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

Correlated biodiversity change between plant and insect assemblages resurveyed after 80 years across a dynamic habitat mosaic

Historical data on co-occurring taxa are extremely rare. As such, the extent to which distinct co-occurring taxa experience similar long-term patterns in species richness and compositional change (e.g., when exposed to a changing environment) is not clear. Using data from a diverse ecological community surveyed in the 1930s and resurveyed in the 2010s, we investigated whether local plant and insect assemblages displayed cross-taxon congruence-that is, spatiotemporal correlation in species richness and compositional change-across six co-occurring taxa: vascular plants, non-vascular plants, grasshoppers and crickets (Orthoptera), ants (Hymenoptera: Formicinae), hoverflies (Diptera: Syrphidae), and dragonflies and damselflies (Odonata). All taxa exhibited high levels of turnover across the ca. 80-year time period. Despite minimal observed changes at the level of the whole study system, species richness displayed widespread cross-taxon congruence (i.e., correlated temporal change) across local assemblages within the study system. Hierarchical logistic regression models suggest a role for shared responses to environmental change underlying cross-taxon correlations and highlight stronger correlations between vascular plants and their direct consumers, suggesting a possible role for biotic interactions between these groups. These results provide an illustration of cross-taxon congruence in biodiversity change using data unique in its combination of temporal and taxonomic scope, and highlight the potential for cascading and comparable effects of environmental change (abiotic and biotic) on co-occurring plant and insect communities. However, analyses of historical resurveys based on currently available data come with inherent uncertainties. As such, this study highlights a need for well-designed experiments, and monitoring programs incorporating co-occurring taxa, to determine the underlying mechanisms and prevalence of congruent biodiversity change as anthropogenic environmental change accelerates apace.

Correlation and Influence of Seasonal Variation of Diet with Gut Microbiota Diversity and Metabolism Profile of Chipmunk

Tamias Sibiricus is the only member of the genus Tamias, a significant and vigorous seed distributor and vital food for their predators. No information is known about the strict diet, gut microbiota structure, and metabolism profile of chipmunks and how they diversify seasonally. The above factors, as well as flexibility toward seasonal shifts, are critical in defining its growth rates, health, survivorship, and population stability. This study explored the diet, gut microbiota composition, and chipmunk metabolism. Additionally, the influence of different seasons was also investigated by using next-generation sequencing. Results revealed that seasons strongly affected a diet: streptophyte accounted for 37% in spring, which was lower than in summer (34.3%) and autumn (31.4%). Further, Ascomycota was observed at 43.8% in spring, which reduced to 36.6% in summer and the lowest (31.3%) in autumn. Whereas, nematodes showed maximum abundance from spring (15.8%) to summer (20.6%) and autumn (24.1%). These results signify the insectivorous nature of the chipmunk in summer and autumn. While herbivorous and fungivorous nature in spring. The DNA analysis revealed that chipmunk mainly feeds on fungi, including Aspergillus and Penicillium genus. Similar to diet composition, the microbiome also exhibited highly significant dissimilarity (p < 0.001, R = 0.235) between spring/autumn and spring/summer seasons. Proteobacteria (35.45%), Firmicutes (26.7%), and Bacteroidetes (23.59%) were shown to be the better discriminators as they contributed the most to causing differences between seasons. Moreover, PICRUSt showed that the assimilation of nutrients were also varied seasonally. The abundance of carbohydrates, lipids, nucleotides, xenobiotics, energy, terpenoids, and polyketides metabolism was higher in spring than in other seasons. Our study illustrates that seasonal reconstruction in the chipmunk diet has a significant role in shaping temporal variations in gut microbial community structure and metabolism profile.

