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.     

Persistence and stochasticity are key determinants of genetic diversity in plants associated with banded iron formation inselbergs

The high species endemism characteristic of many of the world's terrestrial island systems provides a model for studying evolutionary patterns and processes, yet there has been no synthesis of studies to provide a systematic evaluation of terrestrial island systems in this context. The banded iron formations (BIFs) of south‐western Australia are ancient terrestrial island formations occurring within a mosaic of alluvial clay soils, sandplains and occasional granite outcropping, across an old, gently undulating, highly weathered, plateau. Notably, these BIFs display exceptionally high beta plant diversity. Here, we address the determinants and consequences of genetic diversity for BIF‐associated plant species through a comprehensive review of all studies on species distribution modelling, phylogenetics, phylogeography, population genetics, life‐history traits and ecology. The taxa studied are predominantly narrowly endemic to individual or a few BIF ranges, but some have more regional distributions occurring both on and off BIFs. We compared genetic data for these BIF‐endemic species to other localised species globally to assess whether the unique history and ancestry of BIF landscapes has driven distinct genetic responses in plants restricted to this habitat. We also assessed the influence of life‐history parameters on patterns of genetic diversity. We found that BIF‐endemic species display similar patterns of genetic diversity and structure to other species with localised distributions. Despite often highly restricted distributions, large effective population size or clonal reproduction appears to provide these BIF‐endemic species with ecological and evolutionary resilience to environmental stochasticity. We conclude that persistence and stochasticity are key determinants of genetic diversity and its spatial structure within BIF‐associated plant species, and that these are key evolutionary processes that should be considered in understanding the biogeography of inselbergs worldwide.     

A roadmap to plant functional island biogeography

Island biogeography is the study of the spatio-temporal distribution of species, communities, assemblages or ecosystems on islands and other isolated habitats. Island diversity is structured by five classes of process: dispersal, establishment, biotic interactions, extinction and evolution. Classical approaches in island biogeography focused on species richness as the deterministic outcome of these processes. This has proved fruitful, but species traits can potentially offer new biological insights into the processes by which island life assembles and why some species perform better at colonising and persisting on islands. Functional traits refer to morphological and phenological characteristics of an organism or species that can be linked to its ecological strategy and that scale up from individual plants to properties of communities and ecosystems. A baseline hypothesis is for traits and ecological strategies of island species to show similar patterns as a matched mainland environment. However, strong dispersal, environmental and biotic-interaction filters as well as stochasticity associated with insularity modify this baseline. Clades that do colonise often embark on distinct ecological and evolutionary pathways, some because of distinctive evolutionary forces on islands, and some because of the opportunities offered by freedom from competitors or herbivores or the absence of mutualists. Functional traits are expected to be shaped by these processes. Here, we review and discuss the potential for integrating functional traits into island biogeography. While we focus on plants, the general considerations and concepts may be extended to other groups of organisms. We evaluate how functional traits on islands relate to core principles of species dispersal, establishment, extinction, reproduction, biotic interactions, evolution and conservation. We formulate existing knowledge as 33 working hypotheses. Some of these are grounded on firm empirical evidence, others provide opportunities for future research. We organise our hypotheses under five overarching sections. Section A focuses on plant functional traits enabling species dispersal to islands. Section B discusses how traits help to predict species establishment, successional trajectories and natural extinctions on islands. Section C reviews how traits indicate species biotic interactions and reproduction strategies and which traits promote intra-island dispersal. Section D discusses how evolution on islands leads to predictable changes in trait values and which traits are most susceptible to change. Section E debates how functional ecology can be used to study multiple drivers of global change on islands and to formulate effective conservation measures. Islands have a justified reputation as research models. They illuminate the forces operating within mainland communities by showing what happens when those forces are released or changed. We believe that the lens of functional ecology can shed more light on these forces than research approaches that do not consider functional differences among species.     

Towards an integrative understanding of soil biodiversity

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species–energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale‐dependent nature of soil biodiversity.     

