Delayed compensation for missing keystone species by colonization

Beyond single-species models: leveraging multispecies forecasts to navigate the dynamics of ecological predictability

Background

Forecasting the responses of natural populations to environmental change is a key priority in the management of ecological systems. This is challenging because the dynamics of multi-species ecological communities are influenced by many factors. Populations can exhibit complex, nonlinear responses to environmental change, often over multiple temporal lags. In addition, biotic interactions, and other sources of multi-species dependence, are major contributors to patterns of population variation. Theory suggests that near-term ecological forecasts of population abundances can be improved by modelling these dependencies, but empirical support for this idea is lacking.

Methods

We test whether models that learn from multiple species, both to estimate nonlinear environmental effects and temporal interactions, improve ecological forecasts compared to simpler single species models for a semi-arid rodent community. Using dynamic generalized additive models, we analyze time series of monthly captures for nine rodent species over 25 years.

Results

Model comparisons provide strong evidence that multi-species dependencies improve both hindcast and forecast performance, as models that captured these effects gave superior predictions than models that ignored them. We show that changes in abundance for some species can have delayed, nonlinear effects on others, and that lagged, nonlinear effects of temperature and vegetation greenness are key drivers of changes in abundance for this system.

Conclusions

Our findings highlight that multivariate models are useful not only to improve near-term ecological forecasts but also to ask targeted questions about ecological interactions and drivers of change. This study emphasizes the importance of jointly modelling species' shared responses to the environment and their delayed temporal interactions when teasing apart community dynamics.

Transferability of ecological forecasting models to novel biotic conditions in a long-term experimental study

Ecological forecasting models play an increasingly important role for managing natural resources and assessing our fundamental knowledge of processes driving ecological dynamics. As global environmental change pushes ecosystems beyond their historical conditions, the utility of these models may depend on their transferability to novel conditions. Because species interactions can alter resource use, timing of reproduction, and other aspects of a species' realized niche, changes in biotic conditions, which can arise from community reorganization events in response to environmental change, have the potential to impact model transferability. Using a long-term experiment on desert rodents, we assessed model transferability under novel biotic conditions to better understand the limitations of ecological forecasting. We show that ecological forecasts can be less accurate when the models generating them are transferred to novel biotic conditions and that the extent of model transferability can depend on the species being forecast. We also demonstrate the importance of incorporating uncertainty into forecast evaluation with transferred models generating less accurate and more uncertain forecasts. These results suggest that how a species perceives its competitive landscape can influence model transferability and that when uncertainties are properly accounted for, transferred models may still be appropriate for decision making. Assessing the extent of the transferability of forecasting models is a crucial step to increase our understanding of the limitations of ecological forecasts.

Scaling approaches and macroecology provide a foundation for assessing ecological resilience in the Anthropocene

In the Anthropocene, intensifying ecological disturbances pose significant challenges to our predictive capabilities for ecosystem responses. Macroecology-which focuses on emergent statistical patterns in ecological systems-unveils consistent regularities in the organization of biodiversity and ecosystems. These regularities appear in terms of abundance, body size, geographical range, species interaction networks, or the flux of matter and energy. This paper argues for moving beyond qualitative resilience metaphors, such as the 'ball and cup', towards a more quantitative macroecological framework. We suggest a conceptual and theoretical basis for ecological resilience that integrates macroecology with a stochastic diffusion approximation constrained by principles of biological symmetry. This approach provides an alternative novel framework for studying ecological resilience in the Anthropocene. We demonstrate how our framework can effectively quantify the impacts of major disturbances and their extensive ecological ramifications. We further show how biological scaling insights can help quantify the consequences of major disturbances, emphasizing their cascading ecological impacts. The nature of these impacts prompts a re-evaluation of our understanding of resilience. Emphasis on regularities of ecological assemblages can help illuminate resilience dynamics and offer a novel basis to predict and manage the impacts of disturbance in the Anthropocene more efficiently. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives

Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.