Looking for compensation at multiple scales in a wetland bird community

Compensatory dynamics, during which community composition shifts despite a near-constant total community size, are usually rare: Synchronous dynamics prevail in natural communities. This is a puzzle for ecologists, because of the key role of compensation in explaining the relation between biodiversity and ecosystem functioning. However, most studies so far have considered compensation in either plants or planktonic organisms, so that evidence for the generality of such synchrony is limited. Here, we extend analyses of community-level synchrony to wetland birds. We analyze a 35-year monthly survey of a community where we suspected that compensation might occur due to potential competition and changes in water levels, favoring birds with different habitat preferences. We perform both year-to-year analyses by season, using a compensation/synchrony index, and multiscale analyses using a wavelet-based measure, which allows for both scale- and time-dependence. We analyze synchrony both within and between guilds, with guilds defined either as tightknit phylogenetic groups or as larger functional groups. We find that abundance and biomass compensation are rare, likely due to the synchronizing influence of climate (and other drivers) on birds, even after considering several temporal scales of covariation (during either cold or warm seasons, above or below the annual scale). Negative covariation in abundance at the guild or community level did only appear at the scale of a few months or several years. We also found that synchrony varies with taxonomic and functional scale: The rare cases where compensation appeared consistently in year-to-year analyses were between rather than within functional groups. Our results suggest that abundance compensation may have more potential to emerge between broad functional groups rather than between species, and at relatively long temporal scales (multiple years for vertebrates), above that of the dominant synchronizing driver.

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 variability in population and community dynamics

Populations and communities fluctuate in their overall numbers through time, and the magnitude of fluctuations in individual species may scale to communities. However, the composite variability at the community scale is expected to be tempered by opposing fluctuations in individual populations, a phenomenon often called the portfolio effect. Understanding population variability, how it scales to community variability, and the spatial scaling in this variability are pressing needs given shifting environmental conditions and community composition. We explore evidence for portfolio effects using null community simulations and a large collection of empirical community time series from the BioTIME database. Additionally, we explore the relative roles of habitat type and geographic location on population and community temporal variability. We find strong portfolio effects in our theoretical community model, but weak effects in empirical data, suggesting a role for shared environmental responses, interspecific competition, or a litany of other factors. Furthermore, we observe a clear latitudinal signal - and differences among habitat types - in population and community variability. Together, this highlights the need to develop realistic models of community dynamics, and hints at spatial, and underlying environmental, gradients in variability in both population and community dynamics.

Factors driving California pocket mice (Chaetodipus californicus) population dynamics

Understanding how demographic parameters respond to climatic variables is essential for predicting species’ response to changing environmental conditions. The California pocket mouse (Chaetodipus californicus) is an inhabitant of coastal-central California oak (Quercus spp.) woodland that is undergoing a rapid anthropogenic transformation while also facing effects of global climate change. We analyzed the population dynamics of the California pocket mouse by applying Pradel’s temporal symmetry model to a 10-year (2004 – 2013) capture–mark–recapture data set to estimate survival and recruitment rates and realized population growth rate. The overall monthly apparent survival probability (ϕ) was 0.76 ± 0.01 SE and was slightly higher in the dry season (0.79 ± 0.02 SE) than the wet season (0.74 ± 0.01 SE). Coefficients of variation (CV) of temperature and rainfall (with and without a one-season lag), average seasonal temperature, and regional climatic variation (El Niño index) positively influenced ϕ. Overall monthly recruitment rate (f) was 0.17 ± 0.01 SE but varied seasonally; f was substantially higher during the dry season (0.39 ± 0.04 SE) than the wet season (0.09 ± 0.02 SE). Average seasonal temperature, CV of temperature and rainfall (without a one-season lag), and total seasonal rainfall (with a one-season lag) positively influenced recruitment, whereas regional climatic variation (El Niño index), total seasonal rainfall (without a one-season lag), and CV of rainfall (with a one-season lag) had a negative effect on f. Monthly realized population growth rate (λ) was 1.00 ± 0.02 SE for the entire study period, but it varied temporally. Our study provides the first estimates of demographic parameters for the California pocket mouse and tests for the influence of climatic variables on these parameters. Although the California pocket mouse population remained relatively stable during our study (as indicated by λ = 1.00), changing climate and anthropogenic influences on California oak woodland could adversely influence demographic parameters and population dynamics and might also indicate effects of climate change on its ecologically sensitive habitat.

