Leaf quality, predators, and stochastic processes in the assembly of a diverse herbivore community

Ecological communities are structured by both deterministic, niche-based processes and stochastic processes such as dispersal. A pressing issue in ecology is to determine when and for which organisms each of these types of processes is important in community assembly. The roles of deterministic and stochastic processes have been studied for a variety of communities, but very few researchers have addressed their contribution to insect herbivore community structure. Insect herbivore niches are often described as largely shaped by the antagonistic pressures of predation and host plant defenses. However host plants are frequently discrete patches of habitat, and their spatial arrangement can affect herbivore dispersal patterns. We studied the roles of predation, host plant quality, and host spatial proximity for the assembly of a diverse insect herbivore community on Quercus alba (white oak) across two growing seasons. We examined abundances of feeding guilds to determine if ecologically similar species responded similarly to variation in niches. Most guilds responded similarly to leaf quality, preferring high-nitrogen, low-tannin host plants, particularly late in the growing season, while bird predation had little impact on herbivore abundance. The communities on the high-quality plants tended to be larger and, in some cases, have greater species richness. We analyzed community composition by correlating indices of community similarity with predator presence, leaf quality similarity, and host plant proximity. Birds did not affect community composition. Community similarity was significantly associated with distance between host plants and uncorrelated with leaf quality similarity. Thus although leaf quality significantly affected the total abundance of herbivores on a host plant, in some cases leading to increased species richness, dispersal limitation may weaken this relationship. The species composition of these communities may be driven by stochastic processes rather than variation in host plant characteristics or differential predation by insectivorous birds.     

In search of quorum effects in metacommunity structure: species co-occurrence analyses

Alternative models of community assembly emphasize regional, stochastic, dispersal-based processes or local, deterministic, niche-based processes. Community ecology's historical focus on local processes implicitly assumes that local processes surpass regional processes over time or across space to derive nonrandom metacommunity structure (i.e., a quorum effect). Quorum effects are expected late in succession among nearby sites, whereas quorum effects are not expected early in succession among distant sites. I conducted a meta-analysis of zooplankton data sets encompassing time scales of one to thousands of years and spatial scales of <1 m to thousands of kilometers. Species co-occurrence analyses statistically evaluated presence/absence patterns relative to random patterns obtained with Monte Carlo null models. A series of weighted analyses was conducted and alternative randomization algorithms and null models were evaluated. Most zooplankton metacommunities were randomly structured in unweighted analyses, and the distribution of significant structure did not follow quorum effect predictions. Weighted analyses (e.g., by habitat area) revealed significant, nonrandom structure in most zooplankton metacommunities, but the distribution of significant structure still did not adhere well to quorum effect predictions. Finally, additional weighting for study scale (number of sites) nullified most significant area-weighted structure, and again, the distribution of significant structure did not follow quorum effect predictions. Overall, a quorum effect was not supported, perhaps related to zooplankton life histories and energetics and/or the quorum effect itself. Results at the presence/absence level of resolution indicated that local processes did not generally override regional processes over time or across space to drive community structure. A full integration of dispersal- and niche-based concepts in metacommunity dynamics will be most fruitful for unraveling community assembly. Species co-occurrence analyses were scale dependent (habitat area and study size). Future analyses should use weights for important factors (e.g., habitat area), and meta-analyses should include study scale as an additional factor contributing to apparent patterns.     

Seed arrival and ecological filters interact to assemble high-diversity plant communities

