The many dimensions of phytochemical diversity: linking theory to practice

Research on the ecological and evolutionary roles of phytochemicals has recently progressed from studying single compounds to examining chemical diversity itself. A key conceptual advance enabling this progression is the use of species diversity metrics for quantifying phytochemical diversity. In this perspective, we extend the theory developed for species diversity to further our understanding of what exactly phytochemical diversity is and how its many dimensions impact ecological and evolutionary processes. First, we discuss the major dimensions of phytochemical diversity – richness, evenness, functional diversity, and alpha, gamma and beta diversity. We describe their potential independent roles in biotic interactions and the practical challenges associated with their analysis. Second, we re‐analyse the published and unpublished datasets to reveal that the phytochemical diversity experienced by an organism (or observed by a researcher) depends strongly on the scale of the interaction and the total amount of phytochemicals involved. We argue that we must account for these frames of reference to meaningfully understand diversity. Moving from a general notion of phytochemical diversity as a single measure to a precise definition of its multidimensional and multiscale nature yields overlooked testable predictions that will facilitate novel insights about the evolutionary ecology of plant biotic interactions.     

Stability and synchrony across ecological hierarchies in heterogeneous metacommunities: linking theory to data

Understanding stability across ecological hierarchies is critical for landscape management in a changing world. Recent studies showed that synchrony among lower‐level components is key to scaling temporal stability across two hierarchical levels, whether spatial or organizational. But an extended framework that integrates both spatial scale and organizational level simultaneously is required to clarify the sources of ecosystem stability at large scales. However, such an extension is far from trivial when taking into account the spatial heterogeneities in real‐world ecosystems. In this paper, we develop a partitioning framework that bridges variability and synchrony measures across spatial scales and organizational levels in heterogeneous metacommunities. In this framework, metacommunity variability is expressed as the product of local‐scale population variability and two synchrony indices that capture the temporal coherence across species and space, respectively. We develop an R function ‘var.partition’ and apply it to five types of desert plant communities to illustrate our framework and test how diversity shapes synchrony and variability at different hierarchical levels. As the observation scale increased from local populations to metacommunities, the temporal variability of plant productivity was reduced mainly by factors that decreased species synchrony. Species synchrony decreased from local to regional scales, and spatial synchrony decreased from species to community levels. Local and regional species diversity were key factors that reduced species synchrony at the two scales. Moreover, beta diversity contributed to decreasing spatial synchrony among communities. We conclude that our new framework offers a valuable toolbox for future empirical studies to disentangle the mechanisms and pathways by which ecological factors influence stability at large scales.     

Dispersal promotes compensatory dynamics and stability in forced metacommunities

Understanding the factors that govern the stability of populations and communities has gained increasing importance as habitat fragmentation and environmental perturbations continue to escalate due to human activities. Dispersal is commonly viewed as essential to the maintenance of diversity in spatially subdivided communities, but few experiments have explored how dispersal interacts with the spatiotemporal components of environmental perturbations to determine community-level stability. We examined these processes using an experimental planktonic system composed of three competing species of zooplankton. We subjected zooplankton metacommunities to varying levels of dispersal and pH perturbations that varied in their degree of spatial synchrony. We show that dispersal can reverse the destabilizing effects of environmental forcing when perturbations are spatially asynchronous. Asynchrony in pH perturbations generated spatially and temporally varying species refugia that promoted source-sink dynamics and allowed prolonged persistence of zooplankton species that were otherwise extirpated in synchronously varying metacommunities. This, in turn, increased local species diversity, promoted compensatory population dynamics, and enhanced local community-level stability. Our results indicate that patterns of spatial covariation in environmental variability are critical to predicting the effects of dispersal on the dynamics and persistence of communities.     

Species diversity in neutral metacommunities: a network approach

Biologists seek an understanding of the processes underlying spatial biodiversity patterns. Neutral theory links those patterns to dispersal, speciation and community drift. Here, we advance the spatially explicit neutral model by representing the metacommunity as a network of smaller communities. Analytic theory is presented for a set of equilibrium diversity patterns in networks of communities, facilitating the exploration of parameter space not accessible by simulation. We use this theory to evaluate how the basic properties of a metacommunity – connectivity, size, and speciation rate – determine overall metacommunity γ -diversity, and how that is partitioned into α - and β -components. We find spatial structure can increase γ -diversity relative to a well-mixed model, even when θ is held constant. The magnitude of deviations from the well-mixed model and the partitioning into α - and β -diversity is related to the ratio of migration and speciation rates. γ -diversity scales linearly with metacommunity size even as α - and β -diversity scale nonlinearly with size.     