Universal rules of life: metabolic rates, biological times and the equal fitness paradigm

Here we review and extend the equal fitness paradigm (EFP) as an important step in developing and testing a synthetic theory of ecology and evolution based on energy and metabolism. The EFP states that all organisms are equally fit at steady state, because they allocate the same quantity of energy, ~ 22.4 kJ/g/generation to the production of offspring. On the one hand, the EFP may seem tautological, because equal fitness is necessary for the origin and persistence of biodiversity. On the other hand, the EFP reflects universal laws of life: how biological metabolism - the uptake, transformation and allocation of energy - links ecological and evolutionary patterns and processes across levels of organisation from: (1) structure and function of individual organisms, (2) life history and dynamics of populations, and (3) interactions and coevolution of species in ecosystems. The physics and biology of metabolism have facilitated the evolution of millions of species with idiosyncratic anatomy, physiology, behaviour and ecology but also with many shared traits and tradeoffs that reflect the single origin and universal rules of life.

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.

It's a trap: Optimizing detection of rare small mammals

Improving detection probabilities for rare species is critical when assessing presence or habitat associations. Our goal was to create a new small mammal trapping protocol that improved detection of rare species, such as the olive-backed pocket mouse (Perognathus fasciatus). We used three trap and bait types and trapped an area 4.4 times larger than the standard grid. We also assessed the effect of captures of non-target species on detection probability of pocket mice. Regardless of species, trap success was higher for Havaharts. We found that bait and trap type selection varied significantly by species, with pocket mice showing strongest selection for Havahart traps baited with bird seed. Increasing grid size, while maintaining a similar trapping effort, resulted in higher detection probability, although our analyses showed that effective grids can be about three-quarters of the size we use to achieve similar results. We were also able to demonstrate that by deploying a combination of different traps and baits it is possible to overcome the potential effect of non-target species (e.g., deer mice, Peromyscus maniculatus) on the detection probability of pocket mice. Our results show that simple changes to standard small-mammal trapping methods can dramatically increase the detectability of rare and elusive small mammals. Increasing detection probability of rare components of a community can improve the results and understanding of future studies.

The distribution and role of functional abundance in cross-scale resilience

The cross-scale resilience model suggests that system-level ecological resilience emerges from the distribution of species' functions within and across the spatial and temporal scales of a system. It has provided a quantitative method for calculating the resilience of a given system and so has been a valuable contribution to a largely qualitative field. As it is currently laid out, the model accounts for the spatial and temporal scales at which environmental resources and species are present and the functional roles species play but does not inform us about how much resource is present or how much function is provided. In short, it does not account for abundance in the distribution of species and their functional roles within and across the scales of a system. We detail the ways in which we would expect species' abundance to be relevant to the cross-scale resilience model based on the extensive abundance literature in ecology. We also put forward a series of testable hypotheses that would improve our ability to anticipate and quantify how resilience is generated, and how ecosystems will (or will not) buffer recent rapid global changes. This stream of research may provide an improved foundation for the quantitative evaluation of ecological resilience.

Improving estimates of environmental change using multilevel regression models of Ellenberg indicator values

