Stuart Bearhop

Source partitioning using stable isotopes: coping with too much variation.

Background Stable isotope analysis is increasingly being utilised across broad areas of ecology and biology. Key to much of this work is the use of mixing models to estimate the proportion of sources contributing to a mixture such as in diet estimation. Methodology By accurately reflecting natural variation and uncertainty to generate robust probability estimates of source proportions, the application of Bayesian methods to stable isotope mixing models promises to enable researchers to address an array of new questions, and approach current questions with greater insight and honesty. Conclusions We outline a framework that builds on recently published Bayesian isotopic mixing models and present a new open source R package, SIAR. The formulation in R will allow for continued and rapid development of this core model into an all-encompassing single analysis suite for stable isotope research.

Comparing isotopic niche widths among and within communities: SIBER – Stable Isotope Bayesian Ellipses in R

1. The use of stable isotope data to infer characteristics of community structure and niche width of community members has become increasingly common. Although these developments have provided ecologists with new perspectives, their full impact has been hampered by an inability to statistically compare individual communities using descriptive metrics. 2. We solve these issues by reformulating the metrics in a Bayesian framework. This reformulation takes account of uncertainty in the sampled data and naturally incorporates error arising from the sampling process, propagating it through to the derived metrics. 3. Furthermore, we develop novel multivariate ellipse-based metrics as an alternative to the currently employed Convex Hull methods when applied to single community members. We show that unlike Convex Hulls, the ellipses are unbiased with respect to sample size, and their estimation via Bayesian inference allows robust comparison to be made among data sets comprising different sample sizes. 4. These new metrics, which we call SIBER (Stable Isotope Bayesian Ellipses in R), open up more avenues for direct comparison of isotopic niches across communities. The computational code to calculate the new metrics is implemented in the free-to-download package Stable Isotope Analysis for the R statistical environment.

A niche for isotopic ecology

Fifty years ago, GE Hutchinson defined the ecological niche as a hypervolume in n-dimensional space with environmental variables as axes. Ecologists have recently developed renewed interest in the concept, and technological advances now allow us to use stable isotope analyses to quantify these niche dimensions. Analogously, we define the isotopic niche as an area (in δ-space) with isotopic values (δ-values) as coordinates. To make isotopic measurements comparable to other niche formulations, we propose transforming δ-space to p-space, where axes represent relative proportions of isotopically distinct resources incorporated into an animals tissues. We illustrate the isotopic niche with two examples: the application of historic ecology to conservation biology and ontogenetic niche shifts. Sustaining renewed interest in the niche requires novel methods to measure the variables that define it. Stable isotope analyses are a natural, perhaps crucial, tool in contemporary studies of the ecological niche.

Applying stable isotopes to examine food-web structure: an overview of analytical tools

Stable isotope analysis has emerged as one of the primary means for examining the structure and dynamics of food webs, and numerous analytical approaches are now commonly used in the field. Techniques range from simple, qualitative inferences based on the isotopic niche, to Bayesian mixing models that can be used to characterize food‐web structure at multiple hierarchical levels. We provide a comprehensive review of these techniques, and thus a single reference source to help identify the most useful approaches to apply to a given data set. We structure the review around four general questions: (1) what is the trophic position of an organism in a food web?; (2) which resource pools support consumers?; (3) what additional information does relative position of consumers in isotopic space reveal about food‐web structure?; and (4) what is the degree of trophic variability at the intrapopulation level? For each general question, we detail different approaches that have been applied, discussing the strengths and weaknesses of each. We conclude with a set of suggestions that transcend individual analytical approaches, and provide guidance for future applications in the field.

Carry‐over effects as drivers of fitness differences in animals

1. Carry-over effects occur when processes in one season influence the success of an individual in the following season. This phenomenon has the potential to explain a large amount of variation in individual fitness, but so far has only been described in a limited number of species. This is largely due to difficulties associated with tracking individuals between periods of the annual cycle, but also because of a lack of research specifically designed to examine hypotheses related to carry-over effects. 2. We review the known mechanisms that drive carry-over effects, most notably macronutrient supply, and highlight the types of life histories and ecological situations where we would expect them to most often occur. We also identify a number of other potential mechanisms that require investigation, including micronutrients such as antioxidants. 3. We propose a series of experiments designed to estimate the relative contributions of extrinsic and intrinsic quality effects in the pre-breeding season, which in turn will allow an accurate estimation of the magnitude of carry-over effects. To date this has proven immensely difficult, and we hope that the experimental frameworks described here will stimulate new avenues of research vital to advancing our understanding of how carry-over effects can shape animal life histories. 4. We also explore the potential of state-dependent modelling as a tool for investigating carry-over effects, most notably for its ability to calculate optimal rates of acquisition of a multitude of resources over the course of the annual cycle, and also because it allows us to vary the strength of density-dependent relationships which can alter the magnitude of carry-over effects in either a synergistic or agonistic fashion. 5. In conclusion carry-over effects are likely to be far more widespread than currently indicated, and they are likely to be driven by a multitude of factors including both macro- and micronutrients. For this reason they could feasibly be responsible for a large amount of the observed variation in performance among individuals, and consequently warrant a wealth of new research designed specifically to decompose components of variation in fitness attributes related to processes across and within seasons.