Shifts in competitive structures can drive variation in species' phenology

For many species, a well documented response to anthropogenic climate change is a shift in various aspects of its life history, including its timing or phenology. Often, these phenological shifts are associated with changes in abiotic factors used as proxies for resource availability or other suitable conditions. Resource availability, however, can also be impacted by competition, but the impact of competition on phenology is less studied than abiotic drivers. We fit generalized additive models (GAMs) to a long-term experimental dataset on small mammals monitored in the southwestern United States and show that altered competitive landscapes can drive shifts in breeding timing and prevalence, and that, relative to a dominant competitor, other species exhibit less specific responses to environmental factors. These results suggest that plasticity of phenological responses, which is often described in the context of annual variation in abiotic factors, can occur in response to biotic context as well. Variation in phenological responses under different biotic conditions shown here further demonstrates that a more nuanced understanding of shifting biotic interactions is useful to better understand and predict biodiversity patterns in a changing world.

Maintenance of community function through compensation breaks down over time in a desert rodent community

Understanding the ecological processes that maintain community function in systems experiencing species loss, and how these processes change over time, is key to understanding the relationship between community structure and function and predicting how communities may respond to perturbations in the Anthropocene. Using a 30‐year experiment on desert rodents, we show that the impact of species loss on community‐level energy use has changed repeatedly and dramatically over time, due to (1) the addition of new species to the community, and (2) a reduction in functional redundancy among the same set of species. Although strong compensation, initially driven by the dispersal of functionally redundant species to the local community, occurred in this system from 1997 to 2010, since 2010, compensation has broken down due to decreasing functional overlap within the same set of species. Simultaneously, long‐term changes in sitewide community composition due to niche complementarity have decoupled the dynamics of compensation from the overall impact of species loss on community‐level energy use. Shifting, context‐dependent compensatory dynamics, such as those demonstrated here, highlight the importance of explicitly long‐term, metacommunity, and eco‐evolutionary perspectives on the link between species‐level fluctuations and community function in a changing world.

Temporal changes in species composition affect a ubiquitous species' use of habitat patches

Across landscapes, shifts in species composition often co-occur with shifts in structural or abiotic habitat features, making it difficult to disentangle the role of competitors and environment on assessments of patch quality. Using over two decades of rodent community data from a long-term experiment, we show that a small, ubiquitous granivore (Chaetodipus penicillatus) shifted its use of different experimental treatments with the establishment of a novel competitor, C. baileyi. Shifts in residency, probability of movement between patches, and the arrival of new individuals in patches altered which treatment supported the highest abundances of C. penicillatus. Our results suggest that the establishment of a new species worsened the quality of the originally preferred treatment, likely by impacting resource availability. Paradoxically, the presence of the new species also increased C. penicillatus' use of the less preferred treatment, potentially through shifts in the competitive network on those plots.

Rodent burrow network dynamics under human-induced landscape transformation from desert to steppe in Kalmykian rangelands

Rodents play an important role in rangelands through the engineering of extensive burrow systems, which provides key habitats for many animal and plant species. We have analyzed the long-term variation in the abundance and distribution of rodent burrows in grazing ecosystems of southern Russia (Kalmykia) under the landscape change from desert to steppe caused by the drastic reduction of livestock after the collapse of the USSR in the early 1990s. We conducted burrow surveys in the "desert" (1980) and "steppe" (2017) periods on 19 3-km transects. We found considerable changes in burrow abundance and distribution, as well as evidence of desert habitat fragmentation and isolation caused by the expansion of tall-grass communities. Burrows of the open-dwelling diurnal ground squirrel (Spermophilus pygmaeus), the dominant and the keystone species during the "desert" period, almost completely disappeared from the rodent burrow network by 2017, indicating significant habitat loss. In contrast, the burrows of the folivorous social vole (Microtus socialis) which was rare in the 1980s, became abundant and ubiquitously distributed. The burrow density of the desert-dwelling psammophilous midday gerbil (Meriones meridianus) decreased, while the distances between occupied patches increased, indicating desert habitat fragmentation and loss of population connectivity. Burrows of the folivorous tamarisk gerbils (M. tamariscinus) were recorded only sporadically in both 1980 and 2017. The observed changes in the rodent burrow network, the key component of grazing ecosystems, correlate with rodent species ecology and can have long-term and important consequences for ecosystem functioning.