Ellenberg indicator values (EIVs) are a widely used metric in plant ecology comprising a semi-quantitative description of species' ecological requirements. Typically, point estimates of mean EIV scores are compared over space or time to infer differences in the environmental conditions structuring plant communities-particularly in resurvey studies where no historical environmental data are available. However, the use of point estimates as a basis for inference does not take into account variance among species EIVs within sampled plots and gives equal weighting to means calculated from plots with differing numbers of species. Traditional methods are also vulnerable to inaccurate estimates where only incomplete species lists are available.We present a set of multilevel (hierarchical) models-fitted with and without group-level predictors (e.g., habitat type)-to improve precision and accuracy of plot mean EIV scores and to provide more reliable inference on changing environmental conditions over spatial and temporal gradients in resurvey studies. We compare multilevel model performance to GLMMs fitted to point estimates of mean EIVs. We also test the reliability of this method to improve inferences with incomplete species lists in some or all sample plots. Hierarchical modeling led to more accurate and precise estimates of plot-level differences in mean EIV scores between time-periods, particularly for datasets with incomplete records of species occurrence. Furthermore, hierarchical models revealed directional environmental change within ecological habitat types, which less precise estimates from GLMMs of raw mean EIVs were inadequate to detect. The ability to compute separate residual variance and adjusted R 2 parameters for plot mean EIVs and temporal differences in plot mean EIVs in multilevel models also allowed us to uncover a prominent role of hydrological differences as a driver of community compositional change in our case study, which traditional use of EIVs would fail to reveal. Assessing environmental change underlying ecological communities is a vital issue in the face of accelerating anthropogenic change. We have demonstrated that multilevel modeling of EIVs allows for a nuanced estimation of such from plant assemblage data changes at local scales and beyond, leading to a better understanding of temporal dynamics of ecosystems. Further, the ability of these methods to perform well with missing data should increase the total set of historical data which can be used to this end.

Linking phytoplankton community metabolism to the individual size distribution

Quantifying variation in ecosystem metabolism is critical to predicting the impacts of environmental change on the carbon cycle. We used a metabolic scaling framework to investigate how body size and temperature influence phytoplankton community metabolism. We tested this framework using phytoplankton sampled from an outdoor mesocosm experiment, where communities had been either experimentally warmed (+ 4 °C) for 10 years or left at ambient temperature. Warmed and ambient phytoplankton communities differed substantially in their taxonomic composition and size structure. Despite this, the response of primary production and community respiration to long- and short-term warming could be estimated using a model that accounted for the size- and temperature dependence of individual metabolism, and the community abundance-body size distribution. This work demonstrates that the key metabolic fluxes that determine the carbon balance of planktonic ecosystems can be approximated using metabolic scaling theory, with knowledge of the individual size distribution and environmental temperature.

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.

Functional and numerical responses of shrews to competition vary with mouse density

For decades, ecologists have debated the importance of biotic interactions (e.g., competition) and abiotic factors in regulating populations. Competition can influence patterns of distribution, abundance, and resource use in many systems but remains difficult to measure. We quantified competition between two sympatric small mammals, Keen's mice (Peromyscus keeni) and dusky shrews (Sorex monticolus), in four habitat types on Prince of Wales Island in Southeast Alaska. We related shrew density to that of mice using standardized regression models while accounting for habitat variables in each year from 2010-2012, during which mice populations peaked (2011) and then crashed (2012). Additionally, we measured dietary overlap and segregation using stable isotope analysis and kernel utilization densities and estimated the change in whole community energy consumption among years. We observed an increase in densities of dusky shrews after mice populations crashed in 2012 as expected under competitive release. In addition, competition coefficients revealed that the influence of Keen's mice was dependent on their density. Also in 2012, shrew diets shifted, indicating that they were able to exploit resources previously used by mice. Nonetheless, increases in shrew numbers only partially compensated for the community energy consumption because, as insectivores, they are unlikely to utilize all food types consumed by their competitors. In pre-commercially thinned stands, which exhibit higher diversity of resources compared to other habitat types, shrew populations were less affected by changes in mice densities. These spatially and temporally variable interactions between unlikely competitors, observed in a relatively simple, high-latitude island ecosystem, highlight the difficulty in assessing the role of biotic factors in structuring communities.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China

BACKGROUND

One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach.

RESULTS

As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which considered the spatial dispersion of species generated a taxonomic structure which proved to be more consistent with that in the observed community. As sampling sizes increased from 20 m × 20 m to 50 m × 50 m, the magnitudes of SESs of taxonomic ratios increased. Based on the phylogenetic analysis, we found that the Jiaohe plot was phylogenetically clustered at almost all scales. We detected significant phylogenetically overdispersion at the 20 m × 20 m and 30 m × 30 m scales in the Liangshui plot.

