Showing papers in "Ecology in 2012"

Coverage‐based rarefaction and extrapolation: standardizing samples by completeness rather than size

Abstract: We propose an integrated sampling, rarefaction, and extrapolation methodology to compare species richness of a set of communities based on samples of equal completeness (as measured by sample coverage) instead of equal size. Traditional rarefaction or extrapolation to equal-sized samples can misrepresent the relationships between the richnesses of the communities being compared because a sample of a given size may be sufficient to fully characterize the lower diversity community, but insufficient to characterize the richer community. Thus, the traditional method systematically biases the degree of differences between community richnesses. We derived a new analytic method for seamless coverage-based rarefaction and extrapolation. We show that this method yields less biased comparisons of richness between communities, and manages this with less total sampling effort. When this approach is integrated with an adaptive coverage-based stopping rule during sampling, samples may be compared directly without rarefaction, so no extra data is taken and none is thrown away. Even if this stopping rule is not used during data collection, coverage-based rarefaction throws away less data than traditional size-based rarefaction, and more efficiently finds the correct ranking of communities according to their true richnesses. Several hypothetical and real examples demonstrate these advantages.

Uses and misuses of bioclimatic envelope modeling

Abstract: Bioclimatic envelope models use associations between aspects of climate and species' occurrences to estimate the conditions that are suitable to maintain viable populations. Once bioclimatic envelopes are characterized, they can be applied to a variety of questions in ecology, evolution, and conservation. However, some have questioned the usefulness of these models, because they may be based on implausible assumptions or may be contradicted by empirical evidence. We review these areas of contention, and suggest that criticism has often been misplaced, resulting from confusion between what the models actually deliver and what users wish that they would express. Although improvements in data and methods will have some effect, the usefulness of these models is contingent on their appropriate use, and they will improve mainly via better awareness of their conceptual basis, strengths, and limitations.

Responses of soil microbial communities to water stress: results from a meta-analysis

Abstract: Soil heterotrophic respiration and nutrient mineralization are strongly affected by environmental conditions, in particular by moisture fluctuations triggered by rainfall events. When soil moisture decreases, so does decomposers' activity, with microfauna generally undergoing stress sooner than bacteria and fungi. Despite differences in the responses of individual decomposer groups to moisture availability (e.g., bacteria are typically more sensitive than fungi to water stress), we show that responses of decomposers at the community level are different in soils and surface litter, but similar across biomes and climates. This results in a nearly constant soil-moisture threshold corresponding to the point when biological activity ceases, at a water potential of about -14 MPa in mineral soils and -36 MPa in surface litter. This threshold is shown to be comparable to the soil moisture value where solute diffusion becomes strongly inhibited in soil, while in litter it is dehydration rather than diffusion that likely limits biological activity around the stress point. Because of these intrinsic constraints and lack of adaptation to different hydro-climatic regimes, changes in rainfall patterns (primary drivers of the soil moisture balance) may have dramatic impacts on soil carbon and nutrient cycling.

Cross-validation of species distribution models: removing spatial sorting bias and calibration with a null model.

Abstract: Species distribution models are usually evaluated with cross-validation. In this procedure evaluation statistics are computed from model predictions for sites of presence and absence that were not used to train (fit) the model. Using data for 226 species, from six regions, and two species distribution modeling algorithms (Bioclim and MaxEnt), I show that this procedure is highly sensitive to "spatial sorting bias": the difference between the geographic distance from testing-presence to training-presence sites and the geographic distance from testing-absence (or testing-background) to training-presence sites. I propose the use of pairwise distance sampling to remove this bias, and the use of a null model that only considers the geographic distance to training sites to calibrate cross-validation results for remaining bias. Model evaluation results (AUC) were strongly inflated: the null model performed better than MaxEnt for 45% and better than Bioclim for 67% of the species. Spatial sorting bias and area under the receiver-operator curve (AUC) values increased when using partitioned presence data and random-absence data instead of independently obtained presence-absence testing data from systematic surveys. Pairwise distance sampling removed spatial sorting bias, yielding null models with an AUC close to 0.5, such that AUC was the same as null model calibrated AUC (cAUC). This adjustment strongly decreased AUC values and changed the ranking among species. Cross-validation results for different species are only comparable after removal of spatial sorting bias and/or calibration with an appropriate null model.

