). We factorially manipulated the presence or absence of two interspecific competitors: juvenile cut-throat trout (Oncorhynchus clarki) and prickly sculpin (Cottus asper). Consistent with the classic niche variation hypothesis, release from trout competition increased stickleback population niche width via increased among-individual variation, while individual niche widths remained unchanged. In contrast, release from sculpin competition had no effect on population niche width, because increased individual niche widths were offset by decreased between-individual variation. Our results confirm that ecological release from interspecific competition can lead to increases in niche width, and that these changes can occur on behavioural time scales. Importantly, we find that changes in population niche width are decoupled from changes in the niche widths of individuals within the population.

Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems

A generic mechanism--networked buffering--is proposed for the generation of robust traits in complex systems. It requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role within a system and 2) agents are degenerate, i.e. there exists partial overlap in the functional capabilities of agents. Given these prerequisites, degenerate systems can readily produce a distributed systemic response to local perturbations. Reciprocally, excess resources related to a single function can indirectly support multiple unrelated functions within a degenerate system. In models of genome:proteome mappings for which localized decision-making and modularity of genetic functions are assumed, we verify that such distributed compensatory effects cause enhanced robustness of system traits. The conditions needed for networked buffering to occur are neither demanding nor rare, supporting the conjecture that degeneracy may fundamentally underpin distributed robustness within several biotic and abiotic systems. For instance, networked buffering offers new insights into systems engineering and planning activities that occur under high uncertainty. It may also help explain recent developments in understanding the origins of resilience within complex ecosystems.

Evolution towards oscillation or stability in a predator-prey system

We studied a prey-predator system in which both species evolve. We discuss here the conditions that result in coevolution towards a stable equilibrium or towards oscillations. First, we show that a stable equilibrium or population oscillations with small amplitude is likely to occur if the prey's (host's) defence is effective when compared with the predator's (parasite's) attacking ability at equilibrium, whereas large-amplitude oscillations are likely if the predator's (parasite's) attacking ability exceeds the prey's (host's) defensive ability. Second, a stable equilibrium is more likely if the prey's defensive trait evolves faster than the predator's attack trait, whereas population oscillations are likely if the predator's trait evolves faster than that of the prey. Third, when the adaptation rates of both species are similar, the amplitude of the fluctuations in their abundances is small when the adaptation rate is either very slow or very fast, but at an intermediate rate of adaptation the fluctuations have a large amplitude. We also show the case in which the prey's abundance and trait fluctuate greatly, while those of the predator remain almost unchanged. Our results predict that populations and traits in host-parasite systems are more likely than those in prey-predator systems to show large-amplitude oscillations.

Structural dynamics and robustness of food webs

Food web structure plays an important role when determining robustness to cascading secondary extinctions. However, existing food web models do not take into account likely changes in trophic interactions ('rewiring') following species loss. We investigated structural dynamics in 12 empirically documented food webs by simulating primary species loss using three realistic removal criteria, and measured robustness in terms of subsequent secondary extinctions. In our model, novel trophic interactions can be established between predators and food items not previously consumed following the loss of competing predator species. By considering the increase in robustness conferred through rewiring, we identify a new category of species--overlap species--which promote robustness as shown by comparing simulations incorporating structural dynamics to those with static topologies. The fraction of overlap species in a food web is highly correlated with this increase in robustness; whereas species richness and connectance are uncorrelated with increased robustness. Our findings underline the importance of compensatory mechanisms that may buffer ecosystems against environmental change, and highlight the likely role of particular species that are expected to facilitate this buffering.

The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour

Species extinctions pose serious threats to the functioning of ecological communities worldwide. We used two qualitative and quantitative pollination networks to simulate extinction patterns following three removal scenarios: random removal and systematic removal of the strongest and weakest interactors. We accounted for pollinator behaviour by including potential links into temporal snapshots (12 consecutive 2-week networks) to reflect mutualists' ability to 'switch' interaction partners (re-wiring). Qualitative data suggested a linear or slower than linear secondary extinction while quantitative data showed sigmoidal decline of plant interaction strength upon removal of the strongest interactor. Temporal snapshots indicated greater stability of re-wired networks over static systems. Tolerance of generalized networks to species extinctions was high in the random removal scenario, with an increase in network stability if species formed new interactions. Anthropogenic disturbance, however, that promote the extinction of the strongest interactors might induce a sudden collapse of pollination networks.