CONCLUSIONS

The results suggest that the effect of abiotic filtering is greater than the effects of interspecific competition in shaping the local community at almost all scales. Local processes influence the taxonomic structures, but their combined effects vary with the spatial scale. The taxonomic approach provides similar insights as the phylogenetic approach, especially when we applied a more conservative null model. Analysing taxonomic structure may be a useful tool for communities where well-resolved phylogenetic data are not available.

Community-level regulation of temporal trends in biodiversity

Many theoretical models of community dynamics predict that species richness (S) and total abundance (N) are regulated in their temporal fluctuations. We present novel evidence for widespread regulation of biodiversity. For 59 plant and animal assemblages from around the globe monitored annually for a decade or more, the majority exhibited regulated fluctuations compared to the null hypothesis of an unconstrained random walk. However, there was little evidence for statistical artifacts, regulation driven by correlations with average annual temperature, or local-scale compensatory fluctuations in S or N. In the absence of major environmental perturbations, such as urbanization or cropland transformation, species richness and abundance may be buffered and exhibit some resilience in their temporal trajectories. These results suggest that regulatory processes are occurring despite unprecedented environmental change, highlighting the need for community-level assessment of biodiversity trends, as well as extensions of existing theory to address open source pools and shifting environmental conditions.

Extra-metabolic energy use and the rise in human hyper-density

Humans, like all organisms, are subject to fundamental biophysical laws. Van Valen predicted that, because of zero-sum dynamics, all populations of all species in a given environment flux the same amount of energy on average. Damuth's 'energetic equivalence rule' supported Van Valen´s conjecture by showing a tradeoff between few big animals per area with high individual metabolic rates compared to abundant small species with low energy requirements. We use metabolic scaling theory to compare variation in densities and individual energy use in human societies to other land mammals. We show that hunter-gatherers occurred at densities lower than the average for a mammal of our size. Most modern humans, in contrast, concentrate in large cities at densities up to four orders of magnitude greater than hunter-gatherers, yet consume up to two orders of magnitude more energy per capita. Today, cities across the globe flux greater energy than net primary productivity on a per area basis. This is possible by importing enormous amounts of energy and materials required to sustain hyper-dense, modern humans. The metabolic rift with nature created by modern cities fueled largely by fossil energy poses formidable challenges for establishing a sustainable relationship on a rapidly urbanizing, yet finite planet.

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.

Fifteen forms of biodiversity trend in the Anthropocene

Humans are transforming the biosphere in unprecedented ways, raising the important question of how these impacts are changing biodiversity. Here we argue that our understanding of biodiversity trends in the Anthropocene, and our ability to protect the natural world, is impeded by a failure to consider different types of biodiversity measured at different spatial scales. We propose that ecologists should recognize and assess 15 distinct categories of biodiversity trend. We summarize what is known about each of these 15 categories, identify major gaps in our current knowledge, and recommend the next steps required for better understanding of trends in biodiversity.

The landscape of fear: the missing link to understand top-down and bottom-up controls of prey abundance?

Identifying factors that may be responsible for regulating the size of animal populations is a cornerstone in understanding population ecology. The main factors that are thought to influence population size are either resources (bottom-up), or predation (top-down), or interspecific competition (parallel). However, there are highly variable and often contradictory results regarding their relative strengths and influence. These varied results are often interpreted as indicating "shifting control" among the three main factors, or a complex, nonlinear relationship among environmental variables, resource availability, predation, and competition. We argue here that there is a "missing link" in our understanding of predator-prey dynamics. We explore whether the landscape-of-fear model can help us clarify the inconsistencies and increase our understanding of the roles, extent, and possible interactions of top-down, bottom-up, and parallel factors on prey population abundance. We propose two main predictions derived from the landscape-of-fear model: (1) for a single species, we suggest that as the makeup of the landscape of fear changes from relatively safe to relatively risky, bottom-up impacts switch from strong to weak as top-down impacts go from weak to strong; (2) for two or more species, interspecific competitive interactions produce various combinations of bottom-up, top-down, and parallel impacts depending on the dominant competing species and whether the landscapes of fear are shared or distinctive among competing species. We contend that these predictions could successfully explain many of the complex and contradictory results of current research. We test some of these predictions based on long-term data for small mammals from the Chihuahuan Desert in the United States, and Mexico. We conclude that the landscape-of-fear model does provide reasonable explanations for many of the reported studies and should be tested further to better understand the effects of bottom-up, top-down, and parallel factors on population dynamics.