Measuring diversity: the importance of species similarity

Abstract: Realistic measures of biodiversity should reflect not only the relative abundances of species, but also the differences between them. We present a natural family of diversity measures taking both factors into account. This is not just another addition to the already long list of diversity indices. Instead, a single formula subsumes many of the most popular indices, including Shannon's, Simpson's, species richness, and Rao's quadratic entropy. These popular indices can then be used and understood in a unified way, and the relationships between them are made plain. The new measures are, moreover, effective numbers, so that percentage changes and ratio comparisons of diversity value are meaningful. We advocate the use of diversity profiles, which provide a faithful graphical representation of the shape of a community; they show how the perceived diversity changes as the emphasis shifts from rare to common species. Communities can usefully be compared by comparing their diversity profiles. We show by example that this is a far more subtle method than any relying on a single statistic. Some ecologists view diversity indices with suspicion, questioning whether they are biologically meaningful. By dropping the naive assumption that distinct species have nothing in common, working with effective numbers, and using diversity profiles, we arrive at a system of diversity measurement that should lay much of this suspicion to rest.

Woody encroachment decreases diversity across North American grasslands and savannas

Abstract: Woody encroachment is a widespread and acute phenomenon affecting grasslands and savannas worldwide. We performed a meta-analysis of 29 studies from 13 different grassland/savanna communities in North America to determine the consequences of woody encroachment on plant species richness. In all 13 communities, species richness declined with woody plant encroachment (average decline = 45%). Species richness declined more in communities with higher precipitation (r2 = 0.81) and where encroachment was associated with a greater change in annual net primary productivity (ANPP; r2 = 0.69). Based on the strong positive correlation between precipitation and ANPP following encroachment (r2 = 0.87), we hypothesize that these relationships occur because water-limited woody plants experience a greater physiological and demographic release as precipitation increases. The observed relationship between species richness and ANPP provides support for the theoretical expectation that a trade-off occurs between richness and productivity in herbaceous communities. We conclude that woody plant encroachment leads to significant declines in species richness in North American grassland/savanna communities.

Flexible and practical modeling of animal telemetry data: hidden Markov models and extensions

Abstract: We discuss hidden Markov-type models for fitting a variety of multistate random walks to wildlife movement data. Discrete-time hidden Markov models (HMMs) achieve considerable computational gains by focusing on observations that are regularly spaced in time, and for which the measurement error is negligible. These conditions are often met, in particular for data related to terrestrial animals, so that a likelihood-based HMM approach is feasible. We describe a number of extensions of HMMs for animal movement modeling, including more flexible state transition models and individual random effects (fitted in a non-Bayesian framework). In particular we consider so-called hidden semi-Markov models, which may substantially improve the goodness of fit and provide important insights into the behavioral state switching dynamics. To showcase the expediency of these methods, we consider an application of a hierarchical hidden semi-Markov model to multiple bison movement paths.

Mapping the niche space of soil microorganisms using taxonomy and traits

Abstract: The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.

Phylogenetic diversity promotes ecosystem stability

Abstract: Ecosystem stability in variable environments depends on the diversity of form and function of the constituent species. Species phenotypes and ecologies are the product of evolution, and the evolutionary history represented by co-occurring species has been shown to be an important predictor of ecosystem function. If phylogenetic distance is a surrogate for ecological differences, then greater evolutionary diversity should buffer ecosystems against environmental variation and result in greater ecosystem stability. We calculated both abundance-weighted and unweighted phylogenetic measures of plant community diversity for a long-term biodiversity–ecosystem function experiment at Cedar Creek, Minnesota, USA. We calculated a detrended measure of stability in aboveground biomass production in experimental plots and showed that phylogenetic relatedness explained variation in stability. Our results indicate that communities where species are evenly and distantly related to one another are more stable compared to c...

Interactions among lignin, cellulose, and nitrogen drive litter chemistry-decay relationships.

