12,394 research outputs found
Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model
Food webs, networks of feeding relationships among organisms, provide
fundamental insights into mechanisms that determine ecosystem stability and
persistence. Despite long-standing interest in the compartmental structure of
food webs, past network analyses of food webs have been constrained by a
standard definition of compartments, or modules, that requires many links
within compartments and few links between them. Empirical analyses have been
further limited by low-resolution data for primary producers. In this paper, we
present a Bayesian computational method for identifying group structure in food
webs using a flexible definition of a group that can describe both functional
roles and standard compartments. The Serengeti ecosystem provides an
opportunity to examine structure in a newly compiled food web that includes
species-level resolution among plants, allowing us to address whether groups in
the food web correspond to tightly-connected compartments or functional groups,
and whether network structure reflects spatial or trophic organization, or a
combination of the two. We have compiled the major mammalian and plant
components of the Serengeti food web from published literature, and we infer
its group structure using our method. We find that network structure
corresponds to spatially distinct plant groups coupled at higher trophic levels
by groups of herbivores, which are in turn coupled by carnivore groups. Thus
the group structure of the Serengeti web represents a mixture of trophic guild
structure and spatial patterns, in contrast to the standard compartments
typically identified in ecological networks. From data consisting only of nodes
and links, the group structure that emerges supports recent ideas on spatial
coupling and energy channels in ecosystems that have been proposed as important
for persistence.Comment: 28 pages, 6 figures (+ 3 supporting), 2 tables (+ 4 supporting
Bayesian Models for Spatially Explicit Interactions Between Neighbouring Plants
Interactions between neighbouring plants drive population and community dynamics in terrestrial ecosystems. Understanding these interactions is critical for both fundamental and applied ecology. Spatial approaches to model neighbour interactions are necessary, as interaction strength depends on the distance between neighbouring plants. Recent Bayesian advancements, including the Hamiltonian Monte Carlo algorithm, offer the flexibility and speed to fit models of spatially explicit neighbour interactions. We present a guide for parameterizing these models in the Stan programming language and demonstrate how Bayesian computation can assist ecological inference on plantâplant interactions.
Modelling plant neighbour interactions presents several challenges for ecological modelling. First, nonlinear models for distance decay can be prone to identifiability problems, resulting in lack of model convergence. Second, the pairwise data structure of plantâplant interaction matrices often leads to large matrices that demand high computational power. Third, hierarchical structure in plantâplant interaction data is ubiquitous, including repeated measurements within field plots, species and individuals. Hierarchical terms (e.g. ârandom effectsâ) can result in model convergence problems caused by correlations between coefficients. We explore modelling solutions for these challenges with examples representing spatial data on plant demographic rates: growth, survival and recruitment.
We show that ragged matrices reduce computational challenges inherent to pairwise matrices, resulting in higher efficiency across data types. We also demonstrate how metrics for model convergence, including divergent transitions and effective sample size, can help diagnose problems that result from complex nonlinear structures. Finally, we explore when to use different model structures for hierarchical terms, including centred and non-centred parameterizations. We provide reproducible examples written in Stan to enable ecologists to fit and troubleshoot a broad range of neighbourhood interaction models.
Spatially explicit models are increasingly central to many ecological questions. Our work illustrates how novel Bayesian tools can provide flexibility, speed and diagnostic capacity for fitting plant neighbour models to large, complex datasets. The methods we demonstrate are applicable to any dataset that includes a response variable and locations of observations, from forest inventory plots to remotely sensed imagery. Further developments in statistical models for neighbour interactions are likely to improve our understanding of plant population and community ecology across systems and scales
Isotopic niche variability in macroconsumers of the East Scotia Ridge (Southern Ocean) hydrothermal vents: What more can we learn from an ellipse?
Aspects of between-individual trophic niche width can be explored through the isotopic niche concept. In many cases isotopic variability can be influenced by the scale of sampling and biological characteristics including body size or sex. Sample size-corrected (SEAc) and Bayesian (SEAb) standard ellipse areas and generalised least squares (GLS) models were used to explore the spatial variability of δ13C and δ15N in Kiwa tyleri (decapod), Gigantopelta chessoia (peltospirid gastropod) and Vulcanolepas scotiaensis (stalked barnacle) collected from 3 hydrothermal vent field sites (E2, E9N and E9S) on the East Scotia Ridge (ESR), Southern Ocean. SEAb only revealed spatial differences in isotopic niche area in male K. tyleri. However, the parameters used to draw the SEAc, eccentricity (E) and angle of the major SEAc axis to the x-axis (θ), indicated spatial differences in the relationships between δ13C and δ15N in all 3 species. The GLS models indicated that there were spatial differences in isotope-length trends, which were related to E and θ of the SEAc. This indicated that E and θ were potentially driven by underlying trophic and biological processes that varied with body size. Examination of the isotopic niches using standard ellipse areas and their parameters in conjunction with length-based analyses provided a means by which a proportion of the isotopic variability within each species could be described. We suggest that the parameters E and θ offer additional ecological insight that has so far been overlooked in isotopic niche studies
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