Size-energy relationships in ecological communities

Hypotheses that relate body size to energy use are of particular interest in community ecology and macroecology because of their potential to facilitate quantitative predictions about species interactions and to clarify complex ecological patterns. One prominent size-energy hypothesis, the energetic equivalence hypothesis, proposes that energy use from shared, limiting resources by populations or size classes of foragers will be independent of body size. Alternative hypotheses propose that energy use will increase with body size, decrease with body size, or peak at an intermediate body size. Despite extensive study, however, size-energy hypotheses remain controversial, due to a lack of directly-measured data on energy use, a tendency to confound distinct scaling relationships, and insufficient attention to the ecological contexts in which predicted relationships are likely to occur. Our goal, therefore, was to directly evaluate size-energy hypotheses while clarifying how results would differ with alternate methods and assumptions. We comprehensively tested size-energy hypotheses in a vertebrate frugivore guild in a tropical forest in Madagascar. Our test of size-energy hypotheses, which is the first to examine energy intake directly, was consistent with the energetic equivalence hypothesis. This finding corresponds with predictions of metabolic theory and models of energy distribution in ecological communities, which imply that body size does not confer an advantage in competition for energy among populations or size classes of foragers. This result was robust to different assumptions about energy regulation. Our results from direct energy measurement, however, contrasted with those obtained with conventional methods of indirect inference from size-density relationships, suggesting that size-density relationships do not provide an appropriate proxy for size-energy relationships as has commonly been assumed. Our research also provides insights into mechanisms underlying local size-energy relationships and has important implications for predicting species interactions and for understanding the structure and dynamics of ecological communities.

An Experimental Test of Competition among Mice, Chipmunks, and Squirrels in Deciduous Forest Fragments

Mixed hardwood forests of the northeast United States support a guild of granivorous/omnivorous rodents including gray squirrels (Sciurus carolinensis), eastern chipmunks (Tamias striatus), and white-footed mice (Peromyscus leucopus). These species coincide geographically, co-occur locally, and consume similar food resources. Despite their idiosyncratic responses to landscape and patch variables, patch occupancy models suggest that competition may influence their respective distributions and abundances, and accordingly their influence on the rest of the forest community. Experimental studies, however, are wanting. We present the result of a large-scale experiment in which we removed white-footed mice or gray squirrels from small, isolated forest fragments in Dutchess County, New York, and added these mammals to other fragments in order to alter the abundance of these two species. We then used mark-recapture analyses to quantify the population-level and individual-level effects on resident mice, squirrels, and chipmunks. Overall, we found little evidence of competition. There were essentially no within-season numerical responses to changes in the abundance of putative competitors. Moreover, while individual-level responses (apparent survival and capture probability) did vary with competitor densities in some models, these effects were often better explained by site-specific parameters and were restricted to few of the 19 sites we studied. With only weak or nonexistent competition among these three common rodent species, we expect their patterns of habitat occupancy and population dynamics to be largely independent of one another.