Food-chain length and adaptive foraging

Food-chain length, the number of feeding links from the basal species to the top predator, is a key characteristic of biological communities. However, the determinants of food-chain length still remain controversial. While classical theory predicts that food-chain length should increase with increasing resource availability, empirical supports of this prediction are limited to those from simple, artificial microcosms. A positive resource availability-chain length relationship has seldom been observed in natural ecosystems. Here, using a theoretical model, we show that those correlations, or no relationships, may be explained by considering the dynamic food-web reconstruction induced by predator's adaptive foraging. More specifically, with foraging adaptation, the food-chain length becomes relatively invariant, or even decreases with increasing resource availability, in contrast to a non-adaptive counterpart where chain length increases with increasing resource availability; and that maximum chain length more sharply decreases with resource availability either when species richness is higher or potential link number is larger. The interactive effects of resource availability, adaptability and community complexity may explain the contradictory effects of resource availability in simple microcosms and larger ecosystems. The model also explains the recently reported positive effect of habitat size on food-chain length as a result of increased species richness and/or decreased connectance owing to interspecific spatial segregation.

Googling food webs: can an eigenvector measure species' importance for coextinctions?

A major challenge in ecology is forecasting the effects of species' extinctions, a pressing problem given current human impacts on the planet. Consequences of species losses such as secondary extinctions are difficult to forecast because species are not isolated, but interact instead in a complex network of ecological relationships. Because of their mutual dependence, the loss of a single species can cascade in multiple coextinctions. Here we show that an algorithm adapted from the one Google uses to rank web-pages can order species according to their importance for coextinctions, providing the sequence of losses that results in the fastest collapse of the network. Moreover, we use the algorithm to bridge the gap between qualitative (who eats whom) and quantitative (at what rate) descriptions of food webs. We show that our simple algorithm finds the best possible solution for the problem of assigning importance from the perspective of secondary extinctions in all analyzed networks. Our approach relies on network structure, but applies regardless of the specific dynamical model of species' interactions, because it identifies the subset of coextinctions common to all possible models, those that will happen with certainty given the complete loss of prey of a given predator. Results show that previous measures of importance based on the concept of "hubs" or number of connections, as well as centrality measures, do not identify the most effective extinction sequence. The proposed algorithm provides a basis for further developments in the analysis of extinction risk in ecosystems.

Host niches and defensive extended phenotypes structure parasitoid wasp communities

Oak galls are spectacular extended phenotypes of gallwasp genes in host oak tissues and have evolved complex morphologies that serve, in part, to exclude parasitoid natural enemies.

Parasitoids and their insect herbivore hosts have coevolved to produce diverse communities comprising about a third of all animal species. The factors structuring these communities, however, remain poorly understood. An emerging theme in community ecology is the need to consider the effects of host traits, shaped by both natural selection and phylogenetic history, on associated communities of natural enemies. Here we examine the impact of host traits and phylogenetic relatedness on 48 ecologically closed and species-rich communities of parasitoids attacking gall-inducing wasps on oaks. Gallwasps induce the development of spectacular and structurally complex galls whose species- and generation-specific morphologies are the extended phenotypes of gallwasp genes. All the associated natural enemies attack their concealed hosts through gall tissues, and several structural gall traits have been shown to enhance defence against parasitoid attack. Here we explore the significance of these and other host traits in predicting variation in parasitoid community structure across gallwasp species. In particular, we test the “Enemy Hypothesis,” which predicts that galls with similar morphology will exclude similar sets of parasitoids and therefore have similar parasitoid communities. Having controlled for phylogenetic patterning in host traits and communities, we found significant correlations between parasitoid community structure and several gall structural traits (toughness, hairiness, stickiness), supporting the Enemy Hypothesis. Parasitoid community structure was also consistently predicted by components of the hosts' spatiotemporal niche, particularly host oak taxonomy and gall location (e.g., leaf versus bud versus seed). The combined explanatory power of structural and spatiotemporal traits on community structure can be high, reaching 62% in one analysis. The observed patterns derive mainly from partial niche specialisation of highly generalist parasitoids with broad host ranges (>20 hosts), rather than strict separation of enemies with narrower host ranges, and so may contribute to maintenance of the richness of generalist parasitoids in gallwasp communities. Though evolutionary escape from parasitoids might most effectively be achieved via changes in host oak taxon, extreme conservatism in this trait for gallwasps suggests that selection is more likely to have acted on gall morphology and location. Any escape from parasitoids associated with evolutionary shifts in these traits has probably only been transient, however, due to subsequent recruitment of parasitoid species already attacking other host galls with similar trait combinations.