Factors That Influence Assimilation Rates and Fractionation of Nitrogen and Carbon Stable Isotopes in Avian Blood and Feathers

By switching great skuas Catharacta skua from one isotopically distinct diet to another, we measured diet‐tissue discrimination factors and tested the assumption that dietary nitrogen and carbon isotope signatures are incorporated into blood and feathers at similar rates. We also examined the effects of metabolic rate and looked for evidence of isotopic routing. We found that blood δ15N and δ13C signatures altered after the diet switch at similar rates (14.4 d and 15.7 d, respectively). Qualitative analyses imply that the same was true with feathers. Mass balance calculations suggest that only a small amount of lipid is likely to be involved in the synthesis of blood and feathers. Differences in diet‐tissue discrimination factors before and after the diet switch may mean that toward the end of the experiment, some of the nutrients for blood synthesis had been coming from stores. Repeated measures mixed models provided evidence that increases in metabolic rate might accelerate fractional turnover rates in blood. There is a need for more laboratory‐based experimental isotope studies in order to address further questions that this study has raised.

Food for thought: supplementary feeding as a driver of ecological change in avian populations

Every year, millions of households provide huge quantities of supplementary food to wild birds. While alteration of the natural dynamics of food supply represents a major intervention in avian ecology, we have a remarkably limited understanding of the impacts of this widespread pastime. Here, we examine the many and varied responses of birds to supplementary feeding at backyard feeders – in large-scale management projects and in focused academic studies – and evaluate population responses to the bird-feeding phenomenon. Our review encompasses a wide range of species, from songbirds to raptors, and compares provisioning with a variety of foods, at different times of year and in different locations. We consider positive impacts, such as aiding species conservation programs, and negative ones, such as increased risk of disease transmission. It seems highly likely that natural selection is being artificially perturbed, as feeding influences almost every aspect of bird ecology, including reproduction, behavior...

Changes in fisheries discard rates and seabird communities.

It is clear that discards from commercial fisheries are a key food resource for many seabird species around the world. But predicting the response of seabird communities to changes in discard rates is problematic and requires historical data to elucidate the confounding effects of other, more ‘natural’ ecological processes. In the North Sea, declining stocks, changes in technical measures, changes in population structure and the establishment of a recovery programme for cod (Gadus morhua) will alter the amount of fish discarded. This region also supports internationally important populations of seabirds, some of which feed extensively, but facultatively, on discards, in particular on undersized haddock (Melanogrammus aeglefinus) and whiting (Merlangius merlangus). Here we use long-term data sets from the northern North Sea to show that there is a direct link between discard availability and discard use by a generalist predator and scavenger—the great skua (Stercorarius skua). Reduced rates of discarding, particularly when coupled with reduced availability of small shoaling pelagic fish such as sandeel (Ammodytes marinus), result in an increase in predation by great skuas on other birds. This switching of prey by a facultative scavenger presents a potentially serious threat to some seabird communities.

Stable isotope ratios indicate that body condition in migrating passerines is influenced by winter habitat

Although predicted some time ago, there has been little success in demonstrating that the overall fitness of migratory birds depends on the combined influences of their experiences over all seasons. We used stable carbon isotope signatures (δ13C) in the claws of migrating black–throated blue warblers Dendroica caerulescens to infer their wintering habitats and investigated whether winter habitat selection can be linked to condition during migration. Resident bird species with low δ13C corresponded to selection of more mesic habitats, and migrating birds with low δ13C were in better condition than conspecifics with higher δ13C signatures. These findings concur with empirical observations on the wintering grounds, where dominants (mostly males) tend to exclude subordinates from mesic areas (considered to be high–quality habitats). We believe that variation in condition during migration may be one of the key factors determining differences in arrival times and condition at the breeding areas, which in turn have a major influence on reproductive success.

Erroneous behaviour of MixSIR, a recently published Bayesian isotope mixing model: a discussion of Moore & Semmens (2008)

The application of Bayesian methods to stable isotopic mixing problems, including inference of diet has the potential to revolutionise ecological research. Using simulated data we show that a recently published model MixSIR fails to correctly identify the true underlying dietary proportions more than 50% of the time and fails with increasing frequency as additional unquantified error is added. While the source of the fundamental failure remains elusive, mitigating solutions are suggested for dealing with additional unquantified variation. Moreover, MixSIR uses a formulation for a prior distribution that results in an opaque and unintuitive covariance structure.