Species diversity and community similarity in fluctuating environments: parametric approaches using species abundance distributions

Here we review recent advances in characterizing pattern of variation in community structure in space and time based on parametric approaches utilizing the full distribution of abundances of species rather than some summary indices. Assessment of biodiversity based on the structure of rank-abundance plots or simple species diversity indices, which describe properties of the sample of individuals, may reveal limited information about the underlying species abundance distribution of the community because the number of individuals counted are dependent on the sampling intensity. For instance, assuming Poisson sampling and an underlying lognormal species abundance distribution implies that observed abundances (counts) are a sample from a Poisson lognormal distribution. A convenient property of this distribution is that the estimate of σ(2) can be used as an inverse measure of species diversity in a community as well as the number of unobserved species can be estimated approximately without bias for unknown sampling intensities. If two communities can be described by a bivariate lognormal species abundance model, then the correlation between the log abundances of species in the two communities is an index of similarity that can be estimated without knowledge of sampling intensities using the bivariate Poisson lognormal distribution. This method is even applicable as an approximation when the abundance distribution deviates from the lognormal. An analysis of the interrelationship between the parameters of the lognormal species abundance distribution in communities of species from a wide variety of taxa shows that the canonical hypothesis of Preston in general, for a given number of species, gives far too large variances in the distribution of log abundances. A general feature in community dynamics is that a large component of the variance in the species abundance distribution is caused by heterogeneity among species in the population dynamics as well as environmental noise. This pattern is in contrast to the assumptions of the neutral theory of community dynamics. The choice of species abundance distribution should be a consequence of specific assumptions about the dynamics of the species. We suggest that such specific assumptions for the choice of species abundance model will facilitate more robust comparisons of changes in community structure in time and space.

Reversal in the relationship between species richness and turnover in a phytoplankton community

Negative relationships between species richness and the rate of compositional turnover are common, suggesting that diverse communities have greater stability than depauperate ones; however, the mechanistic basis for this pattern is still widely debated. Species richness and turnover can covary either because they are mechanistically linked or because they share common environmental drivers. Few empirical studies have combined long-term changes in community composition with multiple drivers of environmental change, and so little is known about how the underlying mechanisms of species coexistence interact with changes in the mean and variability of environmental conditions. Here, we use a 33 year long time series (1976-2008) of phytoplankton community composition from Lake Zurich, to examine how environmental variation influences the relationship between richness and annual turnover. We find that the relationship between richness and annual turnover reverses midway through the time series (1992-1993), leading to a hump-shaped relationship between species richness and annual turnover. Using structural equation modeling we show that annual turnover and diversity are independently associated with different drivers of environmental change. Furthermore, we find that the observed annual sequences of community assembly give rise to rates of species accumulation that are more heterogeneous through time than expected by chance, likely owing to a high proportion of species showing significant autocorrelation and to strong positive covariation in the occurrences of species.

Phylogenetic structure illuminates the mechanistic role of environmental heterogeneity in community organization

1. Diversity begets diversity. Numerous published positive correlations between environmental heterogeneity and species diversity indicate ubiquity of this phenomenon. Nonetheless, most assessments of this relationship are phenomenological and provide little insight into the mechanism whereby such positive association results. 2. Two unresolved issues could better illuminate the mechanistic basis to diversity begets diversity. First, as environmental heterogeneity increases, both productivity and the species richness that contributes to that productivity often increase in a correlated fashion thus obscuring the primary driver. Second, it is unclear how species are added to communities as diversity increases and whether additions are trait based. 3. We examined these issues based on 31 rodent communities in the central Mojave Desert. At each site, we estimated rodent species richness and characterized environmental heterogeneity from the perspectives of standing primary productivity and number of seed resources. We further examined the phylogenetic structure of communities by estimating the mean phylogenetic distance (MPD) among species and by comparing empirical phylogenetic distances to those based on random assembly from a regional species pool. 4. The relationship between rodent species diversity and environmental heterogeneity was positive and significant. Moreover, diversity of resources accounted for more unique variation than did total productivity, suggesting that variety and not total amount of resource was the driver of increased rodent diversity. Relationships between environmental heterogeneity and phylogenetic distance were negative and significant; species were significantly phylogenetically over-dispersed in communities of low environmental heterogeneity and became more clumped as environmental heterogeneity increased. 5. Results suggest that species diversity increases with environmental heterogeneity because a wider variety of resources allow greater species packing within communities.

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.