Predicting food-web structure with metacommunity models

Synthesis Metacommunity theory aims to elucidate the relative influence of local and regional-scale processes in generating diversity patterns across the landscape. Metacommunity research has focused largely on assemblages of competing organisms within a single trophic level. Here, we test the ability of metacommunity models to predict the network structure of the aquatic food web found in the leaves of the northern pitcher plant Sarracenia purpurea. The species-sorting and patch-dynamics models most accurately reproduced nine food web properties, suggesting that local-scale interactions play an important role in structuring Sarracenia food webs. Our approach can be applied to any well-resolved food web for which data are available from multiple locations. The metacommunity framework explores the relative influence of local and regional-scale processes in generating diversity patterns across the landscape. Metacommunity models and empirical studies have focused mostly on assemblages of competing organisms within a single trophic level. Studies of multi-trophic metacommunities are predominantly restricted to simplified trophic motifs and rarely consider entire food webs. We tested the ability of the patch-dynamics, species-sorting, mass-effects, and neutral metacommunity models, as well as three hybrid models, to reproduce empirical patterns of food web structure and composition in the complex aquatic food web found in the northern pitcher plant Sarracenia purpurea. We used empirical data to determine regional species pools and estimate dispersal probabilities, simulated local food-web dynamics, dispersed species from regional pools into local food webs at rates based on the assumptions of each metacommunity model, and tested their relative fits to empirical data on food-web structure. The species-sorting and patch-dynamics models most accurately reproduced nine food web properties, suggesting that local-scale interactions were important in structuring Sarracenia food webs. However, differences in dispersal abilities were also important in models that accurately reproduced empirical food web properties. Although the models were tested using pitcher-plant food webs, the approach we have developed can be applied to any well-resolved food web for which data are available from multiple locations. © 2012 The Authors. Oikos © 2012 Nordic Society Oikos

Local to Continental-Scale Variation in the Richness and Composition of an Aquatic Food Web

Organismic and Evolutionary Biolog

Sensitivity of codispersion to noise and error in ecological and environmental data

Codispersion analysis is a new statistical method developed to assess spatial covariation between two spatial processes that may not be isotropic or stationary. Its application to anisotropic ecological datasets have provided new insights into mechanisms underlying observed patterns of species distributions and the relationship between individual species and underlying environmental gradients. However, the performance of the codispersion coefficient when there is noise or measurement error ("contamination") in the data has been addressed only theoretically. Here, we use Monte Carlo simulations and real datasets to investigate the sensitivity of codispersion to four types of contamination commonly seen in many real-world environmental and ecological studies. Three of these involved examining codispersion of a spatial dataset with a contaminated version of itself. The fourth examined differences in codisperson between plants and soil conditions, where the estimates of soil characteristics were based on complete or thinned datasets. In all cases, we found that estimates of codispersion were robust when contamination, such as data thinning, was relatively low (<15\%), but were sensitive to larger percentages of contamination. We also present a useful method for imputing missing spatial data and discuss several aspects of the codispersion coefficient when applied to noisy data to gain more insight about the performance of codispersion in practice.Comment: 20 pages, 14 figure

Geographic Variation in Network Structure of a Nearctic Aquatic Food Web

Aim: The network structure of food webs plays an important role in the maintenance of diversity and ecosystem functioning in ecological communities. Previous research has found that ecosystem size, resource availability, assembly history and biotic interactions can potentially drive food web structure. However, the relative influence of climatic variables that drive broad-scale biogeographic patterns of species richness and composition has not been explored for food web structure. In this study, we assess the influence of broad-scale climatic variables in addition to known drivers of food web structure on replicate observations of a single aquatic food web, sampled from the leaves of the pitcher plant (Sarracenia purpurea), at different geographic sites across a broad latitudinal and climatic range. Location: Using standardized sampling methods, we conducted an extensive ‘snapshot’ survey of 780 replicated aquatic food webs collected from the leaves of the pitcher plant S. purpurea at 39 sites from northern Florida to Newfoundland and westward to eastern British Columbia. Methods: We examined correlations of 15 measures of food web structure at the pitcher and site scales with geographic variation in temperature and precipitation, concentrations of nutrients from atmospheric nitrogen deposition, resource availability, ecosystem size and the abundance of the pitcher plant mosquito (Wyeomyia smithii), a potential keystone species. Results: At the scale of a single pitcher plant leaf, linkage density, species richness, measures of chain length and the proportion of omnivores in a web all increased with pitcher volume. Linkage density and species richness were greater at high-latitude sites, which experience low mean temperatures and precipitation and high annual variation in both of these variables. At the site scale, variation in 8 of the 15 food web metrics decreased at higher latitudes, and variation in measures of chain length increased with the abundance of mosquitoes. Main conclusions: Ecosystem size and climatic variables related to latitude were most strongly correlated with network structure of the Sarracenia food web. However, in spite of large sample sizes, thorough standardized sampling and the large geographic extent of the survey, even the best-fitting models explained less than 40% of the variation in food web structure. In contrast to biogeographic patterns of species richness, food web structure was largely independent of broad-scale climatic variables. The large proportion of unexplained variance in our analyses suggests that stochastic assembly may be an important determinant of local food web structure.Organismic and Evolutionary Biolog

Degradation of cognitive timing mechanisms in behavioural variant frontotemporal dementia.