Long-term community change through multiple rapid transitions in a desert rodent community

While studies increasingly document long-term change in community composition, whether long-term change occurs gradually or via rapid reorganization events remains unclear. We used Latent Dirichlet Allocation (LDA) and a change-point model to examine the long-term dynamics of a desert rodent community undergoing compositional change over a 38-yr span. Our approach detected three rapid reorganization events, where changes in the relative abundances of dominant and rare species occurred, and a separate period of increased variance in the structure of the community. These events coincided with time periods, possibly related to climate events, where the total abundance of rodents was extremely low. There are a variety of processes that could link low abundance events with a higher probability of rapid ecological transitions, including higher importance of stochastic processes (i.e., competitive interactions or priority effects) and the removal of structuring effects of competitive dominants or incumbent species. Continued study of the dynamics of community change will provide important information not only on the processes structuring communities, but will also provide guidance for forecasting how communities will undergo change in the future.

Top predator absence enhances leaf breakdown in an intermittent stream

Current biodiversity loss is characterized by the extinction of top predators, but small-bodied freshwater fish are often overlooked in research and conservation management even when threatened because they usually lack commercial value. Therefore, the ecosystem impacts of their possible loss remain mostly unknown. We assessed whether the presence/absence of an endangered predatory fish (Barbus meridionalis (A. Risso, 1827)) in an intermittent stream affects leaf fungal biomass and leaf quality (i.e. leaf carbon:nitrogen ratio and leaf toughness), macroinvertebrate assemblages colonizing leaf packs, and leaf breakdown rates. We conducted a leaf bag experiment comparing a control reach with a population of B. meridionalis with an adjacent upstream fishless reach. In the fishless reach, leaf fungal biomass and microbially mediated breakdown rate were lower compared to the control reach. This was probably caused by the lack of the bottom-up stimulation through nutrient recycling by fish. Shredders and scrapers were found at higher abundance and biomass in the fishless compared to the control reach, and the whole macroinvertebrate community composition changed with fish absence. Consequently, macroinvertebrate mediated leaf breakdown was faster in the fishless than in the control reach, not only compensating for the lower microbially mediated leaf breakdown in the fishless reach, but accelerating the overall leaf breakdown rate. Our study contributes to understand the potential cascading effects produced by the extirpation of endangered small-bodied fish.

Decline of the Endangered Morro Bay Kangaroo Rat in California

The Morro Bay kangaroo rat Dipodomys heermanni morroensis occurs in the vicinity of Morro Bay (specifically in and near Los Osos) in western San Luis Obispo County in coastal central California. It was listed as endangered pursuant to the U.S. Endangered Species Conservation Act in 1970 and subsequently the U.S. Endangered Species Act in 1973. Field research from the late 1950s to the mid-1980s has documented a rapid population decline. Despite many efforts, researchers have not captured the Morro Bay kangaroo rat since 1986, and the last captive individual died in 1993. We review the biology and conservation status of the Morro Bay kangaroo rat, including taxonomy and genetics, soil type and burrows, history of decline, primary causes of decline, breeding in the wild and in captivity, habitat restoration, and threats. In particular, there are two primary causes of decline. First, development (urban, agricultural, and industrial) has resulted in direct loss of habitat. Second, in the absence of fire, the early seral stages of coastal dune scrub (optimal habitat) have matured to later successional stages of vegetation, which are denser and with substantially fewer annual food plants, and which negatively impact the locomotion of kangaroo rats and change the diversity of the small mammal community with a likely increase in competition. In 2016 only pockets of habitat remain, with optimal habitat comprising an estimated 1% of the historical geographic range. Although researchers have not demonstrated predation by domestic cats, it is likely a major threat and we suspect it has contributed to the decline based upon a review of the literature. In 2011 we observed potential signs of the Morro Bay kangaroo rat at two historical areas, which suggests it may be persisting at extremely low densities in a few isolated colonies. In addition, we could not obtain permission to survey on four private properties with potential habitat. In consideration of the vast loss and fragmentation of its habitat, along with the continuing and pervasive threats, the Morro Bay kangaroo rat is clearly conservation-reliant. We believe that without urgent human intervention, the Morro Bay kangaroo rat will soon become extinct if it is not already.