Abstract: Litter decay rates often correlate with the initial ratios of lignin:nitrogen (N) or lignin:cellulose in litter. However, the chemical and microbial mechanisms that give rise to these patterns are still unclear. To identify these mechanisms, we studied the decomposition of a model plant system, Arabidopsis thaliana, in which plants were manipulated to have low levels of lignin, cellulose, or litter N. Nitrogen fertilizer often increases the loss of cellulose, but it suppresses the breakdown of lignin in plant litter. To understand the mechanisms driving these patterns, we decomposed plants in litterbags for one year in control and N-fertilized plots in an Alaskan boreal forest. We found that litter N had a positive effect on total mass loss because it increased the loss of lignin, N, and soluble C. Lignin had a negative effect on rates of total litter mass loss due to decreases in the loss of cellulose and hemicellulose. Cellulose had a positive effect on lignin loss, supporting the concept of a "priming effect" for lignin breakdown. However, the low-cellulose plants also lost more of their original cellulose compared to the other plant types, indicating that decomposers mined the litter for cellulose despite the presence of lignin. Low-lignin litter had higher fungal biomass and N-acetyl glucosaminidase (NAG, a chitinase) activity, suggesting that lignin restricted fungal growth and may have influenced competitive interactions between decomposers. Nitrogen fertilization increased NAG activity in the early stages of decay. In the later stages, N fertilization led to increased cellulase activity on the litters and tended to reduce lignin losses. The transition over time from competition among decomposers to high cellulase activity and suppressed lignin loss under N fertilization suggests that, in N-limited systems, N fertilization may alter decomposer community structure by favoring a shift toward cellulose- and mineral-N users.

Gradient forests: calculating importance gradients on physical predictors

Abstract: In ecological analyses of species and community distributions there is interest in the nature of their responses to environmental gradients and in identifying the most important environmental variables, which may be used for predicting patterns of biodiversity. Methods such as random forests already exist to assess predictor importance for individual species and to indicate where along gradients abundance changes. However, there is a need to extend these methods to whole assemblages, to establish where along the range of these gradients the important compositional changes occur, and to identify any important thresholds or change points. We develop such a method, called "gradient forest," which is an extension of the random forest approach. By synthesizing the cross-validated R2 and accuracy importance measures from univariate random forest analyses across multiple species, sampling devices, and surveys, gradient forest obtains a monotonic function of each predictor that represents the compositional turnover along the gradient of the predictor. When applied to a synthetic data set, the method correctly identified the important predictors and delineated where the compositional change points occurred along these gradients. Application of gradient forest to a real data set from part of the Great Barrier Reef identified mud fraction of the sediment as the most important predictor, with highest compositional turnover occurring at mud fraction values around 25%, and provided similar information for other predictors. Such refined information allows for more accurate capturing of biodiversity patterns for the purposes of bioregionalization, delineation of protected areas, or designing of biodiversity surveys.

Effects of warming and grazing on soil N availability, species composition, and ANPP in an alpine meadow

Abstract: Uncertainty about the effects of warming and grazing on soil nitrogen (N) availability, species composition, and aboveground net primary production (ANPP) limits our ability to predict how global carbon sequestration will vary under future warming with grazing in alpine regions. Through a controlled asymmetrical warming (1.2/1.7 degrees C during daytime/nighttime) with a grazing experiment from 2006 to 2010 in an alpine meadow, we found that warming alone and moderate grazing did not significantly affect soil net N mineralization. Although plant species richness significantly decreased by 10% due to warming after 2008, we caution that this may be due to the transient occurrence or disappearance of some rare plant species in all treatments. Warming significantly increased graminoid cover, except in 2009, and legume cover after 2008, but reduced non-legume forb cover in the community. Grazing significantly decreased cover of graminoids and legumes before 2009 but increased forb cover in 2010. Warming significantly increased ANPP regardless of grazing, whereas grazing reduced the response of ANPP to warming. N addition did not affect ANPP in both warming and grazing treatments. Our findings suggest that soil N availability does not determine ANPP under simulated warming and that heavy grazing rather than warming causes degradation of the alpine meadows.