Two prominent mechanisms proposed to structure biodiversity are niche-based ecological filtering and chance arrival of propagules from the species pool. Seed arrival is hypothesized to play a particularly strong role in high-diversity plant communities with large potential species pools and many rare species, but few studies have explored how seed arrival and local ecological filters interactively assemble species-rich communities in space and time. We experimentally manipulated seed arrival and multiple ecological filters in high-diversity, herbaceous-dominated groundcover communities in longleaf pine savannas, which contain the highest small-scale species richness in North America (up to > 40 species/m2). We tested three hypotheses: (1) local communities constitute relatively open-membership assemblages, in which increased seed arrival from the species pool strongly increases species richness; (2) ecological filters imposed by local fire intensity and soil moisture influence recruitment and richness of immigrating species; and (3) ecological filters increase similarity in the composition of immigrating species. In a two-year factorial field experiment, we manipulated local fire intensity by increasing pre-fire fuel loads, soil moisture using rain shelters and irrigation, and seed arrival by adding seeds from the local species pool. Seed arrival increased species richness regardless of fire intensity and soil moisture but interacted with both ecological filters to influence community assembly. High-intensity fire decreased richness of resident species, suggesting an important abiotic filter. In contrast, high-intensity fire increased recruitment and richness of immigrating species, presumably by decreasing effects of other ecological filters (competition and resource limitation) in postfire environments. Drought decreased recruitment and richness of immigrating species, whereas wet soil conditions increased recruitment but decreased or had little effect on richness. Moreover, some ecological filters (wet soil conditions and, to a lesser extent, high-intensity fire) increased similarity in the composition of immigrating species, illustrating conditions that influence deterministic community assembly in species-rich communities. Our experiment provides insights into how dispersal-assembly mechanisms may interact with niche-assembly mechanisms in space (spatial variation in disturbance) and time (temporal variation in resource availability) to structure high-diversity communities and can help guide conservation of threatened longleaf pine ecosystems in the face of habitat fragmentation and environmental change.     

Hierarchical analysis of species distributions and abundance across environmental gradients

Abiotic and biotic processes operate at multiple spatial and temporal scales to shape many ecological processes, including species distributions and demography. Current debate about the relative roles of niche-based and stochastic processes in shaping species distributions and community composition reflects, in part, the challenge of understanding how these processes interact across scales. Traditional statistical models that ignore autocorrelation and spatial hierarchies can result in misidentification of important ecological covariates. Here, we demonstrate the utility of a hierarchical modeling framework for testing hypotheses about the importance of abiotic factors at different spatial scales and local spatial autocorrelation for shaping species distributions and abundances. For the two orchid species studied, understory light availability and soil moisture helped to explain patterns of presence and abundance at a microsite scale (<4 m2), while soil organic content was important at a population scale (<400 m2). The inclusion of spatial autocorrelation is shown to alter the magnitude and certainty of estimated relationships between abundance and abiotic variables, and we suggest that such analysis be used more often to explore the relationships between species life histories and distributions. The hierarchical modeling framework is shown to have great potential for elucidating ecological relationships involving abiotic and biotic processes simultaneously at multiple scales.     

Compositional divergence and convergence in arbuscular mycorrhizal fungal communities

In spite of the controversy that they have generated, neutral models provide ecologists with powerful tools for creating dynamic predictions about beta-diversity in ecological communities. Ecologists can achieve an understanding of the assembly rules operating in nature by noting when and how these predictions are met or not met. This is particularly valuable for those groups of organisms that are challenging to study under natural conditions (e.g., bacteria and fungi). Here, we focused on arbuscular mycorrhizal fungal (AMF) communities and performed an extensive literature search that allowed us to synthesize the information in 19 data sets with the minimal requisites for creating a null hypothesis in terms of community dissimilarity expected under neutral dynamics. In order to achieve this task, we calculated the first estimates of neutral parameters for several AMF communities from different ecosystems. Communities were shown either to be consistent with neutrality or to diverge or converge with respect to the levels of compositional dissimilarity expected under neutrality. These data support the hypothesis that divergence occurs in systems where the effect of limited dispersal is overwhelmed by anthropogenic disturbance or extreme biological and environmental heterogeneity, whereas communities converge when systems have the potential for niche divergence within a relatively homogeneous set of environmental conditions. Regarding the study cases that were consistent with neutrality, the sampling designs employed may have covered relatively homogeneous environments in which the effects of dispersal limitation overwhelmed minor differences among AMF taxa that would lead to environmental filtering. Using neutral models we showed for the first time for a soil microbial group the conditions under which different assembly processes may determine different patterns of beta-diversity. Our synthesis is an important step showing how the application of general ecological theories to a model microbial taxon has the potential to shed light on the assembly and ecological dynamics of communities.     

