Effects of Phylogenetic Relatedness on Fluctuation-Dependent and Fluctuation-Independent Coexistence Mechanisms in Multispecies Communities

AbstractEvolutionary relatedness may hinder stable coexistence due to similar niches and nonlinear responses to competition. The mechanisms driving stability may respond differently to phylogenetic distance. Related species may be synchronic (have similar demographic responses over time), affecting fluctuation-dependent mechanisms: the storage effect should destabilize coexistence, and relative nonlinearity should be stronger due to increased fluctuations in competition. We tested these hypotheses using invasion analysis based on a model parameterized for 19 plant species from a semiarid grassland. Although weakly, coexistence stability increased with phylogenetic distance. Stabilization through fluctuation-independent niche differentiation was stronger between distant relatives as a result of weaker competition. Synchronicity was higher between close relatives, having the expected negative effects on the storage effect's contribution to coexistence. Relative nonlinearity was strong at both ends of the phylogenetic relatedness gradient but not in the middle. This may be the result of different nonlinear responses between distant relatives and of stronger fluctuations in competition due to synchronicity between closer relatives. The effect of phylogenetic distance on coexistence was almost negligible when pairwise species were analyzed, in accordance with previous research. Phylogenetic distance became more important as more species interacted, however, suggesting that evolutionary relatedness may be influential in species-rich communities.

A general theory of coexistence and extinction for stochastic ecological communities

We analyze a general theory for coexistence and extinction of ecological communities that are influenced by stochastic temporal environmental fluctuations. The results apply to discrete time (stochastic difference equations), continuous time (stochastic differential equations), compact and non-compact state spaces and degenerate or non-degenerate noise. In addition, we can also include in the dynamics auxiliary variables that model environmental fluctuations, population structure, eco-environmental feedbacks or other internal or external factors. We are able to significantly generalize the recent discrete time results by Benaim and Schreiber (J Math Biol 79:393-431, 2019) to non-compact state spaces, and we provide stronger persistence and extinction results. The continuous time results by Hening and Nguyen (Ann Appl Probab 28(3):1893-1942, 2018a) are strengthened to include degenerate noise and auxiliary variables. Using the general theory, we work out several examples. In discrete time, we classify the dynamics when there are one or two species, and look at the Ricker model, Log-normally distributed offspring models, lottery models, discrete Lotka-Volterra models as well as models of perennial and annual organisms. For the continuous time setting we explore models with a resource variable, stochastic replicator models, and three dimensional Lotka-Volterra models.

Quantifying the relative importance of variation in predation and the environment for species coexistence

Coexistence and food web theory are two cornerstones of the long-standing effort to understand how species coexist. Although competition and predation are known to act simultaneously in communities, theory and empirical study of these processes continue to be developed largely independently. Here, we integrate modern coexistence theory and food web theory to simultaneously quantify the relative importance of predation and environmental fluctuations for species coexistence. We first examine coexistence in a theoretical, multitrophic model, adding complexity to the food web using machine learning approaches. We then apply our framework to a stochastic model of the rocky intertidal food web, partitioning empirical coexistence dynamics. We find the main effects of both environmental fluctuations and variation in predator abundances contribute substantially to species coexistence. Unexpectedly, their interaction tends to destabilise coexistence, leading to new insights about the role of bottom-up vs. top-down forces in both theory and the rocky intertidal ecosystem.

The role of seasonal timing and phenological shifts for species coexistence

Shifts in the phenologies of coexistence species are altering the temporal structure of natural communities worldwide. However, predicting how these changes affect the structure and long-term dynamics of natural communities is challenging because phenology and coexistence theory have largely proceeded independently. Here, I propose a conceptual framework that incorporates seasonal timing of species interactions into a well-studied competition model to examine how changes in phenologies influence long-term dynamics of natural communities. Using this framework I demonstrate that persistence and coexistence conditions strongly depend on the difference in species' mean phenologies and how this difference varies across years. Consequently, shifts in mean and interannual variation in relative phenologies of species can fundamentally alter the outcome of interactions and the potential for persistence and coexistence of competing species. These effects can be predicted by how per-capita effects scale with differences in species' phenologies. I outline how this approach can be parameterized with empirical systems and discuss how it fits within the context of current coexistence theory. Overall, this synthesis reveals that phenology of species interactions can play a crucial yet currently understudied role in driving coexistence and biodiversity patterns in natural systems and determine how species will respond to future climate change.