Proposing a resolution to debates on diversity partitioning

Abstract: There have been intense debates about the decomposition of regional diversity (gamma) into its within-community component (alpha) and between-community component (beta). Although a recent Ecology Forum achieved consensus in the use of "numbers equivalents" (Hill numbers) as the proper choice of diversity measure, three related major issues were still left unresolved. (1) What is the precise meaning of the "independence" or "statistical independence" of alpha diversity and beta diversity? (2) Which partitioning (additive vs. multiplicative) should be used for a given application? (3) What is the proper formula for alpha diversity, as there are two formulas in the literature? This paper proposes a possible resolution to each of these issues. For the first issue, we clarify the definitions of "independence" and "statistical independence" from two perspectives so that confusion about this issue can be cleared up. We also discuss the causes of dependence, so that the dependence relationship between any two diversity components in both partitioning schemes can be rigorously justified by theory and also intuitively understood by simulation. For the second issue, both multiplicative and additive beta diversities based on Hill numbers are useful measures and quantify different aspects of communities. However, neither can be directly applied to compare relative compositional similarity or differentiation across multiple regions with different numbers of communities because multiplicative beta diversity depends on the number of communities, and additive beta diversity additionally depends on alpha (equivalently, on gamma). Such dependences should be removed. We propose transformations to remove these dependences, and we show that the transformed multiplicative beta and additive beta both lead to the same classes of measures, which are always in a range of [0, 1] and thus can be used to compare relative similarity or differentiation among communities across multiple regions. These similarity measures include multiple-community generalizations of the Sorenson, Jaccard, Horn, and Morisita-Horn measures. For the third issue, we present some observations including a finding about which alpha formula produces independent alpha and beta components. These may help to resolve the choice of a proper formula for alpha diversity. Some related issues are also briefly discussed.

Life history theory predicts fish assemblage response to hydrologic regimes

Abstract: The hydrologic regime is regarded as the primary driver of freshwater ecosystems, structuring the physical habitat template, providing connectivity, framing biotic interactions, and ultimately selecting for specific life histories of aquatic organisms. In the present study, we tested ecological theory predicting directional relationships between major dimensions of the flow regime and life history composition of fish assemblages in perennial free-flowing rivers throughout the continental United States. Using long-term discharge records and fish trait and survey data for 109 stream locations, we found that 11 out of 18 relationships (61%) tested between the three life history strategies (opportunistic, periodic, and equilibrium) and six hydrologic metrics (two each describing flow variability, predictability, and seasonality) were statistically significant (P ≤ 0.05) according to quantile regression. Our results largely support a priori hypotheses of relationships between specific flow indices and relative prevalence of fish life history strategies, with 82% of all significant relationships observed supporting predictions from life history theory. Specifically, we found that (1) opportunistic strategists were positively related to measures of flow variability and negatively related to predictability and seasonality, (2) periodic strategists were positively related to high flow seasonality and negatively related to variability, and (3) the equilibrium strategists were negatively related to flow variability and positively related to predictability. Our study provides important empirical evidence illustrating the value of using life history theory to understand both the patterns and processes by which fish assemblage structure is shaped by adaptation to natural regimes of variability, predictability, and seasonality of critical flow events over broad biogeographic scales.

Revisiting the Evolution of Ecological Specialization, With Emphasis on Insect-Plant Interactions

Abstract: Ecological specialization is a fundamental and well-studied concept, yet its great reach and complexity limit current understanding in important ways. More than 20 years after the publication of D. J. Futuyma and G. Moreno's oft-cited, major review of the topic, we synthesize new developments in the evolution of ecological specialization. Using insect–plant interactions as a model, we focus on important developments in four critical areas: genetic architecture, behavior, interaction complexity, and macroevolution. We find that theory based on simple genetic trade-offs in host use is being replaced by more subtle and complex pictures of genetic architecture, and multitrophic interactions have risen as a necessary framework for understanding specialization. A wealth of phylogenetic data has made possible a more detailed consideration of the macroevolutionary dimension of specialization, revealing (among other things) bidirectionality in transitions between generalist and specialist lineages. Technological advances, including genomic sequencing and analytical techniques at the community level, raise the possibility that the next decade will see research on specialization spanning multiple levels of biological organization in non-model organisms, from genes to populations to networks of interactions in natural communities. Finally, we offer a set of research questions that we find to be particularly pressing and fruitful for future research on ecological specialization.

Phenological tracking enables positive species responses to climate change

Abstract: Earlier spring phenology observed in many plant species in recent decades provides compelling evidence that species are already responding to the rising global temperatures associated with anthropogenic climate change. There is great variability among species, however, in their phenological sensitivity to temperature. Species that do not phenologically “track” climate change may be at a disadvantage if their growth becomes limited by missed interactions with mutualists, or a shorter growing season relative to earlier-active competitors. Here, we set out to test the hypothesis that phenological sensitivity could be used to predict species performance in a warming climate, by synthesizing results across terrestrial warming experiments. We assembled data for 57 species across 24 studies where flowering or vegetative phenology was matched with a measure of species performance. Performance metrics included biomass, percent cover, number of flowers, or individual growth. We found that species that advanced thei...

