Implications of scale for patterns and processes in stream ecology

Abstract Although the scale-dependence of ecological patterns and processes is recognized by freshwater ecologists, current knowledge of scale effects is rudimentary and non-quantitative. We review issues of spatial and temporal scale in this paper to highlight conceptual problems relating to scale and some potential solutions. We present examples of how the spatial scale of a study influences observed patterns and their interpretation, and discuss how the size of an experimental arena influences the degree to which the dynamics of studied populations are influenced by exchange processes (immigration and emigration). The results of small-scale field experiments in streams will often be strongly influenced by the per capita exchange rates of organisms and differences in exchange rates may explain differences in the perceived effects of stream manipulations across scales. Spatial extent also influences the amount of spatial heterogeneity within a study site or arena, with important consequences for the outcome of predator-prey interactions. We suggest that changes in the availability of prey refuges may help explain why predator manipulations in streams appear to weaken as arena size increases. We also recommend that new techniques for decomposing and quantifying spatial heterogeneity be applied to characterize scale-dependent variation in freshwater systems. Lastly, we discuss the pitfalls of mismatching the temporal scale of experiments and models. Models incorporating spatial heterogeneity and the behaviour of organisms are needed to predict the short-term outcome of perturbations in streams, whereas models predicting long-term dynamics will need to integrate the impacts of episodic disturbance and all life history stages of organisms. In general, we recommend that freshwater ecologists undertake more multi-scale sampling and experimentation to examine patterns and processes at multiple scales, and make greater attempts to match the scales of their observations and experiments to the characteristic scales of the phenomena that they investigate.     

Dispersal scales up the biodiversity–productivity relationship in an experimental source-sink metacommunity

The influence of biodiversity on ecosystem functioning is a major concern of ecological research. However, the biodiversity–ecosystem functioning relationship has very often been studied independently from the mechanisms allowing coexistence. By considering the effects of dispersal and niche partitioning on diversity, the metacommunity perspective predicts a spatial scale-dependence of the shape of the relationship. Here, we present experimental evidence of such scale-dependent patterns. After approximately 500 generations of diversification in a spatially heterogeneous environment, we measured functional diversity (FD) and productivity at both local and regional scales in experimental source-sink metacommunities of the bacterium Pseudomonas fluorescens SBW25. At the regional scale, environmental heterogeneity yielded high levels of FD and we observed a positive correlation between diversity and productivity. At the local scale, intermediate dispersal increased local FD through a mass effect but there was no correlation between diversity and productivity. These experimental results underline the importance of considering the mechanisms maintaining biodiversity and the appropriate spatial scales in understanding its relationship with ecosystem functioning.     

Integrating methods that investigate how complementarity influences ecosystem functioning

Separating the mechanisms that influence ecosystem functioning has been a goal of recent high profile experiments. Integrating the various experimental and analytical methods that attempt this goal across terrestrial and aquatic ecosystems, as well as careful definition of 'complementarity', produces novel insights and valuable lessons about new directions for research. (1) Experimental designs differ in temporal scale and whether standing stock or another ecosystem process was the response variable. (2) Mathematically identical variables in different designs have contrasting ecological interpretations. For example, different sets of ecological processes can contribute to different variables in different experimental designs. (3) The frequency of transgressive overyielding of standing stock (e.g. total above ground biomass) in polycultures implies little about the prevalence of transgressive overyielding in other ecosystem processes. (4) Measuring the contribution to ecosystem functioning of individual species, rather than just total ecosystem functioning of a polyculture, is not essential for estimating effects of complementarity. (5) Further research will profit from distinguishing standing stock from all other ecosystem functions. (6) None of the analytic methods can distinguish the effects of individual processes or mechanisms such as resource use differentiation, facilitation, or allelopathy, for which additional experimental treatments are required.     

Scale-dependence of movement rates in stream invertebrates

We used analytical models and random walk simulations in a one-dimensional habitat to study the scale-dependence of migration rates in stream invertebrates. Our models predict that per capita migration rate is inversely proportional to patch length when patches are large compared to the scale of movements. When patches are small the scale-dependence is weaker and primarily determined by the length of individual movements (steps) relative to patch size. Laboratory experiments using isopods ( Asellus aquaticus L . ) and mayfly nymphs ( Baetis sp.) confirmed that the strength of the scale-dependence decreased with increasing step length.
For the case when step length distributions follow an exponential probability distribution, which is often the case for stream organisms, we provide a simple model that allows the scale-dependence to be predicted from the mean step length. We fitted this model to published field data on drift densities at different downstream distances from a net that blocks the drift from upstream areas. Agreement between model and data was excellent in most cases. We then used already published data on the length of induced drift movements to predict the scale-dependence that was observed in block experiments performed in the same system. Predicted and observed scale-dependence showed very close agreement.
We conclude that our models and published data on drift distances can be used to calculate the expected scale-dependence of per capita emigration rates for a large number of taxa under a wide range of environmental conditions.     