Landscape issues in plant ecology

In the last decade, we have seen the emergence and consolidation of a conceptual framework that recognizes the landscape as an ecological unit of interest. Plant ecologists have long emphasized landscape-scale issues, but there has been no recent attempt to define how landscape concepts are now integrated in vegetation studies. To help define common research paradigms in both landscape and plant ecology, we discuss issues related to three main landscape concepts in vegetation researches, reviewing theoretical influences and emphasizing recent developments. We first focus on environmental relationships, documenting how vegetation patterns emerge from the influence of local abiotic conditions. The landscape is the physical environment. Disturbances are then considered, with a particular attention to human-driven processes that often overrule natural dynamics. The landscape is a dynamic space. As environmental and historical processes generate heterogeneous patterns, we finally move on to stress current evidence relating spatial structure and vegetation dynamics. This relates to the concept of a landscape as a patch-corridor-matrix mosaic. Future challenges involve: 1) the capacity to evaluate the relative importance of multiple controlling processes at broad spatial scale; 2) better assessment of the real importance of the spatial configuration of landscape elements for plant species and finally; 3) the integration of natural and cultural processes and the recognition of their interdependence in relation to vegetation management issues in human landscapes.     

Phylofloristics: an example from the Lesser Antilles

Aims The last decade has seen many plant ecologists integrating phylogenetic analysis into ecology to explain patterns of species co-occurrence and compositional similarity across assemblages. Despite the advances in this area, there are still some challenges that need to be addressed. One challenge is that most of the phylogenetic studies of plant assemblages have focused only on a small proportion of all of the vascular plants that co-occur (e.g. woody plants), while much of the remaining co-occurring flora has been ignored.Methods Here we introduce an analytical approach that we term phylofloristics that analyzes the compositional similarity of floras in relation to spatial and environmental gradients to understand their assembly. As an illustration, we assembled a large phylogenetic tree for the flora of the Lesser Antilles and evaluated the patterns of floristic and phylofloristic similarity among the island-specific floras. We analyzed the relationship of these similarities with spatial and environmental distance and compared the results for non-endemic and endemic lineages.Important findings The results show a major influence of environmental heterogeneity on the assembly of island floras and far less evidence for the importance of dispersal limitation of lineages and species. This study highlights the importance of incorporating broader taxonomic sampling to improve our understanding of assembly processes in ecology. We expect future phylofloristic studies will improve the approach we have taken by generating more refined phylogenetic trees and by incorporating phylogeographic information.     

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment

A central challenge in ecology is to understand the relative importance of processes that shape diversity patterns. Compared with aboveground biota, little is known about spatial patterns and processes in soil organisms. Here we examine the spatial structure of communities of small soil eukaryotes to elucidate the underlying stochastic and deterministic processes in the absence of environmental gradients at a local scale. Specifically, we focus on the fine-scale spatial autocorrelation of prominent taxonomic and functional groups of eukaryotic microbes. We collected 123 soil samples in a nested design at distances ranging from 0.01 to 64 m from three boreal forest sites and used 454 pyrosequencing analysis of Internal Transcribed Spacer for detecting Operational Taxonomic Units of major eukaryotic groups simultaneously. Among the main taxonomic groups, we found significant but weak spatial variability only in the communities of Fungi and Rhizaria. Within Fungi, ectomycorrhizas and pathogens exhibited stronger spatial structure compared with saprotrophs and corresponded to vegetation. For the groups with significant spatial structure, autocorrelation occurred at a very fine scale (<2 m). Both dispersal limitation and environmental selection had a weak effect on communities as reflected in negative or null deviation of communities, which was also supported by multivariate analysis, that is, environment, spatial processes and their shared effects explained on average <10% of variance. Taken together, these results indicate a random distribution of soil eukaryotes with respect to space and environment in the absence of environmental gradients at the local scale, reflecting the dominant role of drift and homogenizing dispersal.     

Understanding ecological change across large spatial,temporal and taxonomic scales: integrating data and methods in light of theory