Herbivorous insects, such as the wasps that induce trees to make galls, and the parasitoids that attack (and ultimately kill) the wasps comprise about a third of all animal species, but it remains unclear what determines the structure of these complex coevolving communities. Here, we analyzed 48 parasitoid communities attacking different cynipid wasps that live and feed on oak trees. These communities are diverse and “closed,” with each centered upon the characteristic gall induced by a given cynipid wasp species. The often spectacular and complex galls are extended phenotypes of gallwasp genes and have been suggested to evolve as gallwasp defenses against their parasitoid enemies—“the Enemy Hypothesis.” Our analysis showed that similar parasitoid communities occurred on galls with similar structural traits (e.g., toughness, hairiness, stickiness), supporting the Enemy Hypothesis. We also found similar communities on galls that co-occur frequently in time and space; in particular, those occurring on the same oak species and same plant organ (e.g., leaf, bud, seed). Our results suggest that cynipid wasps might escape particular parasitoids via evolutionary shifts in the structure or location of their galls. However, escape may often be transient due to recruitment of new enemies already attacking other host galls with similar trait combinations.

Functional links and robustness in food webs

The robustness of ecosystems to species losses is a central question in ecology, given the current pace of extinctions and the many species threatened by human impacts, including habitat destruction and climate change. Robustness from the perspective of secondary extinctions has been addressed in the context of food webs to consider the complex network of species interactions that underlie responses to perturbations. In-silico removal experiments have examined the structural properties of food webs that enhance or hamper the robustness of ecosystems to species losses, with a focus on the role of hubs, the most connected species. Here we take a different approach and focus on the role of the connections themselves. We show that trophic links can be divided into functional and redundant based on their contribution to robustness. The analysis of empirical webs shows that hubs are not necessarily the most important species as they may hold many redundant links. Furthermore, the fraction of functional connections is high and constant across systems regardless of size and interconnectedness. The main consequence of this scaling pattern is that ecosystem robustness can be considerably reduced by species extinctions even when these do not result in any secondary extinctions. This introduces the possibility of tipping points in the collapse of ecosystems.

The more food webs change, the more they stay the same

Here, we synthesize a number of recent empirical and theoretical papers to argue that food-web dynamics are characterized by high amounts of spatial and temporal variability and that organisms respond predictably, via behaviour, to these changing conditions. Such behavioural responses on the landscape drive a highly adaptive food-web structure in space and time. Empirical evidence suggests that underlying attributes of food webs are potentially scale-invariant such that food webs are characterized by hump-shaped trophic structures with fast and slow pathways that repeat at different resolutions within the food web. We place these empirical patterns within the context of recent food-web theory to show that adaptable food-web structure confers stability to an assemblage of interacting organisms in a variable world. Finally, we show that recent food-web analyses agree with two of the major predictions of this theory. We argue that the next major frontier in food-web theory and applied food-web ecology must consider the influence of variability on food-web structure.