Multistate occupancy modeling improves understanding of amphibian breeding dynamics in the Greater Yellowstone Area

Discerning the determinants of species occurrence across landscapes is fundamental to their conservation and management. In spatially and climatologically complex landscapes, explaining the dynamics of occurrence can lead to improved understanding of short- vs. long-term trends and offer novel insight on local vs. regional change. We examined the changes in occupancy for two species of anurans with different life histories over a decade using hundreds of wetland sites in Yellowstone and Grand Teton National Parks. To account for the joint dynamics of wetland drying and amphibian breeding, we adopted a multistate occupancy model as a means to investigate mechanistic relationships of observed occurrence patterns with climatological drivers of wetland hydrologic variability. This approach allowed us to decompose occupancy dynamics into habitat changes caused by wetland drying and amphibian breeding activity, conditional on available water and previous breeding state. Over our 10-yr time series, we observed considerable variability in climate drivers and the proportion of dry wetlands. Boreal chorus frogs (Pseudacris maculata) were more responsive to changes in wetland inundation status than Columbia spotted frogs (Rana luteiventris), as indicated by higher breeding colonization probabilities under favorable (wet) conditions. Both species had high probabilities of breeding persistence in permanently inundated wetlands with prior breeding. Despite the absence of multi-year drought in our time series, mechanistic relationships described here offer insights on how future climate variation may result in reduced and/or shifted occurrence patterns for pond-breeding anurans in the Greater Yellowstone Area. Further, our modeling approach may prove valuable in evaluating determinants of occurrence for other species that are dependent on wetlands or other dynamic habitats.

No trade-offs in interspecific interference ability and predation susceptibility in newt larvae

Coexistence of species with similar requirements is allowed, among others, through trade-offs between competitive ability and other ecological traits. Although interspecific competition is based on two mechanisms, exploitation of resources and physical interference, trade-off studies largely consider only species' ability to exploit resources. Using a mesocosm experiment, we examined the trade-off between interference competition ability and susceptibility to predation in larvae of two newt species, Ichthyosaura alpestris and Lissotriton vulgaris. In the presence of heterospecifics, L. vulgaris larvae slowed somatic growth and developmental rates, and experienced a higher frequency of injuries than in conspecific environments which suggests asymmetrical interspecific interference. During short-term predation trials, L. vulgaris larvae suffered higher mortality than I. alpestris. Larvae of the smaller species, L. vulgaris, had both lower interference and antipredator performance than the larger I. alpestris, which suggests a lack of trade-off between interference competition ability and predator susceptibility. We conclude that interference competition may produce a positive rather than negative relationship with predation susceptibility, which may contribute to the elimination of subordinate species from common habitats.

How spatial structure and neighbor uncertainty promote mutualists and weaken black queen effects

The ubiquity of cooperative cross-feeding (a resource-exchange mutualism) raises two related questions: Why is cross-feeding favored over self-sufficiency, and how are cross-feeders protected from non-producing cheaters? The Black Queen Hypothesis suggests that if leaky resources are costly, then there should be selection for either gene loss or self-sufficiency, but selection against mutualistic inter-dependency. Localized interactions have been shown to protect mutualists against cheaters, though their effects in the presence of self-sufficient organisms are not well understood. Here we develop a stochastic spatial model to examine how spatial effects alter the predictions of the Black Queen Hypothesis. Microbes need two essential resources to reproduce, which they can produce themselves (at a cost) or take up from neighbors. Additionally, microbes need empty sites to give birth into. Under well mixed mean-field conditions, the cross-feeders will always be displaced by a non-producer and a self-sufficient microbe. However, localized interactions have two effects that favor production. First, a microbe that interacts with a small number of neighbors will not always receive the essential resources it needs; this effect slightly harms cross-feeders but greatly harms non-producers. Second, microbes tend to displace other microbes that produce resources they need; this effect also slightly harms cross-feeders but greatly harms non-producers. Our work therefore suggests localized interactions produce an accelerating cost of non-production. Thus, the right trade-off between the cost of producing resources and the cost of sometimes being resource-limited can favor mutualistic inter-dependence over both self-sufficiency and non-production.

Predator Persistence through Variability of Resource Productivity in Tritrophic Systems

The trophic structure of species communities depends on the energy transfer between trophic levels. Primary productivity varies strongly through time, challenging the persistence of species at higher trophic levels. Yet resource variability has mostly been studied in systems with only one or two trophic levels. We test the effect of variability in resource productivity in a tritrophic model system including a resource, a size-structured consumer, and a size-specific predator. The model complies with fundamental principles of mass conservation and the body-size dependence of individual-level energetics and predator-prey interactions. Surprisingly, we find that resource variability may promote predator persistence. The positive effect of variability on the predator arises through periods with starvation mortality of juvenile prey, which reduces the intraspecific competition in the prey population. With increasing variability in productivity and starvation mortality in the juvenile prey, the prey availability increases in the size range preferred by the predator. The positive effect of prey mortality on the trophic transfer efficiency depends on the biologically realistic consideration of body size-dependent and food-dependent functions for growth and reproduction in our model. Our findings show that variability may promote the trophic transfer efficiency, indicating that environmental variability may sustain species at higher trophic levels in natural ecosystems.