The difficulty of integrating multiple theories, data and methods has slowed progress towards making unified inferences of ecological change generalizable across large spatial, temporal and taxonomic scales. However, recent progress towards a theoretical synthesis now provides a guiding framework for organizing and integrating all primary data and methods for spatiotemporal assemblage‐level inference in ecology. In this paper, we describe how recent theoretical developments can provide an organizing paradigm for linking advances in data collection and methodological frameworks across disparate ecological sub‐disciplines and across large spatial and temporal scales. First, we summarize the set of fundamental processes that determine change in multispecies assemblages across spatial and temporal scales by reviewing recent theoretical syntheses of community ecology. Second, we review recent advances in data and methods across the main sub‐disciplines concerned with ecological inference across large spatial, temporal and taxonomic scales, and organize them based on the primary fundamental processes they include, rather than the spatiotemporal scale of their inferences. Finally, we highlight how iteratively focusing on only one fundamental process at a time, but combining all relevant spatiotemporal data and methods, may reduce the conceptual challenges to integration among ecological sub‐disciplines. Moreover, we discuss a number of avenues for decreasing the practical barriers to integration among data and methods. We aim to reconcile the recent convergence of decades of thinking in community ecology and macroecology theory with the rapid progress in spatiotemporal approaches for assemblage‐level inference, at a time where a robust understanding of spatiotemporal change in ecological assemblages is more crucial than ever to conserve biodiversity.     

Linking community and ecosystem dynamics through spatial ecology

Classical approaches to food webs focus on patterns and processes occurring at the community level rather than at the broader ecosystem scale, and often ignore spatial aspects of the dynamics. However, recent research suggests that spatial processes influence both food web and ecosystem dynamics, and has led to the idea of 'metaecosystems'. However, these processes have been tackled separately by 'food web metacommunity' ecology, which focuses on the movement of traits, and 'landscape ecosystem' ecology, which focuses on the movement of materials among ecosystems. Here, we argue that this conceptual gap must be bridged to fully understand ecosystem dynamics because many natural cases demonstrate the existence of interactions between the movements of traits and materials. This unification of concepts can be achieved under the metaecosystem framework, and we present two models that highlight how this framework yields novel insights. We then discuss patches, limiting factors and spatial explicitness as key issues to advance metaecosystem theory. We point out future avenues for research on metaecosystem theory and their potential for application to biological conservation.     

Synthesizing traditional biogeography with microbial ecology: the importance of dormancy

The discovery of biogeographical patterns among microbial communities has led to a focus on the empirical evaluation of the importance of dispersal limitation in microbial biota. As a result, the spatial distribution of microbial diversity has been increasingly studied while the synthesis of biogeographical theory with microbial ecology remains undeveloped. To make biogeographical theory relevant to microbial ecology, microbial traits that potentially affect the distribution of microbial diversity need to be considered. Given that many microorganisms in natural environments are in a state of dormancy and that dormancy is an important microbial fitness trait, I provide a first attempt to account for the effects of dormancy on microbial biogeography by treating dormancy as a fundamental biogeographical response. I discuss the effects of dormancy on the equilibrium theory of island biogeography and on the unified neutral theory of biodiversity and biogeography, and suggest how the equilibrium theory of island biogeography can produce predictions approaching those of the Baas‐Becking hypothesis (i.e. everything is everywhere, but the environment selects). In addition, I present a conceptual model of the unified neutral theory of biodiversity and biogeography, generalized to account for dormancy, from which a full model can be constructed for species with or without dormant life history stages.     

A phylogenetic perspective on species diversity, β‐diversity and biogeography for the microbial world

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high‐altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β‐diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High‐altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β‐diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β‐diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter‐ and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies.     

Spatial scale and evolutionary history determine the degree of taxonomic homogenization across island bird assemblages

It is widely documented that human activities have elevated the extirpation of natural populations as well as the successful introduction to new areas of non-native species. These dual processes of introduction and extirpation can change the similarity of communities, but the direction and magnitude these changes take are likely to depend on the manner in which introductions and extirpations occur, the spatial scale at which the changes are measured, and the initial similarity of the communities before the human-induced drivers occurred. Here, we explore patterns of extirpation and introduction and their influence on the similarity of global oceanic island bird assemblages from four different Oceans (Atlantic, Caribbean, Indian, Pacific). We show that different historical patterns of introduction and extirpation have produced varying trends in compositional similarity both between islands within archipelagos and between islands across different archipelagos within the same ocean. Patterns of bird assemblage convergence (i.e. taxonomic homogenization) or divergence (i.e. taxonomic differentiation) among islands depended on the scale of examination, the evolutionary associations among species of the region, and the cultural history of human colonization. These factors are all likely to be leading to a series of multiple interacting processes that are shaping the complex compositional changes observed among global island bird faunas over time.     