Time-Lag in Responses of Birds to Atlantic Forest Fragmentation: Restoration Opportunity and Urgency

There are few opportunities to evaluate the relative importance of landscape structure and dynamics upon biodiversity, especially in highly fragmented tropical landscapes. Conservation strategies and species risk evaluations often rely exclusively on current aspects of landscape structure, although such limited assumptions are known to be misleading when time-lag responses occur. By relating bird functional-group richness to forest patch size and isolation in ten-year intervals (1956, 1965, 1978, 1984, 1993 and 2003), we revealed that birds with different sensitivity to fragmentation display contrasting responses to landscape dynamics in the Brazilian Atlantic Forest. For non-sensitive groups, there was no time-lag in response: the recent degree of isolation best explains their variation in richness, which likely relates to these species' flexibility to adapt to changes in landscape structure. However, for sensitive bird groups, the 1978 patch area was the best explanatory variable, providing evidence for a 25-year time-lag in response to habitat reduction. Time-lag was more likely in landscapes that encompass large patches, which can support temporarily the presence of some sensitive species, even when habitat cover is relatively low. These landscapes potentially support the most threatened populations and should be priorities for restoration efforts to avoid further species loss. Although time-lags provide an opportunity to counteract the negative consequences of fragmentation, it also reinforces the urgency of restoration actions. Fragmented landscapes will be depleted of biodiversity if landscape structure is only maintained, and not improved. The urgency of restoration action may be even higher in landscapes where habitat loss and fragmentation history is older and where no large fragment remained to act temporarily as a refuge.

Diversity components and assembly patterns of plant functional traits determine community spatial stability under resource gradients in a desert steppe

The diversity–stability relationship has been addressed and debated for decades, but how this relationship is affected by nutrient availability remains contentious. In the present study we assessed the effects of plant diversity, in terms of species richness, functional group composition and functional trait diversity, on the spatial stability of net primary productivity (NPP) following nitrogen and phosphorus application. In addition, we explored how functional traits at the species level contribute to the spatial stability of NPP. The results support the hypothesis that greater diversity leads to higher spatial stability. This relationship was highly dependent on soil nutrient availability, and increasing species richness or functional trait diversity significantly increased spatial variation of NPP under a high N fertilisation level. The effects of high mineral fertilisation rates may perhaps have masked the effects of plant diversity. Although species richness or functional trait diversity of the original and modified communities from which species with particular functional traits had been removed were significantly different, there were no differences in the coefficients of variation in the NPP of those communities. The lack of difference demonstrated that the relationship between spatial variability and biodiversity depended on the measure of diversity applied and that the functional group composition exerted a stronger effect than other diversity measures. Further analyses revealed that spatial stability of NPP was enhanced with increased diversity in vegetative plant height, rooting depth and the presence of legume, and diminished with diversity in the root system type and life cycle under some fertilisation treatments. The present study demonstrates that the relationship between biodiversity and ecosystem functioning is variable with different diversity, identity and environmental factors. Evaluating the contribution of particular traits to community stability will ultimately help us better understand the mechanisms underlying the diversity–stability relationship.

Energy flow and functional compensation in Great Basin small mammals under natural and anthropogenic environmental change

Research on the ecological impacts of environmental change has primarily focused at the species level, leaving the responses of ecosystem-level properties like energy flow poorly understood. This is especially so over millennial timescales inaccessible to direct observation. Here we examine how energy flow within a Great Basin small mammal community responded to climate-driven environmental change during the past 12,800 y, and use this baseline to evaluate responses observed during the past century. Our analyses reveal marked stability in energy flow during rapid climatic warming at the terminal Pleistocene despite dramatic turnover in the distribution of mammalian body sizes and habitat-associated functional groups. Functional group turnover was strongly correlated with climate-driven changes in regional vegetation, with climate and vegetation change preceding energetic shifts in the small mammal community. In contrast, the past century has witnessed a substantial reduction in energy flow caused by an increase in energetic dominance of small-bodied species with an affinity for closed grass habitats. This suggests that modern changes in land cover caused by anthropogenic activities--particularly the spread of nonnative annual grasslands--has led to a breakdown in the compensatory dynamics of energy flow. Human activities are thus modifying the small mammal community in ways that differ from climate-driven expectations, resulting in an energetically novel ecosystem. Our study illustrates the need to integrate across ecological and temporal scales to provide robust insights for long-term conservation and management.