Are we selecting appropriate metrics to assess human impacts on biodiversity?

Biased and subjective choices of metrics to be used in ecological studies could lead researchers to reach misleading conclusions regarding patterns of biodiversity response to human disturbances. Nevertheless, little attention has been given to the choices of variables in the majority of studies published to date. Here, we used the literature concerning land use change effects on dung beetles to assess the extent to which variables commonly employed in ecological studies correspond to those deemed to be most important by researchers of the same studies. Specifically, we examined both biodiversity (response) and environmental (explanatory) metrics from a comprehensive literature review and compared their use with their relative importance, according to a survey of the authors of the studies. Our results highlight marked disparities between researchers opinion expressed in our survey and their choice of variables in published papers. We suggest that these disparities are due to the high costs of sampling and processing some variables, logistical constraints and different perceptions of importance amongst researchers. We highlight the importance of these issues for our understanding of the biodiversity consequences of land use change, and highlight some recommendations for alleviating this issue.     

生物多样性与生态系统功能:最新的进展与动向

生物多样性与生态系统功能的关系及其内在机制是当前生态学领域的重大科学问题。 2 0 0 2年以来人们不再过多地纠缠于“抽样 -互补之争” ,对这一世纪课题的认识又有了新的进展。 (1)人们开始运用已有的知识揭示更大时间和空间尺度上的物种多样性 -生态系统功能关系。多样性作用机制可能存在着动态变化———“抽样向互补转型” :群落建立初期 ,抽样效应是主要的多样性作用机制 ;随时间推移 ,生态位互补成为主要机制。理论研究则预测 :局域尺度上生态系统功能与物种多样性呈现单峰曲线关系 ,在区域尺度上为单调上升关系 ;(2 )非生物因素与多样性 -生产力的交互关系吸引了许多实验研究。人们发现 :物种多样性 -生产力关系可能会受到资源供给率和环境扰动的修正 ,环境因素可能是多样性 -生产力关系的幕后操纵者 ;(3)人们开始重视营养级相互作用对于多样性 -生态系统功能关系的影响 ,生态位互补和抽样假说开始被扩展运用到消费者营养级上 ;(4 )人们开始认真思考物种共存机制在多样性 -生态系统功能关系的形成中所扮演的角色。理论模型研究表明 ,不同的物种共存机制会导致不同的多样性 -生产力关系     

Direct experimental evidence for alternative stable states: a review

A large number of studies have presented empirical arguments for the existence of alternative stable states (ASS) in a wide range of ecological systems. However, most of these studies have used non-manipulative, indirect methods, which findings remain open for alternative explanations. Here, we review the direct evidence for ASS resulting from manipulation experiments. We distinguish four conclusive experimental approaches which test for predictions made by the hysteresis effect: (1) discontinuity in the response to an environmental driving parameter, (2) lack of recovery potential after a perturbation, (3) divergence due to different initial conditions and (4) random divergence. Based on an extensive literature search we found 35 corresponding experiments. We assessed the ecological stability of the reported contrasting states using the minimum turnover of individuals in terms of life span and classified the studies according to 4 categories: (1) experimental system, (2) habitat type, (3) involved organisms and (4) theoretical framework. 13 experiments have directly demonstrated the existence of alternative stable states while 8 showed the absence of ASS in other cases. 14 experiments did not fulfil the requirements of a conclusive test, mostly because they applied a too short time scale. We found a bias towards laboratory experiments compared to field experiments in demonstrating bistability. There was no clear pattern of the distribution of ASS over categories. The absence of ASS in 38% of the tested systems indicates that ASS are just one possibility of how ecological systems can behave. The relevance of the concept of ASS for natural systems is discussed, in particular under consideration of the observed laboratory bias, perturbation frequency and variable environments. It is argued, that even for a permanently transient system, alternative attractors may still be of relevance.     