Littoral macroinvertebrate communities: spatial scale and ecological relationships

SUMMARY 1. Spatial correlations between ecological patterns and processes are thought to be scale-dependent, yet surprisingly few studies have evaluated the correspondence between different levels of spatial scale and ecosystem structure and function.
2. We evaluated the strength of relationships between the benthic macroinvertebrate communities of stony littoral habitats and levels of ecological scale and geographical position, using partial constrained ordination. Our hypothesis was that correlation strength would be inversely related to ecological scale, i.e. habitat > ecosystem > riparian > catchment > ecoregion.
3. The effect of habitat was greater than that of other levels of spatial scale: 23% of the variance in taxonomic composition and 11% of that in functional composition was explained by habitat variables alone. However, greater spatial scales were also important. For example, the combined influence of riparian, catchment and ecoregion classification accounted for 24% (taxonomic) and 11% (functional) of the explained variance.
4. Relationships between organisms and scale variables were, however, non-linear and a substantial amount of the functional variance was hidden in joint effects. These findings were not unexpected, and presumably indicate a close interdependence between local and regional-scale variables.     

Towards a general formalization of encounter rates in ecology

Although encounters between organisms are fundamental to many ecological processes, a general theory of encounters that accounts for random movements and probabilistic events has yet to be proposed. We present a framework for examining probabilistic encounters between arbitrarily moving searchers and immobile targets in continuous space and time. We define and contrast first encounter rates and mean encounter rates, which are generally not equal and depend on several properties of the process, including movement behaviors, the spatial scales of the encounter kernel, spatial distribution and birth–death dynamics of targets, and whether the encounters are destructive. Based on these considerations, we propose a taxonomy of encounter processes and discuss their functional relationships. Analytical approximations in several special cases are derived, leading to inference about general patterns. We identify, for example, cases (nondestructive, mean encounters) in which encounter rates are completely independent of movement velocity or tortuosity, and we quantify the dependence for cases (e.g., hard, first encounters and destructive encounters in a dynamic landscape) where there is a relationship. The analytical results lead to general qualitative conclusions, while the mathematical formalization and taxonomic organization provides a framework for studying and contrasting a broad range of encounter processes in ecology.     

Taxonomic identification bias does not drive patterns of abundance and diversity in theropod dinosaurs

The ability of palaeontologists to correctly diagnose and classify new fossil species from incomplete morphological data is fundamental to our understanding of evolution. Different parts of the vertebrate skeleton have different likelihoods of fossil preservation and varying amounts of taxonomic information, which could bias our interpretations of fossil material. Substantial previous research has focused on the diversity and macroevolution of non-avian theropod dinosaurs. Theropods provide a rich dataset for analysis of the interactions between taxonomic diagnosability and fossil preservation. We use specimen data and formal taxonomic diagnoses to create a new metric, the Likelihood of Diagnosis, which quantifies the diagnostic likelihood of fossil species in relation to bone preservation potential. We use this to assess whether a taxonomic identification bias impacts the non-avian theropod fossil record. We find that the patterns of differential species abundance and clade diversity are not a consequence of their relative diagnosability. Although there are other factors that bias the theropod fossil record that are not investigated here, our results suggest that patterns of relative abundance and diversity for theropods might be more representative of Mesozoic ecology than often considered.     

Fine‐scale Beta‐diversity Patterns Across Multiple Arthropod Taxa Over a Neotropical Latitudinal Gradient

Documenting how diversity patterns vary at fine‐ and broad scales may help answer many questions in theoretical and applied ecology. However, studies tend to compare diversity patterns at the same scale and within the same taxonomic group, which limits the applicability and generality of the results. Here, we have investigated whether vegetation‐dwelling arthropods from different trophic ranks and with distinct life histories (i.e., ants, caterpillars, cockroaches, and spiders) have different beta‐diversity patterns at multiple scales. Specifically, we compared their beta diversity across architecturally distinct plant species (fine‐scale process) and a latitudinal gradient of sites (broad‐scale process) along 2040 km of coastal restinga vegetation in the Neotropics. Over 50 percent of the compositional changes (β‐diversity) in ants, caterpillars, and spiders and 41 percent of those in cockroaches were explained by plant identity within each site. Even groups that do not feed on plant tissues, such as omnivores and predators, were strongly affected by plant identity. Fine‐scale variation was more important than large‐scale processes for all studied groups. Performing a cross‐scale comparison of diversity patterns of groups with distinct life histories helps elucidate how processes that act at regional scales, such as dispersal, interact with local processes to assemble arthropod communities.     