Small but powerful: top predator local extinction affects ecosystem structure and function in an intermittent stream

Top predator loss is a major global problem, with a current trend in biodiversity loss towards high trophic levels that modifies most ecosystems worldwide. Most research in this area is focused on large-bodied predators, despite the high extinction risk of small-bodied freshwater fish that often act as apex consumers. Consequently, it remains unknown if intermittent streams are affected by the consequences of top-predators' extirpations. The aim of our research was to determine how this global problem affects intermittent streams and, in particular, if the loss of a small-bodied top predator (1) leads to a 'mesopredator release', affects primary consumers and changes whole community structures, and (2) triggers a cascade effect modifying the ecosystem function. To address these questions, we studied the top-down effects of a small endangered fish species, Barbus meridionalis (the Mediterranean barbel), conducting an enclosure/exclosure mesocosm experiment in an intermittent stream where B. meridionalis became locally extinct following a wildfire. We found that top predator absence led to 'mesopredator release', and also to 'prey release' despite intraguild predation, which contrasts with traditional food web theory. In addition, B. meridionalis extirpation changed whole macroinvertebrate community composition and increased total macroinvertebrate density. Regarding ecosystem function, periphyton primary production decreased in apex consumer absence. In this study, the apex consumer was functionally irreplaceable; its local extinction led to the loss of an important functional role that resulted in major changes to the ecosystem's structure and function. This study evidences that intermittent streams can be affected by the consequences of apex consumers' extinctions, and that the loss of small-bodied top predators can lead to large ecosystem changes. We recommend the reintroduction of small-bodied apex consumers to systems where they have been extirpated, to restore ecosystem structure and function.

An experimental test of the response of macroecological patterns to altered species interactions

Macroecological patterns such as the species-area relationship (SAR), the species-abundance distribution (SAD), and the species-time relationship (STR) exhibit regular behavior across ecosystems and taxa. However, determinants of these patterns remain poorly understood. Emerging theoretical frameworks for macroecology attempt to understand this regularity by ignoring detailed ecological interactions and focusing on the influence of a small number of community-level state variables, such as species richness and total abundance, on these patterns. We present results from a 15-year rodent removal experiment evaluating the response of three different macroecological patterns in two distinct annual plant communities (summer and winter) to two levels of manipulated seed predation. Seed predator manipulations significantly impacted species composition on all treatments in both communities, but did not significantly impact richness, community abundance, or macroecological patterns in most cases. How'ever, winter community abundance and richness responded significantly to the removal of all rodents. Changes in richness and abundance were coupled with significant shifts in macroecological patterns (SADs, SARs, and STRs). Because altering species interactions only impacted macroecological patterns when the state variables of abundance and richness also changed, we suggest that, in this system, local-scale processes primarily act indirectly through these properties to determine macroecological patterns.

Trophic tangles through time? Opposing direct and indirect effects of an invasive omnivore on stream ecosystem processes

Omnivores can impact ecosystems via opposing direct or indirect effects. For example, omnivores that feed on herbivores and plants could either increase plant biomass due to the removal of herbivores or decrease plant biomass due to direct consumption. Thus, empirical quantification of the relative importance of direct and indirect impacts of omnivores is needed, especially the impacts of invasive omnivores. Here we investigated how an invasive omnivore (signal crayfish, Pacifastacus leniusculus) impacts stream ecosystems. First, we performed a large-scale experiment to examine the short-term (three month) direct and indirect impacts of crayfish on a stream food web. Second, we performed a comparative study of un-invaded areas and areas invaded 90 years ago to examine whether patterns from the experiment scaled up to longer time frames. In the experiment, crayfish increased leaf litter breakdown rate, decreased the abundance and biomass of other benthic invertebrates, and increased algal production. Thus, crayfish controlled detritus via direct consumption and likely drove a trophic cascade through predation on grazers. Consistent with the experiment, the comparative study also found that benthic invertebrate biomass decreased with crayfish. However, contrary to the experiment, crayfish presence was not significantly associated with higher leaf litter breakdown in the comparative study. We posit that during invasion, generalist crayfish replace the more specialized native detritivores (caddisflies), thereby leading to little long-term change in net detrital breakdown. A feeding experiment revealed that these native detritivores and the crayfish were both effective consumers of detritus. Thus, the impacts of omnivores represent a temporally-shifting interplay between direct and indirect effects that can control basal resources.