Robustness of variance and autocorrelation as indicators of critical slowing down

Abstract: Ecosystems close to a critical threshold lose resilience, in the sense that perturbations can more easily push them into an alternative state. Recently, it has been proposed that such loss of resilience may be detected from elevated autocorrelation and variance in the fluctuations of the state of an ecosystem due to critical slowing down; the underlying generic phenomenon that occurs at critical thresholds. Here we explore the robustness of autocorrelation and variance as indicators of imminent critical transitions. We show both analytically and in simulations that variance may sometimes decrease close to a transition. This can happen when environmental factors fluctuate stochastically and the ecosystem becomes less sensitive to these factors near the threshold, or when critical slowing down reduces the ecosystem's capacity to follow high-frequency fluctuations in the environment. In addition, when available data is limited, variance can be systematically underestimated due to the prevalence of low frequencies close to a transition. By contrast, autocorrelation always increases toward critical transitions in our analyses. To exemplify this point, we provide cases of rising autocorrelation and increasing or decreasing variance in time series prior to past climate transitions.

Warming modifies trophic cascades and eutrophication in experimental freshwater communities

Abstract: Climate warming is occurring in concert with other anthropogenic changes to ecosystems. However, it is unknown whether and how warming alters the importance of top-down vs. bottom-up control over community productivity and variability. We performed a 16-month factorial experimental manipulation of warming, nutrient enrichment, and predator presence in replicated freshwater pond mesocosms to test their independent and interactive impacts. Warming strengthened trophic cascades from fish to primary producers, and it decreased the impact of eutrophication on the mean and temporal variation of phytoplankton biomass. These impacts varied seasonally, with higher temperatures leading to stronger trophic cascades in winter and weaker algae blooms under eutrophication in summer. Our results suggest that higher temperatures may shift the control of primary production in freshwater ponds toward stronger top-down and weaker bottom-up effects. The dampened temporal variability of algal biomass under eutrophication at higher temperatures suggests that warming may stabilize some ecosystem processes.

Stoichiometric controls of nitrogen and phosphorus cycling in decomposing beech leaf litter

Abstract: Resource stoichiometry (C:N:P) is an important determinant of litter decomposition. However, the effect of elemental stoichiometry on the gross rates of microbial N and P cycling processes during litter decomposition is unknown. In a mesocosm experiment, beech (Fagus sylvatica L.) litter with natural differences in elemental stoichiometry (C:N:P) was incubated under constant environmental conditions. After three and six months, we measured various aspects of nitrogen and phosphorus cycling. We found that gross protein depolymerization, N mineralization (ammonification), and nitrification rates were negatively related to litter C:N. Rates of P mineralization were negatively correlated with litter C:P. The negative correlations with litter C:N were stronger for inorganic N cycling processes than for gross protein depolymerization, indicating that the effect of resource stoichiometry on intracellular processes was stronger than on processes catalyzed by extracellular enzymes. Consistent with this, extracellular protein depolymerization was mainly limited by substrate availability and less so by the amount of protease. Strong positive correlations between the interconnected N and P pools and the respective production and consumption processes pointed to feed-forward control of microbial litter N and P cycling. A negative relationship between litter C:N and phosphatase activity (and between litter C:P and protease activity) demonstrated that microbes tended to allocate carbon and nutrients in ample supply into the production of extracellular enzymes to mine for the nutrient that is more limiting. Overall, the study demonstrated a strong effect of litter stoichiometry (C:N:P) on gross processes of microbial N and P cycling in decomposing litter; mineralization of N and P were tightly coupled to assist in maintaining cellular homeostasis of litter microbial communities.