The Effects of Dynamical Rates on Species Coexistence in a Variable Environment: The Paradox of the Plankton Revisited

Hutchinson's famous hypothesis for the "paradox of the plankton" has been widely accepted, but critical aspects have remained unchallenged. Hutchinson argued that environmental fluctuations would promote coexistence when the timescale for environmental change is comparable to the timescale for competitive exclusion. Using a consumer-resource model, we do find that timescales of processes are important. However, it is not the time to exclusion that must be compared with the time for environmental change but the time for resource depletion. Fast resource depletion, when resource consumption is favored for different species at different times, strongly promotes coexistence. The time for exclusion is independent of the rate of resource depletion. Therefore, the widely believed predictions of Hutchinson are misleading. Fast resource depletion, as determined by environmental conditions, ensures strong coupling of environmental processes and competition, which leads to enhancement over time of intraspecific competition relative to interspecific competition as environmental shifts favor different species at different times. This critical coupling is measured by the covariance between environment and competition. Changes in this quantity as densities change determine the stability of coexistence and provide the key to rigorous analysis, both theoretically and empirically, of coexistence in a variable environment. These ideas apply broadly to diversity maintenance in variable environments whether the issue is species diversity or genetic diversity and competition or apparent competition.

The relative importance of relative nonlinearity and the storage effect in the lottery model

Although it is likely that many coexistence mechanisms contribute to maintenance of species diversity, most approaches to understanding species coexistence proceed as if only one mechanism would be present. In studies of species coexistence in a temporally fluctuating environment, the storage effect, believed to be the most important coexistence mechanism, has been the focus. Although a different coexistence mechanism--relative nonlinearity--is also predicted to arise frequently with environmental variation, its effect has been overshadowed by the storage effect. The relatively nonlinear growth rates on which the mechanism depends arise simply from differences in life history traits. Many kinds of temporal variation can then interact with these nonlinearity differences to create the relative nonlinearity coexistence mechanism. Much is unknown about when this mechanism is important and its total neglect is not justified. Here, we use the lottery model to provide a much needed quantitative assessment of the relative and combined effects of relative nonlinearity and the storage effect. Our analysis takes advantage of recently developed techniques for quantifying coexistence mechanisms when multiple mechanisms operate in concert. We find that relative nonlinearity is able to contribute substantially to species coexistence in the lottery model when two conditions are satisfied: (1) species must differ greatly in their adult death rates, (2) sensitivity of recruitment to environmental variation must be greater for species with larger adult death rates. In addition, relative nonlinearity has a critical role in compensating for a weakened storage effect when there is high correlation between species in their responses to the varying environment. In some circumstances relative nonlinearity is stronger than the storage effect or is even the sole mechanism of coexistence.

Armstrong-McGehee mechanism revisited: competitive exclusion and coexistence of nonlinear consumers

A number of mechanisms have been proposed to explain the coexistence of species engaging in exploitative competition. The Armstrong-McGehee mechanism relies on different levels of nonlinearity in functional response between competing consumers and their ability to avoid competitive exclusion through temporal resource partitioning during endogenously generated fluctuations. While previous studies have mainly focused on cases where one consumer has nonlinear functional response and the other consumer has linear functional response, our study assessed coexistence and competitive exclusion under a more realistic scenario with two nonlinear consumers. Using analytical and numerical methods we found that the potential of coexistence of the two consumers decreases with increasing nonlinearity in the more linear species; increasing nonlinearity in the more nonlinear species, however, resulted in non-monotonic changes in the parameter space allowing coexistence. When coexistence potential is quantified under the presupposition that each consumer must be able to persist with the resource by itself, coexistence becomes consistently less likely with increasing similarity of the functional responses of the two consumers. Our results suggest that the Armstrong-McGehee mechanism is unlikely to operate as the sole coexistence-promoting mechanism in communities with generally nonlinear consumer-resource interactions. However, its role as a module in more complex systems and in synergy with other factors remains to be established.

Global dynamics of a discrete two-species Lottery-Ricker competition model

In this article, we study the global dynamics of a discrete two-dimensional competition model. We give sufficient conditions on the persistence of one species and the existence of local asymptotically stable interior period-2 orbit for this system. Moreover, we show that for a certain parameter range, there exists a compact interior attractor that attracts all interior points except Lebesgue measure zero set. This result gives a weaker form of coexistence which is referred to as relative permanence. This new concept of coexistence combined with numerical simulations strongly suggests that the basin of attraction of the locally asymptotically stable interior period-2 orbit is an infinite union of connected components. This idea may apply to many other ecological models. Finally, we discuss the generic dynamical structure that gives relative permanence.