A trait-based test for habitat filtering: convex hull volume

Community assembly theory suggests that two processes affect the distribution of trait values within communities: competition and habitat filtering. Within a local community, competition leads to ecological differentiation of coexisting species, while habitat filtering reduces the spread of trait values, reflecting shared ecological tolerances. Many statistical tests for the effects of competition exist in the literature, but measures of habitat filtering are less well-developed. Here, we present convex hull volume, a construct from computational geometry, which provides an n-dimensional measure of the volume of trait space occupied by species in a community. Combined with ecological null models, this measure offers a useful test for habitat filtering. We use convex hull volume and a null model to analyze California woody-plant trait and community data. Our results show that observed plant communities occupy less trait space than expected from random assembly, a result consistent with habitat filtering.     

Studying ecological communities from a neutral standpoint: A review of models’ structure and parameter estimation

Neutral models provide an alternative to niche-based assembly rules of ecological communities by assuming that communities’ properties are shaped by the stochastic interplay between ecological drift, migration and speciation. The recent and ongoing interest about neutral assumptions has produced many developments on the theoretical side, with nevertheless limited echoes in terms of analyses of real-world data. The present review paper aims to help bridge the widening gap between modellers and field ecologists through two objectives. First, to provide a multi-criteria typology of the main neutral models, including those from population genetics that have not yet been transposed to ecology, by considering how the fundamental processes of ecological drift, speciation and migration are modelled and, specifically, how space is taken into account. Second, to review methods recently proposed to estimate models parameters from field data, a point that should be mastered to allow for broader applications.     

The influence of spatial and size scale on phylogenetic relatedness in tropical forest communities

The relative importance of biotic, abiotic, and stochastic processes in structuring ecological communities continues to be a central focus in community ecology. In order to assess the role of phylogenetic relatedness on the nature of biodiversity we first quantified the degree of phylogenetic niche conservatism of several plant traits linked to plant form and function. Next we quantified the degree of phylogenetic relatedness across two fundamental scaling dimensions: plant size and neighborhood size. The results show that phylogenetic niche conservatism is likely widespread, indicating that closely related species are more functionally similar than distantly related species. Utilizing this information we show that three of five tropical forest dynamics plots (FDPs) exhibit similar scale-dependent patterns of phylogenetic structuring using only a spatial scaling axis. When spatial- and size-scaling axes were analyzed in concert, phylogenetic overdispersion of co-occurring species was most important at small spatial scales and in four of five FDPs for the largest size class. These results suggest that phylogenetic relatedness is increasingly important: (1) at small spatial scales, where phylogenetic overdispersion is more common, and (2) in large size classes, where phylogenetic overdispersion becomes more common throughout ontogeny. Collectively, our results highlight the critical spatial and size scales at which the degree of phylogenetic relatedness between constituent species influences the structuring of tropical forest diversity.     

Modeling species co-occurrence by multivariate logistic regression generates new hypotheses on fungal interactions

Signals of species interactions can be inferred from survey data by asking if some species occur more or less often together than what would be expected by random, or more generally, if any structural aspect of the community deviates from that expected from a set of independent species. However, a positive (or negative) association between two species does not necessarily signify a direct or indirect interaction, as it can result simply from the species having similar (or dissimilar) habitat requirements. We show how these two factors can be separated by multivariate logistic regression, with the regression part accounting for species-specific habitat requirements, and a correlation matrix for the positive or negative residual associations. We parameterize the model using Bayesian inference with data on 22 species of wood-decaying fungi acquired in 14 dissimilar forest sites. Our analyses reveal that some of the species commonly found to occur together in the same logs are likely to do so merely by similar habitat requirements, whereas other species combinations are systematically either over- or underrepresented also or only after accounting for the habitat requirements. We use our results to derive hypotheses on species interactions that can be tested in future experimental work.     