Fear of the dark or dinner by moonlight? Reduced temporal partitioning among Africa's large carnivores

Abstract: Africa is home to the last intact guild of large carnivores and thus provides the only opportunity to investigate mechanisms of coexistence among large predator species. Strong asymmetric dominance hierarchies typically characterize guilds of large carnivores; but despite this asymmetry, subdominant species may persist alongside their stronger counterparts through temporal partitioning of habitat and resources. In the African guild, the subdominant African wild dogs and cheetahs are routinely described as diurnal and crepuscular. These activity patterns have been interpreted to result from the need to avoid encounters with the stronger, nocturnal spotted hyenas and lions. However, the idea that diel activity patterns of carnivore species are strongly shaped by competition and predation has recently been challenged by new observations. In a three-year study in the Okavango Delta, we investigated daily activity patterns and temporal partitioning for wild dogs, cheetahs, spotted hyenas and lions by fitting radio collars that continuously recorded activity bursts, to a total of 25 individuals. Analysis of activity patterns throughout the 24-h cycle revealed an unexpectedly high degree of temporal overlap among the four species. This was mainly due to the extensive and previously undescribed nocturnal activity of wild dogs and cheetahs. Their nocturnal activity fluctuated with the lunar cycle, represented up to 40% of the diel activity budget and was primarily constrained by moonlight availability. In contrast, the nocturnal activity patterns of lions and hyenas were unaffected by moonlight and remained constant over the lunar cycle. Our results suggest that other ecological factors such as optimal hunting conditions have shaped the diel activity patterns of subdominant, large predators. We suggest that they are ''starvation driven'' and must exploit every opportunity to obtain a meal. The benefits of activity on moonlit nights therefore offset the risks of encountering night-active predators and competitors.

Functional species pool framework to test for biotic effects on community assembly

Abstract: Functional trait differences among species are increasingly used to infer the effects of biotic and abiotic processes on species coexistence. Commonly, the trait diversity observed within communities is compared to patterns simulated in randomly generated communities based on sampling within a region. The resulting patterns of trait convergence and divergence are assumed to reveal abiotic and biotic processes, respectively. However, biotic processes such as competition can produce both trait divergence and convergence, through either excluding similar species (niche differences, divergence) or excluding dissimilar species (weaker competitor exclusion, convergence). Hence, separating biotic and abiotic processes that can produce identical patterns of trait diversity, or even patterns that neutralize each other, is not feasible with previous methods. We propose an operational framework in which the functional trait dissimilarity within communities (FDcomm) is compared to the corresponding trait dissimilarity expected from the species pool (i.e., functional species pool diversity, FDpool). FDpool includes the set of potential species for a site delimited by the operating environmental and dispersal limitation filters. By applying these filters, the resulting pattern of trait diversity is consistent with biotic processes, i.e., trait divergence (FDcomm > FDpool) indicates niche differentiation, while trait convergence (FDcomm < FDpool) indicates weaker competitor exclusion. To illustrate this framework, with its potential application and constraints, we analyzed both simulated and field data. The functional species pool framework more consistently detected the simulated trait diversity patterns than previous approaches. In the field, using data from plant communities of typical Northern European habitats in Estonia, we found that both niche-based and weaker competitor exclusion influenced community assembly, depending on the traits and community considered. In both simulated and field data, we demonstrated that only by estimating the species pool of a site is it possible to differentiate the patterns of trait dissimilarity produced by operating biotic processes. The framework, which can be applied with both functional and phylogenetic diversity, enables a reinterpretation of community assembly processes. Solving the challenge of defining an appropriate reference species pool for a site can provide a better understanding of community assembly.

Daphne: a dated phylogeny of a large European flora for phylogenetically informed ecological analyses

Abstract: This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, The Netherlands, and Switzerland, totaling 4685 species. The phylogeny thus encompasses all species in the trait databases BIOLFLOR, PLANTATT, and BioBase 2003. The topology of the phylogentic tree is based on a backbone family phylogeny of the Angiosperm Phylogeny Group III. Subsequently, partial phylogenetic subtrees derived from a total of 518 recent molecular studies were manually pruned onto the backbone tree, using multi-gene consensus topologies if possible. Similarly, 1103 internal nodes and the root node were dated based on 261 recent studies. Finally, an ultrametric tree was calculated by placing undated nodes evenly between dated nodes. The phylogeny provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a la...

Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities

Abstract: The study of biodiversity has tended to focus primarily on relatively information-poor measures of species diversity. Recently, many studies of local diversity (alpha diversity) have begun to use measures of functional and phylogenetic alpha diversity. Investigations into the phylogenetic and functional dissimilarity (beta diversity) of communities have been far less numerous, but these dissimilarity measures have the potential to infer the mechanisms underlying community assembly and dynamics. Here, we relate levels of phylogenetic and functional alpha diversity to levels of phylogenetic and functional beta diversity to infer the mechanism or mechanisms responsible for the assembly of tree communities in six forests located in tropical and temperate latitudes. The results show that abiotic filtering plays a role in structuring local assemblages and governing spatial turnover in community composition and that phylogenetic measures of alpha and beta diversity are not strong predictors of functional alpha and beta diversity in the forests studied.