Mechanisms linking diversity,productivity and invasibility in experimental bacterial communities

Decreasing species diversity is thought to both reduce community productivity and increase invasibility to other species. However, it remains unclear whether identical mechanisms drive both diversity-productivity and diversity-invasibility relationships. We found a positive diversity-productivity relationship and negative diversity-invasibility and productivity-invasibility relationships using microcosm communities constructed from spatial niche specialist genotypes of the bacterium Pseudomonas fluorescens. The primary mechanism driving these relationships was a dominance (or selection) effect: more diverse communities were more likely to contain the most productive and least invasible type. Statistical elimination of the dominance effect greatly weakened the diversity-invasibility relationship and eliminated the diversity-productivity relationship, but also revealed the operation of additional mechanisms (niche complementarity, positive and negative interactions) for particular combinations of niche specialists. However, these mechanisms differed for invasibility and productivity responses, resulting in the invasibility-productivity relationship changing from strongly negative to weakly positive. In the absence of the dominance effect, which may be an experimental artefact, decreasing diversity can have unexpected or no effects on ecosystem properties.     

Adaptive sex allocation in birds: the complexities of linking theory and practice

We review some recent theoretical and empirical developments in the study of sex allocation in birds. The advent of reliable molecular sexing techniques has led to a sharp increase in the number of studies that report biased offspring sex ratios in birds. However, compelling evidence for adaptive sex allocation in birds is still very scant. We argue that there are two reasons for this: (i) standard sex allocation models, very helpful in understanding sex allocation of invertebrates, do not sufficiently take the complexities of bird life histories and physiology into account. Recent theoretical work might bring us a step closer to more realistic models; (ii) experimental field and laboratory studies on sex allocation in birds are scarce. Recent experimental work both in the laboratory and in the field shows that this is a promising approach.     

Dispersal rates affect species composition in metacommunities of Sarracenia purpurea inquilines

Dispersal among local communities can have a variety of effects on species composition and diversity at local and regional scales. Local conditions (e.g., resource and predator densities) can have independent effects, as well as interact with dispersal, to alter these patterns. Based on metacommunity models, we predicted that local diversity would show a unimodal relationship with dispersal frequency. We manipulated dispersal frequencies, resource levels, and the presence of predators (mosquito larvae) among communities found in the water-filled leaves of the pitcher plant Sarracenia purpurea. Diversity and abundance of species of the middle trophic level, protozoa and rotifers, were measured. Increased dispersal frequencies significantly increased regional species richness and protozoan abundance while decreasing the variance among local communities. Dispersal frequency interacted with predation at the local community scale to produce patterns of diversity consistent with the model. When predators were absent, we found a unimodal relationship between dispersal frequency and diversity, and when predators were present, there was a flat relationship. Intermediate dispersal frequencies maintained some species in the inquiline communities by offsetting extinction rates. Local community composition and the degree of connectivity between communities are both important for understanding species diversity patterns at local and regional scales.     

Network isolation and local diversity in neutral metacommunities

Biologists seek an understanding of the biological and environmental factors determining local community diversity. Recent advances in metacommunity ecology, and neutral theory in particular, highlight the importance of dispersal processes interacting with the spatial structure of a landscape for generating spatial patterns and maintaining biodiversity. The relative spatial isolation of a community is traditionally thought to have a large influence on local diversity. However, isolation remains an elusive concept to quantify, particularly in metacommunities with complex spatial structure. We represent the metacommunity as a network of local communities, and use network centrality measures to quantify the isolation of a local community. Using spatially explicit neutral theory, we examine how node position predicts variation in alpha diversity across a metacommunity. We find that diversity increases with node centrality in the network, but only when centrality is measured on a given scale in the network that widens with increasing dispersal rates and narrows with increasing evolutionary rates. More generally, complex biodiversity patterns form only when the underlying geography has structure on this critical scale. This provides a framework for understanding the influence of spatial geographic structure on global biodiversity patterns.     

Ecology: linking species diversity and genetic diversity

Although there is a great deal of interest in the biological diversity of species and of genes, it is only recently that researchers have begun to investigate the processes that exert parallel influences on these different levels of diversity.     