Species loss, delayed numerical responses, and functional compensation in an antbird guild

When a community loses species through fragmentation, its total food consumption may drop. Compensatory responses of remaining species, whereby survivors assume roles of extinct competitors, may reduce the impact of species loss through numerical or functional responses. We measured compensatory responses in two remaining antbird species on Barro Colorado Island, Panama, four decades after the loss of their dominant competitor, the Ocellated Antbird, Phaenostictus mcleannani. We compared current abundances and behavior of these two species on Barro Colorado to those reported before the island lost Ocellated Antbirds, and to those in a nearby mainland population where all three species still exist as a space-for-time substitution. The smaller, more subordinate Spotted Antbird, Hylophylax naevioides, responded far more strongly than the larger Bicolored Antbird, Gymnopithys leucaspis, which is functionally more like the Ocellated Antbird. Islandwide density of Spotted Antbirds has more than doubled since the loss of Ocellated Antbirds. Moreover, Spotted Antbirds now spend so much more of their time following ant swarms that their metabolic biomass at these swarms has more than tripled since Ocellated Antbirds disappeared. These responses in Spotted Antbirds were apparently delayed by >20 years. Bicolored Antbirds have not increased substantially in islandwide density or metabolic biomass at ant swarms. We hypothesize that behavioral flexibility, as shown by Spotted Antbirds on Barro Colorado Island, is a major factor governing the extent to which fragmented ecosystems can buffer the impacts of species loss.

Red Queen: from populations to taxa and communities

Biotic interactions via the struggle for control of energy and the interactive effects of biota with their physical environment characterize Van Valen's Red Queen (VRQ). Here, we review new evidence for and against a VRQ view of the world from studies of increasing temporal and spatial scales. Interactions among biota and with the physical environment are important for generating and maintaining diversity on diverse timescales, but detailed mechanisms remain poorly understood. We recommend directly estimating the effect of biota and the physical environment on ecological and evolutionary processes. Promising approaches for elucidating VRQ include using mathematical modelling, controlled experimental systems, sampling and processes-oriented approaches for analysing data from natural systems, while paying extra attention to biotic interactions discernable from the fossil record.

Sin nombre virus and rodent species diversity: a test of the dilution and amplification hypotheses

BACKGROUND

Species diversity is proposed to greatly impact the prevalence of pathogens. Two predominant hypotheses, the "Dilution Effect" and the "Amplification Effect", predict divergent outcomes with respect to the impact of species diversity. The Dilution Effect predicts that pathogen prevalence will be negatively correlated with increased species diversity, while the Amplification Effect predicts that pathogen prevalence will be positively correlated with diversity. For many host-pathogen systems, the relationship between diversity and pathogen prevalence has not be empirically examined.

METHODOLOGY/PRINCIPAL FINDINGS

We tested the Dilution and Amplification Effect hypotheses by examining the prevalence of Sin Nombre virus (SNV) with respect to diversity of the nocturnal rodent community. SNV is directly transmitted primarily between deer mice (Peromyscus maniculatus). Using mark-recapture sampling in the Spring and Fall of 2003-2005, we measured SNV prevalence in deer mice at 16 landscape level sites (3.1 hectares each) that varied in rodent species diversity. We explored several mechanisms by which species diversity may affect SNV prevalence, including reduced host density, reduced host persistence, the presence of secondary reservoirs and community composition. We found a negative relationship between species diversity and SNV prevalence in deer mice, thereby supporting the Dilution Effect hypothesis. Deer mouse density and persistence were lower at sites with greater species diversity; however, only deer mouse persistence was positively correlated with SNV prevalence. Pinyon mice (P. truei) may serve as dilution agents, having a negative effect on prevalence, while kangaroo rats (Dipodomys ordii), may have a positive effect on the prevalence of SNV, perhaps through effects on deer mouse behavior.

CONCLUSIONS/SIGNIFICANCE

While previous studies on host-pathogen systems have found patterns of diversity consistent with either the Dilution or Amplification Effects, the mechanisms by which species diversity influences prevalence have not been investigated. Our study indicates that changes in host persistence, coupled with interspecific interactions, are important mechanisms through which diversity may influence patterns of pathogens. Our results reveal the complexity of rodent community interactions with respect to SNV dynamics.