The current study examined motor timing in frontotemporal dementia (FTD), which manifests as progressive deterioration in social, behavioural and cognitive functions. Twenty-patients fulfilling consensus clinical criteria for behavioural variant FTD (bvFTD), 11 patients fulfilling consensus clinical criteria for semantic-variant primary progressive aphasia (svPPA), four patients fulfilling criteria for nonfluent/agrammatic primary progressive aphasia (naPPA), eight patients fulfilling criteria for Alzheimer׳s disease (AD), and 31 controls were assessed on both an externally- and self-paced finger-tapping task requiring maintenance of a regular, 1500 ms beat over 50 taps. Grey and white matter correlates of deficits in motor timing were examined using voxel-based morphometry (VBM) and diffusion tensor imaging (DTI). bvFTD patients exhibited significant deficits in aspects of both externally- and self-paced tapping. Increased mean inter-response interval (faster than target tap time) in the self-paced task was associated with reduced grey matter volume in the cerebellum bilaterally, right middle temporal gyrus, and with increased axial diffusivity in the right superior longitudinal fasciculus, regions and tracts which have been suggested to be involved in a subcortical-cortical network of structures underlying timing abilities. This suggests that such structures can be affected in bvFTD, and that impaired motor timing may underlie some characteristics of the bvFTD phenotype

Detecting Ecological Patterns Along Environmental Gradients: Alpine Treeline Ecotones

Everyone is familiar with that age-old adage: "a picture is worth a thousand words". Among ecologists, the word "picture" easily could be replaced with the word "pattern", although the significance remains the same: the pattern we observe in a single snapshot more than sums up what could be expressed if we tried to describe all the original events that led to the pattern. One particular class of patterns, spatial patterns, are the backbone of much contemporary ecological research. [...

Species Diversity Associated with Foundation Species in Temperate and Tropical Forests

Foundation species define and structure ecological communities but are difficult to identify before they are declining. Yet, their defining role in ecosystems suggests they should be a high priority for protection and management while they are still common and abundant. We used comparative analyses of six large forest dynamics plots spanning a temperate-to-tropical gradient in the Western Hemisphere to identify statistical “fingerprints” of potential foundation species based on their size-frequency and abundance-diameter distributions, and their spatial association with five measures of diversity of associated woody plant species. Potential foundation species are outliers from the common “reverse-J” size-frequency distribution, and have negative effects on alpha diversity and positive effects on beta diversity at most spatial lags and directions. Potential foundation species also are more likely in temperate forests, but foundational species groups may occur in tropical forests. As foundation species (or species groups) decline, associated landscape-scale (beta) diversity is likely to decline along with them. Preservation of this component of biodiversity may be the most important consequence of protecting foundation species while they are still common

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications

Increased stem density and competition may diminish the positive effects of warming at alpine treeline

The most widespread response to global warming among alpine treeline ecotones is not an upward shift, but an increase in tree density. However, the impact of increasing density on interactions among trees at treeline is not well understood. Here, we test if treeline densification induced by climatic warming leads to increasing intraspecific competition. We mapped and measured the size and age of Smith fir trees growing in two treelines located in the southeastern Tibetan Plateau. We used spatial point-pattern and codispersion analyses to describe the spatial association and covariation among seedlings, juveniles, and adults grouped in 30-year age classes from the 1860s to the present. Effects of competition on tree height and regeneration were inferred from bivariate mark-correlations. Since the 1950s, a rapid densification occurred at both sites in response to climatic warming. Competition between adults and juveniles or seedlings at small scales intensified as density increased. Encroachment negatively affected height growth and further reduced recruitment around mature trees. We infer that tree recruitment at the study treelines was more cold-limited prior to 1950 and shifted to a less temperature-constrained regime in response to climatic warming. Therefore, the ongoing densification and encroachment of alpine treelines could alter the way climate drives their transitions towards subalpine forests.Organismic and Evolutionary Biolog

Using codispersion analysis to quantify and understand spatial patterns in species-environment relationships

• The analysis of spatial patterns in species–environment relationships can provide new insights into the niche requirements and potential co-occurrence of species, but species abundance and environmental data are routinely collected at different spatial scales. Here, we investigate the use of codispersion analysis to measure and assess the scale, directionality and significance of complex relationships between plants and their environment in large forest plots. • We applied codispersion analysis to both simulated and field data on spatially located tree species basal area and environmental variables. The significance of the observed bivariate spatial associations between the basal area of key species and underlying environmental variables was tested using three null models. • Codispersion analysis reliably detected directionality (anisotropy) in bivariate species–environment relationships and identified relevant scales of effects. Null model-based significance tests applied to codispersion analyses of forest plot data enabled us to infer the extent to which environmental conditions, tree sizes and/or tree spatial positions underpinned the observed basal area–environment relationships, or whether relationships were a result of other unmeasured factors. • Codispersion analysis, combined with appropriate null models, can be used to infer hypothesized ecological processes from spatial patterns, allowing us to start disentangling the possible drivers of plant species–environment relationships