Spatial scaling of microbial biodiversity

A central goal in ecology is to understand the spatial scaling of biodiversity. Patterns in the spatial distribution of organisms provide important clues about the underlying mechanisms that structure ecological communities and are central to setting conservation priorities. Although microorganisms comprise much of Earth's biodiversity, little is known about their biodiversity scaling relationships relative to that for plants and animals. Here, we discuss current knowledge of microbial diversity at local and global scales. We focus on three spatial patterns: the distance-decay relationship (how community composition changes with geographic distance), the taxa-area relationship, and the local:global taxa richness ratio. Recent empirical analyses of these patterns for microorganisms suggest that there are biodiversity scaling rules common to all forms of life.     

Spatial hierarchical approach in community ecology: a way beyond high context-dependency and low predictability in local phenomena

Patterns and functioning of communities, which are determined by a set of processes operating at a large variety of spatial and temporal scales, exhibit quite high context-dependency and low predictability at the fine spatial scales at which recent studies have concentrated. More attention to broader scale and across-scale phenomena may be useful to search for general patterns and rules in communities. In this context, it is effective to incorporate hierarchical spatial scale explicitly into the experimental and sampling design of field studies, an approach referred to here as the spatial hierarchical approach, focusing on a particular assemblage in which biological interaction and species life history are well known. The spatial hierarchical approach can provide insight into the effects of scale in operating processes and answers to a number of important questions in community ecology such as: (1) detection of patterns and processes in spatiotemporal variability in communities, including how to explain the partitioning of pattern information of species diversity at a broad scale into finer scales, and the pattern of spatial variability of community properties at the finest spatial scale; (2) evaluation of changes in patterns observed in macroecology at finer scales; (3) testing of models explaining the coexistence of competing species; and (4) detection of latitudinal patterns in spatiotemporal variability in communities and their causal processes.     

Stream insect occupancy-frequency patterns and metapopulation structure

An understanding of the distribution patterns of organisms and the underlying factors is a fundamental goal of ecology. One commonly applied approach to visualize these is the analysis of occupancy-frequency patterns. We used data sets describing stream insect distributions from different regions of North America to analyze occupancy-frequency patterns and assess the effects of spatial scale, sampling intensity, and taxonomic resolution on these patterns. Distributions were dominated by satellite taxa (those occurring in or=90% of sites) determined the overall modality of occupancy-frequency patterns. The proportions of satellite taxa increased with spatial scale and showed positive relationships with sampling intensity (r2=0.74-0.96). Furthermore, analyses of data sets from New York (USA) showed that generic-level assessments underestimated the satellite class and occasionally shifted occupancy-frequency distributions from unimodal to bimodal. Our results indicate that, regardless of species- or generic-level taxonomy, stream insect communities are characterized by satellite species and that the proportion of satellite species increases with spatial scale and sampling intensity. Thus, niche-based models of occupancy-frequency patterns better characterize stream insect communities than metapopulation models such as the core-satellite species hypothesis.     

The combined effects of exogenous and endogenous variability on the spatial distribution of ant communities in a forested ecosystem (Hymenoptera: Formicidae)

Spatial patterns observed in ecosystems have traditionally been attributed to exogenous processes. Recently, ecologists have found that endogenous processes also have the potential to create spatial patterns. Yet, relatively few studies have attempted to examine the combined effects of exogenous and endogenous processes on the distribution of organisms across spatial and temporal scales. Here we aim to do this, by investigating whether spatial patterns of under-story tree species at a large spatial scale (18 ha) influences the spatial patterns of ground foraging ant species at a much smaller spatial scale (20 m by 20 m). At the regional scale, exogenous processes (under-story tree community) had a strong effect on the spatial patterns in the ground-foraging ant community. We found significantly more Camponotus noveboracensis, Formica subsericae, and Lasius alienus species in black cherry (Prunis serotine Ehrh.) habitats. In witch-hazel (Hamamelis virginiana L.) habitats, we similarly found significantly more Myrmica americana, Formica fusca, and Formica subsericae. At smaller spatial scales, we observed the emergence of mosaic ant patches changing rapidly in space and time. Our study reveals that spatial patterns are the result of both exogenous and endogenous forces, operating at distinct scales.