Zero sum, the niche, and metacommunities: long-term dynamics of community assembly

Recent models of community assembly, structure, and dynamics have incorporated, to varying degrees, three mechanistic processes: resource limitation and interspecific competition, niche requirements of species, and exchanges between a local community and a regional species pool. Synthesizing 30 years of data from an intensively studied desert rodent community, we show that all of these processes, separately and in combination, have influenced the structural organization of this community and affected its dynamical response to both natural environmental changes and experimental perturbations. In addition, our analyses suggest that zero-sum constraints, niche differences, and metacommunity processes are inextricably linked in the ways that they affect the structure and dynamics of this system. Explicit consideration of the interaction of these processes should yield a deeper understanding of the assembly and dynamics of other ecological communities. This synthesis highlights the role that long-term data, especially when coupled with experimental manipulations, can play in assessing the fundamental processes that govern the structure and function of ecological communities.

Impact of an extreme climatic event on community assembly

Extreme climatic events are predicted to increase in frequency and magnitude, but their ecological impacts are poorly understood. Such events are large, infrequent, stochastic perturbations that can change the outcome of entrained ecological processes. Here we show how an extreme flood event affected a desert rodent community that has been monitored for 30 years. The flood (i) caused catastrophic, species-specific mortality; (ii) eliminated the incumbency advantage of previously dominant species; (iii) reset long-term population and community trends; (iv) interacted with competitive and metapopulation dynamics; and (v) resulted in rapid, wholesale reorganization of the community. This and a previous extreme rainfall event were punctuational perturbations-they caused large, rapid population- and community-level changes that were superimposed on a background of more gradual trends driven by climate and vegetation change. Captured by chance through long-term monitoring, the impacts of such large, infrequent events provide unique insights into the processes that structure ecological communities.

A niche for neutrality

Ecologists now recognize that controversy over the relative importance of niches and neutrality cannot be resolved by analyzing species abundance patterns. Here, we use classical coexistence theory to reframe the debate in terms of stabilizing mechanisms (niches) and fitness equivalence (neutrality). The neutral model is a special case where stabilizing mechanisms are absent and species have equivalent fitness. Instead of asking whether niches or neutral processes structure communities, we advocate determining the degree to which observed diversity reflects strong stabilizing mechanisms overcoming large fitness differences or weak stabilization operating on species of similar fitness. To answer this question, we propose combining data on per capita growth rates with models to: (i) quantify the strength of stabilizing processes; (ii) quantify fitness inequality and compare it with stabilization; and (iii) manipulate frequency dependence in growth to test the consequences of stabilization and fitness equivalence for coexistence.

REDUCED RODENT BIODIVERSITY DESTABILIZES PLANT POPULATIONS

We tested the hypothesis that species loss at one trophic level will reduce the temporal stability of populations at other trophic levels. We examined the temporal stability of annual plant populations on plots that experimentally manipulated the functional diversity of seed-eating rodent consumers. Experimental reduction of rodent functional diversity destabilized populations of small-seeded plants but had less consistent effects on larger-seeded species. Small-seeded species also exhibited a greater number of years of zero abundance. Thus, experimental reduction of rodent functional diversity resulted in lower plant diversity. The decline in the temporal stability of small-seeded plants likely resulted from increased interspecific competition by large-seeded plants. These results demonstrate that the loss of species at one trophic level can lead to reduced richness at lower trophic levels via competition and reduced temporal stability.

The effect of temporal scale on the outcome of trophic cascade experiments

The outcome of experimental manipulations in ecology should depend on the duration of the experiment. We tested this proposition by examining the results of published trophic cascade experiments in freshwater communities and the results of our own previously unpublished pond experiment. In particular, we analyze the results of 90 published trophic cascade experiments to test the prediction that the outcome of freshwater trophic cascade experiments, in which zooplanktivorous fish are either present or absent, depends on the duration of the experiment. We present evidence that there are quantitative differences in the strength of trophic cascades among different venue types (enclosure, mesocosm, pond, and lake), but that the strength of trophic cascades does not diminish with increasing experiment duration. Despite the large number of studies, there have been few replicated studies of trophic cascades for longer than a summer field season, and none for the time required to estimate the long-term result of press perturbations. We therefore present the results of a 4-year study of trophic cascades in experimental ponds, to test the predictions that the addition of the top predator results in a sustained increase in the phytoplankton biomass. We found that, as predicted by our literature review, there was no decline in the strength of the trophic cascade as the experiment progressed.