Changes in the phytoplankton community at Helgoland, North Sea: lessons from single spot time series analyses

In recent regime shift analyses, the phytoplankton compartment of the marine food web was essentially represented by phytoplankton color or chlorophyll concentration. A detection of changes directly at the species level is highly desirable. The Helgoland Roads data series, a collection of high frequency long-term time series comprising biological and physico-chemical components of the southern North Sea, allow such an investigation at the level of single species. Aiming at a detection and characterization of habitat and community changes in the observation period (1962 until the end of 2008), we selected six species as representatives of certain classes, for example, benthic or neritic species, and applied a combination of novel analysis methods—a fitness-based analysis of the realized niche, a bloom-triggered averaging and a Markovian analysis of co-occurrence and succession patterns—to related abundance time series and concurrent environmental parameter time series. We found a general trend toward enlargement of niche size and shifts of the niche position, interesting salinity patterns around bloom events of two species, and statistically highly significant changes of a phytoplankton community segment after 1965 and after 1998. Interpreting our observations in ecological terms leads to the formulation of testable hypotheses.     

Coexistence of the niche and neutral perspectives in community ecology

The neutral theory for community structure and biodiversity is dependent on the assumption that species are equivalent to each other in all important ecological respects. We explore what this concept of equivalence means in ecological communities, how such species may arise evolutionarily, and how the possibility of ecological equivalents relates to previous ideas about niche differentiation. We also show that the co-occurrence of ecologically similar or equivalent species is not incompatible with niche theory as has been supposed, because niche relations can sometimes favor coexistence of similar species. We argue that both evolutionary and ecological processes operate to promote the introduction and to sustain the persistence of ecologically similar and in many cases nearly equivalent species embedded in highly structured food webs. Future work should focus on synthesizing niche and neutral perspectives rather than dichotomously debating whether neutral or niche models provide better explanations for community structure and biodiversity.     

Small-scale grassland assembly patterns differ above and below the soil surface

The existence of deterministic assembly rules for plant communities remains an important and unresolved topic in ecology. Most studies examining community assembly have sampled aboveground species diversity and composition. However, plants also coexist belowground, and many coexistence theories invoke belowground competition as an explanation for aboveground patterns. We used next-generation sequencing that enables the identification of roots and rhizomes from mixed-species samples to measure coexisting species at small scales in temperate grasslands. We used comparable data from above (conventional methods) and below (molecular techniques) the soil surface (0.1 x 0.1 x 0.1 m volume). To detect evidence for nonrandom patterns in the direction of biotic or abiotic assembly processes, we used three assembly rules tests (richness variance, guild proportionality, and species co-occurrence indices) as well as pairwise association tests. We found support for biotic assembly rules aboveground, with lower variance in species richness than expected and more negative species associations. Belowground plant communities were structured more by abiotic processes, with greater variability in richness and guild proportionality than expected. Belowground assembly is largely driven by abiotic processes, with little evidence for competition-driven assembly, and this has implications for plant coexistence theories that are based on competition for soil resources.     

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

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.     

K-select analysis: a new method to analyse habitat selection in radio-tracking studies

Two kinds of wildlife habitat studies can be distinguished in the literature: hindcasting and forecasting studies. Hindcasting studies aim to emphasize among a large set of habitat variables those that are of interest for the focus species, whereas forecasting studies are intended to predict habitat selection according to a small number of habitat variables for a given area. We provide here a new analytical tool which relies on the concept of ecological niche, the K-select analysis, for hindcasting studies of habitat selection by animals using radio-tracking data. Each habitat variable defines one dimension in the ecological space. For each animal, the difference between the vector of average available habitat conditions and the vector of average used conditions defines the marginality vector. Its size is proportional to the importance of habitat selection, and its direction indicates which variables are selected. By performing a non-centered principal component analysis of the table containing the coordinates of the marginality vectors of each animal (row) on the habitat variables (column), the K-select analysis returns a linear combination of habitat variables for which the average marginality is greatest. It is a synthesis of variables which contributes the most to the habitat selection. As with principal component analysis, the biological significance of the factorial axes is deduced from the loading of variables. An example is provided: habitat selection by wild boar is studied in a Mediterranean habitat using the K-select analysis. The numerous advantages of the analysis (a large number of variables that can be included, individual variability in habitat selection taken into account, a lack of too strict underlying hypotheses) make it a powerful approach in radio-tracking studies designed to identify habitat variables that are selected by animals.     