Dispersal effects on a discrete two-patch model for plant-insect interactions

A two-patch discrete time plant-insect model coupled through insect dispersal is studied. The model is based on three different phases: Plant growth is followed by the dispersal of insects followed by insect attacks. Our objective is to understand how different intensities of dispersal impact both local and global population dynamics of the two-patch model. Special attention is paid to two situations: When the single-patch model (i.e., in the absence of dispersal) is permanent and when the single-patch model exhibits Allee-like effects. The existence and stability of synchronous and asynchronous dynamics between two patches is explored. If the single-patch system is permanent, the permanence of the system in two patches is destroyed by extremely large dispersals and large attacking rates of insects, thus creating multiple attractors. If the single-patch model exhibits Allee-like effects, analytical and numerical results indicate that small intensity of dispersals can generate source-sink dynamics between two patches, while intermediate intensity of dispersals promote the extinction of insects in both patches for certain parameter ranges. Our study suggests a possible biology control strategy to stop the invasion of a pest by controlling its migration between patches.

Testing the Janzen-Connell mechanism: pathogens cause overcompensating density dependence in a tropical tree

The Janzen-Connell hypothesis is a leading explanation for plant-species diversity in tropical forests. It suggests that specialized natural enemies decrease offspring survival at high densities beneath parents, giving locally rarer species an advantage. This mechanism, in its original form, assumes that density dependence is overcompensating: mortality must be disproportionately high at the highest densities, with few offspring recruiting below their parents. We tested this assumption using parallel shadehouse and field density-series experiments on seedlings of a tropical tree, Pleradenophora longicuspis. We found strong, overcompensating mortality driven by fungal pathogens, causing 90% (shadehouse) or 100% (field) mortality within 4 weeks of germination, and generating a negative relationship between initial and final seedling densities. Fungicide treatment led to much lower, density-independent, mortality. Overcompensating mortality was extremely rapid, and could be missed without detailed monitoring. Such dynamics may prevent dead trees from being replaced by conspecifics, promoting coexistence as envisioned by the Janzen-Connell hypothesis.

Persistence in fluctuating environments

Understanding under what conditions interacting populations, whether they be plants, animals, or viral particles, coexist is a question of theoretical and practical importance in population biology. Both biotic interactions and environmental fluctuations are key factors that can facilitate or disrupt coexistence. To better understand this interplay between these deterministic and stochastic forces, we develop a mathematical theory extending the nonlinear theory of permanence for deterministic systems to stochastic difference and differential equations. Our condition for coexistence requires that there is a fixed set of weights associated with the interacting populations and this weighted combination of populations' invasion rates is positive for any (ergodic) stationary distribution associated with a sub collection of populations. Here, an invasion rate corresponds to an average per-capita growth rate along a stationary distribution. When this condition holds and there is sufficient noise in the system, we show that the populations approach a unique positive stationary distribution. Moreover, we show that our coexistence criterion is robust to small perturbations of the model functions. Using this theory, we illustrate that (i) environmental noise enhances or inhibits coexistence in communities with rock-paper-scissor dynamics depending on correlations between interspecific demographic rates, (ii) stochastic variation in mortality rates has no effect on the coexistence criteria for discrete-time Lotka-Volterra communities, and (iii) random forcing can promote genetic diversity in the presence of exploitative interactions.

The interaction between predation and competition

Competition and predation are the most heavily investigated species interactions in ecology, dominating studies of species diversity maintenance. However, these two interactions are most commonly viewed highly asymmetrically. Competition for resources is seen as the primary interaction limiting diversity, with predation modifying what competition does, although theoretical models have long supported diverse views. Here we show, using a comprehensive three-trophic-level model, that competition and predation should be viewed symmetrically: these two interactions are equally able to either limit or promote diversity. Diversity maintenance requires within-species density feedback loops to be stronger than between-species feedback loops. We quantify the contributions of predation and competition to these loops in a simple, interpretable form, showing their equivalent potential to strengthen or weaken diversity maintenance. Moreover, we show that competition and predation can undermine each other, with the tendency of the stronger interaction to promote or limit diversity prevailing. The past failure to appreciate the symmetrical effects and interactions of competition and predation has unduly restricted diversity maintenance studies. A multitrophic perspective should be adopted to examine a greater variety of possible effects of predation than generally considered in the past. Conservation and management strategies need to be much more concerned with the implications of changes in the strengths of trophic interactions.