Complexity in quantitative food webs

Food webs depict who eats whom in communities. Ecologists have examined statistical metrics and other properties of food webs, but mainly due to the uneven quality of the data, the results have proved controversial. The qualitative data on which those efforts rested treat trophic interactions as present or absent and disregard potentially huge variation in their magnitude, an approach similar to analyzing traffic without differentiating between highways and side roads. More appropriate data are now available and were used here to analyze the relationship between trophic complexity and diversity in 59 quantitative food webs from seven studies (14-202 species) based on recently developed quantitative descriptors. Our results shed new light on food-web structure. First, webs are much simpler when considered quantitatively, and link density exhibits scale invariance or weak dependence on food-web size. Second, the "constant connectance" hypothesis is not supported: connectance decreases with web size in both qualitative and quantitative data. Complexity has occupied a central role in the discussion of food-web stability, and we explore the implications for this debate. Our findings indicate that larger webs are more richly endowed with the weak trophic interactions that recent theories show to be responsible for food-web stability.

Food-web structure and ecosystem services: insights from the Serengeti

The central organizing theme of this paper is to discuss the dynamics of the Serengeti grassland ecosystem from the perspective of recent developments in food-web theory. The seasonal rainfall patterns that characterize the East African climate create an annually oscillating, large-scale, spatial mosaic of feeding opportunities for the larger ungulates in the Serengeti; this in turn creates a significant annual variation in the food available for their predators. At a smaller spatial scale, periodic fires during the dry season create patches of highly nutritious grazing that are eaten in preference to the surrounding older patches of less palatable vegetation. The species interactions between herbivores and plants, and carnivores and herbivores, are hierarchically nested in the Serengeti food web, with the largest bodied consumers on each trophic level having the broadest diets that include species from a large variety of different habitats in the ecosystem. The different major habitats of the Serengeti are also used in a nested fashion; the highly nutritious forage of the short grass plains is available only to the larger migratory species for a few months each year. The longer grass areas, the woodlands and kopjes (large partially wooded rocky islands in the surrounding mosaic of grassland) contain species that are resident throughout the year; these species often have smaller body size and more specialized diets than the migratory species. Only the larger herbivores and carnivores obtain their nutrition from all the different major habitat types in the ecosystem. The net effect of this is to create a nested hierarchy of subchains of energy flow within the larger Serengeti food web; these flows are seasonally forced by rainfall and operate at different rates in different major branches of the web. The nested structure that couples sequential trophic levels together interacts with annual seasonal variation in the fast and slow chains of nutrient flow in a way that is likely to be central to the stability of the whole web. If the Serengeti is to be successfully conserved as a fully functioning ecosystem, then it is essential that the full diversity of natural habitats be maintained within the greater Serengeti ecosystem. The best way to do this is by controlling the external forces that threaten the boundaries of the ecosystem and by balancing the economic services the park provides between local, national and international needs. I conclude by discussing how the ecosystem services provided by the Serengeti are driven by species on different trophic levels. Tourism provides the largest financial revenue to the national economy, but it could be better organized to provide more sustained revenue to the park. Ultimately, ecotourism needs to be developed in ways that take lessons from the structure of the Serengeti food webs, and in ways that provide tangible benefits to people living around the park while also improving the experience of all visitors.

Niche evolution, trophic structure, and species turnover in model food webs

The features that govern the stability and persistence of species interaction networks, such as food webs, remain elusive, but recent work suggests that the distribution and strength of trophic links play an important role. Potential omnivory-stability relationships have been investigated and debated extensively, but we still have a relatively poor understanding of how levels of omnivory relate to the stability of diverse food webs. Here, we use an evolutionary assembly model to investigate how different trade-offs in resource use influence both food web structure and dynamic stability during the assembly process. We build on a previous model by allowing speciation along with the evolution of two traits: body size and feeding-niche width. Across a wide range of conditions, the level of omnivory in a food web is positively related to its dynamic instability (variability and species turnover). Parameter values favoring omnivory also allow a wider range of phenotypes to invade, often displacing existing species. This high species turnover leaves signatures in reconstructed phylogenies, with shorter branches connecting extant species in more omnivorous food webs. Our findings suggest that features of the environment may influence both trophic structure and dynamic stability, leading to emergent omnivory-stability relationships.

Systems biology of microbial communities

Microbes exist naturally in a wide range of environments in communities where their interactions are significant, spanning the extremes of high acidity and high temperature environments to soil and the ocean. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.