Habitat Fragmentation Effects on Trophic Processes of Insect-Plant Food Webs

Abstract:  Habitat fragmentation is the transformation of once-extensive landscapes into smaller, isolated remnants surrounded by new types of habitat. There is ample evidence of impoverished biodiversity as a consequence of habitat fragmentation, but its most profound effects may actually result from functional changes in ecological processes such as trophic interactions. We studied the trophic processes of herbivory and parasitism in insect-plant food webs composed of hundreds of species in a fragmented woodland landscape. We recorded all plant species, collected mined leaves, and reared leafminers and parasitoids from 19 woodland remnants. Herbivory and parasitism rates were then analyzed in relation to woodland size and edge or interior location. Herbivory by leaf-mining insects and their overall parasitism rates decreased as woodland remnants became smaller. For each remnant the intensity of both processes differed between edge and interior. Our results provide novel evidence of the magnitude of habitat fragmentation effects, showing they can be so pervasive as to affect trophic processes of highly complex food webs and suggesting a response associated with trophic specialization of the involved organisms as much as with their trophic level.     

Causes of habitat divergence in two species of agamid lizards in arid central Australia

The deserts of central Australia contain richer communities of lizards than any other arid regions, with the highest diversity occurring in sand dune habitats dominated by hummock-forming spinifex grasses. To investigate the mechanisms that permit coexistence, we studied two species of coexisting agamid lizards that exhibit striking divergence in their use of habitat in the Simpson Desert of central Australia. Here, the military dragon Ctenophorus isolepis is restricted primarily to sites providing > 30% cover of hard spinifex Triodia basedowii, whereas the central netted dragon C. nuchalis occurs in areas with much sparser (< 10%) cover. We constructed four mechanistic models to explain this pattern and then derived hypotheses to test them. One hypothesis, that competition restricts each species to its preferred habitat, was rejected after dyad encounters in field enclosures failed to elicit any habitat shift or any overt interactions between the species. Our next hypotheses were that each species exhibits preferences for different thermal environments or different prey types and that each selects the habitats that maximize access to them. Both were supported. C. isolepis preferred lower temperatures when active and specialized in eating ants < 5 mm long and selected spinifex-dominated areas where these requirements were met. In contrast, C. nuchalis preferred higher temperatures and a diversity of prey, both of which were available mostly in open areas. Finally, we used plasticine models to test the hypothesis that each species faced lower risk of predation in its selected habitat. This was partly supported, as models of both species were attacked more often in the open than under spinifex cover. The results show that habitat divergence occurs along several, probably covarying, niche axes. We suggest that different levels of spinifex cover provide the template for a broad range of ecological interactions, allowing lizard species to partition biotic and abiotic resources and achieve the extraordinarily high levels of local diversity that are observed.     

Effects of photoacclimation on the light niche of corals: a process-based approach

The ecology of photosynthetic organisms is influenced by the need to adjust the photosynthetic apparatus to variable light environments (photoacclimation). In this study, we quantified different components of the photoacclimation process for a reef-building coral (Turbinaria mesenterina, Lamarck, 1816): including, variation in absorption cross-section, size of photosynthetic units, turnover time, chlorophyll content, and colony respiration. We used these calibrations to characterize this species’ light niche, and to determine the sensitivity of the niche boundaries to different processes of photoacclimation. Results showed that the breadth of the light niche was most sensitive to the size of the photosynthetic unit, absorption cross-section, and rates of respiration. Habitats with the highest light availability did not lead to maximal energy acquisition. This was because, although corals acclimated to high light have high rates of photosynthesis per unit chlorophyll, their chlorophyll content was strongly reduced. This suggests that potential energetic benefits that could be achieved through increased light harvesting (i.e., increased chlorophyll content) in high-light habitats are outweighed by costs associated with photoprotection. Such costs appear to place an upper bound on the habitat distributions of coral species. Our approach reveals how the photophysiological processes involved in photoacclimation interact to determine the light niche.     