Dispersal stochasticity mediates species richness in source–sink metacommunities

Although it is well‐known that dispersal of organisms within a metacommunity will influence patterns of coexistence and richness, theoretical and experimental studies generally assume that dispersal rates are constant through time. However, dispersal is often a highly variable process that can vary seasonally and/or when stochastic events (e.g. wind storms, droughts, floods) occur. Using a well‐known source–sink metacommunity model, we present novel predictions for local and regional species richness when stochasticity in dispersal is expressly considered. We demonstrate that dispersal stochasticity alters some of the predictions obtained with constant dispersal; the peak of the predicted hump‐shaped relationship between dispersal and local species richness is diminished and shifted towards higher values of dispersal. Dispersal stochasticity increases extinction probabilities of inferior competitor species particularly in metacommunities subjected to severe isolation events (i.e. decreases of dispersal) or homogenization events (i.e. sudden increases of dispersal). Our results emphasize how incorporating dispersal stochasticity into theoretical predictions will broaden our understanding of metacommunities dynamics and their responses to natural and human‐related disturbances.     

Dispersal and species diversity: a meta-analysis

Species diversity in communities of interacting organisms is thought to be enhanced by dispersal, yet mechanisms predicting this have little to say about what effects differing rates of dispersal have on diversity and how dispersal affects diversity at larger spatial scales. I performed meta‐analyses on 23 studies comprising 50 experiments that manipulated species migration and measured community richness or diversity to test three hypotheses: that dispersal increases local diversity; that this effect depends on the rate of dispersal, specifically, that local diversity should be maximized at intermediate dispersal rates or else linearly related to dispersal rate; and that regional diversity may be either unaffected or negatively impacted by dispersal because dispersal tends to homogenize local communities. I found that immigration increased local diversity. Further, in animal studies, diversity appears maximized at intermediate dispersal rates but not with plant studies; however, more standardized studies are needed. Finally, results are ambiguous as to what happens at larger scales, with studies finding either declines or no change in regional diversity with dispersal. Taken together, these results reveal that dispersal has a complex, spatially contingent relationship with patterns of species diversity.     

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.     

Capturing the cornerstones of coral reef resilience: linking theory to practice

Coral reefs can undergo unexpected and dramatic changes in community composition, so called phase shifts. This can have profound consequences for ecosystem services upon which human welfare depends. Understanding of this behavior is in many aspects still in its infancy. Resilience has been argued to provide insurance against unforeseen ecosystem responses in the face of environmental change, and has become a prime goal for the management of coral reefs. However, diverse definitions of resilience can be found in the literature, making its meaning ambiguous. Several studies have used the term as a theoretical framework and concern regarding its practical applicability has been raised. Consequently, operationalizing theory to make resilience observable is an important task, particularly for policy makers and managers dealing with pressing environmental problems. Ultimately this requires some type of empirical assessments, something that has proven difficult due to the multidimensional nature of the concept. Biodiversity, spatial heterogeneity, and connectivity have been proposed as cornerstones of resilience as they may provide insurance against ecological uncertainty. The aim of this article is to provide an overview of the divergent uses of the concept and to propose empirical indicators of the cornerstones of coral reef resilience. These indicators include functional group approaches, the ratios of “good” and “bad” colonizers of space, measurements of spatial heterogeneity, and estimates of potential space availability against grazing capacity. The essence of these operational indicators of resilience is to use them as predictive tools to recognize vulnerability before disturbance occurs that may lead to abrupt phase shifts. Moving toward operationalizing resilience theory is imperative to the successful management of coral reefs in an increasingly disturbed and human-dominated environment. Communicating by Ecology Editor Professor Peter Mumby Order of authors 2–3 is alphabetic     

Dispersal, spatial scale, and species diversity in a hierarchically structured experimental landscape

Although there has been growing interest in the effect of dispersal on species diversity, much remains unknown about how dispersal occurring at multiple scales influences diversity. We used an experimental microbial landscape to determine whether dispersal occurring at two different scales - among local communities and among metacommunities - affects diversity differently. At the local scale, dispersal initially had a positive effect and subsequently a neutral effect on diversity, whereas at the metacommunity and landscape scales, dispersal showed a consistently negative effect. The timing in which dispersal affected beta diversity also differed sharply between local communities and metacommunities. These patterns were explained by scale- and time-dependent effects of dispersal in allowing spread of species and in removing spatial refuges from predators. Our results suggest that the relative contribution of opposing mechanisms by which dispersal affects diversity changes considerably over time and space in hierarchical landscapes in which dispersal occurs at multiple scales.     