Spatially integrated assessment reveals widespread changes in penguin populations on the Antarctic Peninsula.

Abstract: As important marine mesopredators and sensitive indicators of Antarctic ecosystem change, penguins have been a major focus of long-term biological research in the Antarctic. However, the vast majority of such studies have been constrained by logistics and relate mostly to the temporal dynamics of individual breeding populations from which regional trends have been inferred, often without regard for the complex spatial heterogeneity of population processes and the underlying environmental conditions. Integrating diverse census data from 70 breeding sites across 31 years in a robust, hierarchical analysis, we find that trends from intensely studied populations may poorly reflect regional dynamics and confuse interpretation of environmental drivers. Results from integrated analyses confirm that Pygoscelis adeliae (Adelie Penguins) are decreasing at almost all locations on the Antarctic Peninsula. Results also resolve previously contradictory studies and unambiguously establish that P. antarctica (Chinstrap Penguins), thought to benefit from decreasing sea ice, are instead declining regionally. In contrast, another open-water species, P. papua (Gentoo Penguin), is increasing in abundance and expanding southward. These disparate population trends accord with recent mechanistic hypotheses of biological change in the Southern Ocean and highlight limitations of the influential but oversimplified "sea ice" hypothesis. Aggregating population data at the regional scale also allows us to quantify rates of regional population change in a way not previously possible.

Persistent carry‐over effects of planktonic exposure to ocean acidification in the Olympia oyster

Abstract: Predicting impacts of global environmental change is challenging due to the complex life cycles that characterize many terrestrial and aquatic taxa. Different life stages often interact with the physical environment in distinct ways, and a growing body of work suggests that stresses experienced during one life stage can “carry over” to influence subsequent stages. Assessments of population responses to environmental perturbation must therefore consider how effects might propagate across life-history transitions. We investigated consequences of ocean acidification (decreased pH and carbonate saturation) for early life stages of the Olympia oyster (Ostrea lurida), a foundation species in estuaries along the Pacific coast of North America. We reared oysters at three levels of seawater pH, including a control (8.0) and two additional levels (7.9 and 7.8). Oysters were cultured through their planktonic larval period to metamorphosis and into early juvenile life. Larvae reared under pH 7.8 exhibited a 15% decre...

Wolves–coyotes–foxes: a cascade among carnivores

Abstract: Due to the widespread eradication of large canids and felids, top predators in many terrestrial ecosystems are now medium-sized carnivores such as coyotes. Coyotes have been shown to increase songbird and rodent abundance and diversity by suppressing populations of small carnivores such as domestic cats and foxes. The restoration of gray wolves to many parts of North America, however, could alter this interaction chain. Here we use a 30-year time series of wolf, coyote, and fox relative abundance from the state of Minnesota, USA, to show that wolves suppress coyote populations, which in turn releases foxes from top-down control by coyotes. In contrast to mesopredator release theory, which has often considered the consequence of top predator removal in a three-species interaction chain (e.g., coyote-fox-prey), the presence of the top predator releases the smaller predator in a four-species interaction chain. Thus, heavy predation by abundant small predators might be more similar to the historical ecosystem before top-predator extirpation. The restructuring of predator communities due to the loss or restoration of top predators is likely to alter the size spectrum of heavily consumed prey with important implications for biodiversity and human health.

Landscape-scale resources promote colony growth but not reproductive performance of bumble bees