Size-mediated non-trophic interactions and stochastic predation drive assembly and dynamics in a seabird community

Theoretical and empirical evidence suggests that body size is a major life-history trait impacting on the structure and functioning of complex food webs. However, long-term analyses of size-dependent interactions within simpler network modules, for instance, competitive guilds, are scant. Here, we model the assembly dynamics of the largest breeding seabird community in the Mediterranean basin during the last 30 years. This unique data set allowed us to test, through a "natural experiment," whether body size drove the assembly and dynamics of an ecological guild growing from very low numbers after habitat protection. Although environmental stochasticity accounted for most of community variability, the population variance explained by interspecific interactions, albeit small, decreased sharply with increasing body size. Since we found a demographic gradient along a body size continuum, in which population density and stability increase with increasing body size, the numerical effects of interspecific interactions were proportionally higher on smaller species than on larger ones. Moreover, we found that the per capita interaction coefficients were larger the higher the size ratio among competing species, but only for the set of interactions in which the species exerting the effect was greater. This provides empirical evidence for long-term asymmetric interspecific competition, which ultimately prompted the local extinction of two small species during the study period. During the assembly process stochastic predation by generalist carnivores further triggered community reorganizations and global decays in population synchrony, which disrupted the pattern of interspecific interactions. These results suggest that the major patterns detected in complex food webs can hold as well for simpler sub-modules of these networks involving non-trophic interactions, and highlight the shifting ecological processes impacting on assembling vs. asymptotic communities.     

A Method for Setting the Size of Plant Conservation Target Areas

Abstract: Realistic time frames in which management decisions are made often preclude the completion of the detailed analyses necessary for conservation planning. Under these circumstances, efficient alternatives may assist in approximating the results of more thorough studies that require extensive resources and time. We outline a set of concepts and formulas that may be used in lieu of detailed population viability analyses and habitat modeling exercises to estimate the protected areas required to provide desirable conservation outcomes for a suite of threatened plant species. We used expert judgment of parameters and assessment of a population size that results in a specified quasiextinction risk based on simple dynamic models. The area required to support a population of this size is adjusted to take into account deterministic and stochastic human influences, including small-scale disturbance, deterministic trends such as habitat loss, and changes in population density through processes such as predation and competition. We set targets for different disturbance regimes and geographic regions. We applied our methods to Banksia cuneata, Boronia keysii, and Parsonsia dorrigoensis, resulting in target areas for conservation of 1102, 733, and 1084 ha, respectively. These results provide guidance on target areas and priorities for conservation strategies.     

The effects of habitat loss, fragmentation, and community homogenization on resilience in estuaries.

When changes in the frequency and extent of disturbance outstrip the recovery potential of resident communities, the selective removal of species contributes to habitat loss and fragmentation across landscapes. The degree to which habitat change is likely to influence community resilience will depend on metacommunity structure and connectivity. Thus ecological connectivity is central to understanding the potential for cumulative effects to impact upon diversity. The importance of these issues to coastal marine communities, where the prevailing concept of open communities composed of highly dispersive species is being challenged, indicates that these systems may be more sensitive to cumulative impacts than previously thought. We conducted a disturbance-recovery experiment across gradients of community type and environmental conditions to assess the roles of ecological connectivity and regional variations in community structure on the recovery of species richness, total abundance, and community composition in Mahurangi Harbour, New Zealand. After 394 days, significant differences in recovery between sites were apparent. Statistical models explaining a high proportion of the variability (R2 > 0.92) suggested that community recovery rates were controlled by a combination of physical and ecological features operating across spatial scales, affecting successional processes. The dynamic and complex interplay of ecological and environmental processes we observed driving patch recovery across the estuarine landscape are integral to recovery from disturbances in heterogeneous environments. This link between succession/recovery, disturbance, and heterogeneity confirms the utility of disturbance-recovery experiments as assays for cumulative change due to fragmentation and habitat change in estuaries.