Designing ecological climate change impact assessments to reflect key climatic drivers

Identifying the climatic drivers of an ecological system is a key step in assessing its vulnerability to climate change. The climatic dimensions to which a species or system is most sensitive – such as means or extremes – can guide methodological decisions for projections of ecological impacts and vulnerabilities. However, scientific workflows for combining climate projections with ecological models have received little explicit attention. We review Global Climate Model (GCM) performance along different dimensions of change and compare frameworks for integrating GCM output into ecological models. In systems sensitive to climatological means, it is straightforward to base ecological impact assessments on mean projected changes from several GCMs. Ecological systems sensitive to climatic extremes may benefit from what we term the ‘model space’ approach: a comparison of ecological projections based on simulated climate from historical and future time periods. This approach leverages the experimental framework used in climate modeling, in which historical climate simulations serve as controls for future projections. Moreover, it can capture projected changes in the intensity and frequency of climatic extremes, rather than assuming that future means will determine future extremes. Given the recent emphasis on the ecological impacts of climatic extremes, the strategies we describe will be applicable across species and systems. We also highlight practical considerations for the selection of climate models and data products, emphasizing that the spatial resolution of the climate change signal is generally coarser than the grid cell size of downscaled climate model output. Our review illustrates how an understanding of how climate model outputs are derived and downscaled can improve the selection and application of climatic data used in ecological modeling.     

Molecular ecology of parasites: elucidating ecological and microevolutionary processes

We review studies that have used molecular markers to address ecological and microevolutionary processes in parasites. Our goal is to highlight areas of research that may be of particular interest in relation to the parasitic lifestyle, and to draw attention to areas that require additional study. Topics include species identification, phylogeography, host specificity and speciation, population genetic structure, modes of reproduction and transmission patterns, and searching for loci under selection.     

Coralline algae (Rhodophyta) in a changing world: integrating ecological,physiological, and geochemical responses to global change

Coralline algae are globally distributed benthic primary producers that secrete calcium carbonate skeletons. In the context of ocean acidification, they have received much recent attention due to the potential vulnerability of their high‐Mg calcite skeletons and their many important ecological roles. Herein, we summarize what is known about coralline algal ecology and physiology, providing context to understand their responses to global climate change. We review the impacts of these changes, including ocean acidification, rising temperatures, and pollution, on coralline algal growth and calcification. We also assess the ongoing use of coralline algae as marine climate proxies via calibration of skeletal morphology and geochemistry to environmental conditions. Finally, we indicate critical gaps in our understanding of coralline algal calcification and physiology and highlight key areas for future research. These include analytical areas that recently have become more accessible, such as resolving phylogenetic relationships at all taxonomic ranks, elucidating the genes regulating algal photosynthesis and calcification, and calibrating skeletal geochemical metrics, as well as research directions that are broadly applicable to global change ecology, such as the importance of community‐scale and long‐term experiments in stress response.     

Appropriate spatial scales for studies of reef-fish ecology

Abstract Coral-reef systems are conspicuously multi-scalar, with scales set by reef-fish biology, by ecological processes that act upon them and by the architectural patchiness of the coral-reef environment in which they reside. Empirical ecological studies cannot be executed in a way that is independent of spatial scale, and results are inextricably scale-dependent. Further, although the question asked and the measurements planned will suggest appropriate scales, it is often the case in these multi-scalar systems that there is no single correct scale at which to sample. Instead, there must be a process of compromise in designing projects, an awareness of scale in implementing them and careful consideration of the scale-dependence of the results. Some useful principles are presented to help with the process of project design and interpretation.     

Hierarchical partitioning as an interpretative tool in multivariate inference

Abstract Much of biogeography, conservation and evolutionary biology, and ecology involves very large spatial and temporal extents. Direct manipulation to test hypotheses is usually almost impossible at appropriate scales so that multivariate modelling and especially regression are used to draw causal inferences about which ‘independent’ variables influence the distribution and abundances of species. Such inferences clearly are crucial for the successful management of biological resources and for conserving threatened species. A succession of regression approaches has arisen, many of which yield inconsistent implications. The main problem has been the quest for one (the ‘best’ or the ‘optimal’) regression model from which the impacts of independent variables are inferred. This note is to draw the attention of ecologists to a relatively recent method, hierarchical partitioning, that does not aim to identify a best regression model as such but rather uses all models in a regression hierarchy to distinguish those variables that have high independent correlations with the dependent variable. Such variables are likely to be most influential in controlling variation in the dependent variable. Hierarchical partitioning is not to be regarded as a substitute for experimental manipulation when that is appropriate, but it is likely to produce better deductions than common regression approaches in the many ecological situations in which manipulation is impossible or of doubtful value.     

Miniaturizing landscapes to understand species distributions

Species’ geographic distributions shape global patterns of biodiversity and therefore have long been of interest to ecology and conservation. Theory has generated valuable hypotheses about how landscape structure, dispersal, biotic interactions and evolution shape range dynamics, but most predictions have not been tested on real organisms because key variables are difficult to isolate, replicate or manipulate in natural ecosystems. An exciting and rapidly emerging approach is to extend classical microcosm and mesocosm systems to create experimental ‘micro-landscapes’. By enabling researchers to manipulate geographic features of interest, replicate landscapes, control colonization and follow dynamics across evolutionary timescales, micro-landscapes allow explicit tests of the ecological and evolutionary underpinnings of species distributions. Here we review the micro-landscape systems being used to advance biogeography, the major insights they have generated thus far, and the features that limit their application to some scenarios. We end by highlighting important questions about species’ biogeography that are ripe for testing with experimental micro-landscapes, particularly those of immediate concern given rapid global change, such as range contractions and constraints to range expansion.     