Dispersal and life history strategies in epiphyte metacommunities: alternative solutions to survival in patchy,dynamic landscapes

Host trees for obligate epiphytes are dynamic patches that emerge, grow and fall, and metacommunity diversity critically depends on efficient dispersal. Even though species that disperse by large asexual diaspores are strongly dispersal limited, asexual dispersal is common. The stronger dispersal limitation of asexually reproducing species compared to species reproducing sexually via small spores may be compensated by higher growth rates, lower sensitivity to habitat conditions, higher competitive ability or younger reproductive age. We compared growth and reproduction of different groups of epiphytic bryophytes with contrasting dispersal (asexual vs. sexual) and life history strategies (colonists, short- and long-lived shuttle species, perennial stayers) in an old-growth forest stand in the boreo-nemoral region in eastern Sweden. No differences were seen in relative growth rates between asexual and sexual species. Long-lived shuttles had lower growth rates than colonists and perennial stayers. Most groups grew best at intermediate bark pH. Interactions with other epiphytes had a small, often positive effect on growth. Neither differences in sensitivity of growth to habitat conditions nor differences in competitive abilities among species groups were found. Habitat conditions, however, influenced the production of sporophytes, but not of asexual diaspores. Presence of sporophytes negatively affected growth, whereas presence of asexual diaspores did not. Sexual species had to reach a certain colony size before starting to reproduce, whereas no such threshold existed for asexual reproduction. The results indicate that the epiphyte metacommunity is structured by two main trade-offs: dispersal distance vs. reproductive age, and dispersal distance vs. sensitivity to habitat quality. There seems to be a trade-off between growth and sexual reproduction, but not asexual. Trade-offs in species traits may be shaped by conflicting selection pressures imposed by habitat turnover and connectivity rather than by species interactions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao''s estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics (‘Hill diversities''), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao''s estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.     

Predators alter the scaling of diversity in prey metacommunities

Although predator effects on the number of locally coexisting species are well understood, there are few formal predictions of how these local predator effects influence patterns of prey diversity at larger spatial scales. Building on the theory of island biogeography, we develop a simple model that describes how predators can alter the scaling of diversity in prey metacommunities and compares the effects of generalist and specialist predators on regional prey diversity. Generalist predators, which consume prey randomly with respect to species identity, are predicted to reduce α‐diversity and increase β‐diversity thereby maintaining regional diversity (γ‐diversity). Alternatively, specialist predators, which filter out prey species intolerant of predators, are predicted to reduce bothα‐diversity andβ‐diversity by causing the same prey species to be extirpated in each locality, resulting in regional prey species extinctions and lower γ‐diversity. These distinct effects of generalist and specialist predators on prey diversity at different spatial scales are uniquely shaped by the extent of predation within those metacommunities. Overall, our model results make general predictions for how different types of predators can differentially affect prey diversity across spatial scales, allowing a more complete understanding of the possible implications of predator eradications or introductions for biodiversity.     

Empirical approaches to metacommunities: a review and comparison with theory

Metacommunity theory has advanced understanding of how spatial dynamics and local interactions shape community structure and biodiversity. Here, we review empirical approaches to metacommunities, both observational and experimental, pertaining to how well they relate to and test theoretical metacommunity paradigms and how well they capture the realities of natural ecosystems. First, we show that the species-sorting and mass-effects paradigms are the most commonly tested and supported paradigms. Second, the dynamics observed can often be ascribed to two or more of the four non-exclusive paradigms. Third, empirical approaches relate only weakly to the concise assumptions and predictions made by the paradigms. Consequently, we suggest major avenues of improvement for empirical metacommunity approaches, including the integration across theoretical approaches and the incorporation of evolutionary and meta-ecosystem dynamics. We hope for metacommunity ecology to thereby bridge existing gaps between empirical and theoretical work, thus becoming a more powerful framework to understand dynamics across ecosystems.     

Condition‐dependent movement and dispersal in experimental metacommunities

Dispersal and the underlying movement behaviour are processes of pivotal importance for understanding and predicting metapopulation and metacommunity dynamics. Generally, dispersal decisions are condition‐dependent and rely on information in the broad sense, like the presence of conspecifics. However, studies on metacommunities that include interspecific interactions generally disregard condition‐dependence. Therefore, it remains unclear whether and how dispersal in metacommunities is condition‐dependent and whether rules derived from single‐species contexts can be scaled up to (meta)communities. Using experimental protist metacommunities, we show how dispersal and movement depend on and are adjusted by the strength of interspecific interactions. We found that the predicting movement and dispersal in metacommunities requires knowledge on behavioural responses to intra‐ and interspecific interaction strengths. Consequently, metacommunity dynamics inferred directly from single‐species metapopulations without taking interspecific interactions into account are likely flawed. Our work identifies the significance of condition‐dependence for understanding metacommunity dynamics, stability and the coexistence and distribution of species.