Abstract: Variation in the availability of food resources over space and time is a likely driver of how landscape structure and composition affect animal populations. Few studies, however, have directly assessed the spatiotemporal variation in resource availability that arises from landscape pattern, or its effect on populations and population dynamic parameters. We tested the effect of floral resource availability at the landscape scale on the numbers of worker, male, and queen offspring produced by bumble bee, Bombus vosnesenskii, colonies experimentally placed within complex agricultural-natural landscapes. We quantified flower densities in all land use types at different times of the season and then used these data to calculate spatially explicit estimates of floral resources surrounding each colony. Floral availability strongly correlated with landscape structure, and different regions of the landscape showed distinct seasonal patterns of floral availability. The floral resources available in the landscape surrounding a colony positively affected the number of workers and males it produced. Production was more sensitive to early- than to later-season resources. Floral resources did not significantly affect queen production despite a strong correlation between worker number and queen number among colonies. No landscape produced high floral resources during both the early and late season, and seasonal consistency is likely required for greater queen production. Floral resources are important determinants of colony growth and likely affect the pollination services provided by bumble bees at a landscape scale. Spatiotemporal variation in floral resources across the landscape precludes a simple relationship between resources and reproductive success as measured by queens, but nonetheless likely influences the total abundance of bumble bees in our study region.

Sinks for nitrogen inputs in terrestrial ecosystems: a meta‐analysis of 15N tracer field studies

Abstract: Effects of anthropogenic nitrogen (N) deposition and the ability of terrestrial ecosystems to store carbon (C) depend in part on the amount of N retained in the system and its partitioning among plant and soil pools. We conducted a meta-analysis of studies at 48 sites across four continents that used enriched 15N isotope tracers in order to synthesize information about total ecosystem N retention (i.e., total ecosystem 15N recovery in plant and soil pools) across natural systems and N partitioning among ecosystem pools. The greatest recoveries of ecosystem 15N tracer occurred in shrublands (mean, 89.5%) and wetlands (84.8%) followed by forests (74.9%) and grasslands (51.8%). In the short term (< 1 week after 15N tracer application), total ecosystem 15N recovery was negatively correlated with fine-root and soil 15N natural abundance, and organic soil C and N concentration but was positively correlated with mean annual temperature and mineral soil C:N. In the longer term (3-18 months after 15N tracer application), total ecosystem 15N retention was negatively correlated with foliar natural-abundance 15N but was positively correlated with mineral soil C and N concentration and C:N, showing that plant and soil natural-abundance 15N and soil C:N are good indicators of total ecosystem N retention. Foliar N concentration was not significantly related to ecosystem 15N tracer recovery, suggesting that plant N status is not a good predictor of total ecosystem N retention. Because the largest ecosystem sinks for 15N tracer were below ground in forests, shrublands, and grasslands, we conclude that growth enhancement and potential for increased C storage in aboveground biomass from atmospheric N deposition is likely to be modest in these ecosystems. Total ecosystem 15N recovery decreased with N fertilization, with an apparent threshold fertilization rate of 46 kg N x ha(-1) x yr(-1) above which most ecosystems showed net losses of applied 15N tracer in response to N fertilizer addition.

Temporal turnover in the composition of tropical tree communities: functional determinism and phylogenetic stochasticity

Abstract: The degree to which turnover in biological communities is structured by deterministic or stochastic factors and the identities of influential deterministic factors are fundamental, yet unresolved, questions in ecology. Answers to these questions are particularly important for projecting the fate of forests with diverse disturbance histories worldwide. To uncover the processes governing turnover we use species-level molecular phylogenies and functional trait data sets for two long-term tropical forest plots with contrasting disturbance histories: one forest is older-growth, and one was recently disturbed. Having both phylogenetic and functional information further allows us to parse out the deterministic influences of different ecological filters. With the use of null models we find that compositional turnover was random with respect to phylogeny on average, but highly nonrandom with respect to measured functional traits. Furthermore, as predicted by a deterministic assembly process, the older-growth and disturbed forests were characterized by less than and greater than expected functional turnover, respectively. These results suggest that the abiotic environment, which changes due to succession in the disturbed forest, strongly governs the temporal dynamics of disturbed and undisturbed tropical forests. Predicting future changes in the composition of disturbed and undisturbed forests may therefore be tractable when using a functional-trait-based approach.

The natives are restless, but not often and mostly when disturbed

Abstract: The argument that the threat posed by introduced species is overblown is often buttressed by the observation that native species sometimes also become invasive. An examination of the literature on plant invasions in the United States shows that six times more nonnative species have been termed invasive than native species, and that a member of the naturalized nonnative pool is 40 times more likely than a native species to be perceived as invasive. In the great majority of instances in which a native plant species is seen as invasive, the invasion is associated with an anthropogenic disturbance, especially changed fire or hydrological regime, livestock grazing, and changes wrought by an introduced species. These results suggest that natives are significantly less likely than nonnatives to be problematic for local ecosystems.