Integration of ‘omics’ data in aging research: from biomarkers to systems biology

Age is the strongest risk factor for many diseases including neurodegenerative disorders, coronary heart disease, type 2 diabetes and cancer. Due to increasing life expectancy and low birth rates, the incidence of age‐related diseases is increasing in industrialized countries. Therefore, understanding the relationship between diseases and aging and facilitating healthy aging are major goals in medical research. In the last decades, the dimension of biological data has drastically increased with high‐throughput technologies now measuring thousands of (epi) genetic, expression and metabolic variables. The most common and so far successful approach to the analysis of these data is the so‐called reductionist approach. It consists of separately testing each variable for association with the phenotype of interest such as age or age‐related disease. However, a large portion of the observed phenotypic variance remains unexplained and a comprehensive understanding of most complex phenotypes is lacking. Systems biology aims to integrate data from different experiments to gain an understanding of the system as a whole rather than focusing on individual factors. It thus allows deeper insights into the mechanisms of complex traits, which are caused by the joint influence of several, interacting changes in the biological system. In this review, we look at the current progress of applying omics technologies to identify biomarkers of aging. We then survey existing systems biology approaches that allow for an integration of different types of data and highlight the need for further developments in this area to improve epidemiologic investigations.     

Conservation and non-conservation of genetic pathways in eye specification

In this review we highlight two genetic pathways important for eye morphogenesis that are partially conserved between flies and vertebrates. Initially we focus on the ey paradigm and establish which aspects of this genetic hierarchy are conserved in vertebrates. We discuss experiments that evaluate the non-linear relationship amongst the genes of the hierarchy with a concentration on vertebrate functional genetics. We specifically consider the Six genes and their relationship to sine oculis, as tremendous amounts of new data have emerged on this topic. Finally, we highlight similarities between Shh/Hh directed morphogenesis mediated by basic Helix-Loop-Helix factors in vertebrate retinal cell specification and in specification of fly photoreceptors.     

Complex patterns of temperature sensitivity,not ecological traits,dictate diverse species responses to climate change

Despite widespread interest in describing and forecasting the impacts of climate change on species distributions, poor understanding of the climate variables that shape distributions and conflicting perspectives on the role that species traits play in mediating shifts have limited our ability to interpret and project changes in species distributions. Using standardized survey data along the northeast US continental shelf, we assessed the historical exposure and sensitivity of 81 species of marine chordates, arthropods, and molluscs to 24 sea surface temperature (SST) variables in two seasons. By comparing temperature trends in geographies available to species against temperature trends in geographies used by them we were able to identify which variables species track consistently through space and time. Logistic regression analyses were then used to assess whether species traits affected the likelihood of niche tracking while accounting for the season and temporal window in which temperatures were summarized and methodological constraints that might have limited our ability to detect tracking responses. A slight majority of species (52%) clearly shifted their distributions to track at least one temperature variable through space and time. Tracking rates were much lower on a per variable basis (5.1% of 3432 variables), despite widespread exposure to changing temperatures (89.2% of 3432 variables). None of the twelve ecological traits we investigated – including traits related to dispersal ability, ecological specialization, reproductive capacity, and commercial harvest – accounted for differences in tracking responses across species even after accounting for differences in climate exposure. Our results suggest widespread behavioral or physiological flexibility among our study species, or ongoing genetic adaptation to changing temperatures. They also suggest that divergent selection on climate sensitivities of close relatives may limit the utility of ecological traits for predicting distributional responses to future climate change.     

Effects of hydromorphological impacts on river ecosystem functioning: a review and suggestions for assessing ecological impacts

Because of the serious effects of pollution on water supply much closer attention has been paid to water quality than to other aspects of river integrity. However, channel form and water flow are relevant components of river health, and recent evidences show that their impairment threatens the services derived from them. In this article, we review the literature on the effects of common hydromorphological impacts (channel modification and flow modification) on the functioning of river ecosystems. There are evidences that even light hydromorphological impacts can have deep effects on ecosystem functioning, and that different functional variables differ in their responses. Three criteria (relevance, scale and sensitivity) in the selection of functional variables are suggested as a guide for the river scientists and managers to assess the ecological impacts of hydromorphological modifications.