The use of linear mixed effects models (LMMs) is increasingly common in the analysis of biological data. Whilst LMMs offer a flexible approach to modelling a broad range of data types, ecological data are often complex and require complex model structures, and the fitting and interpretation of such models is not always straightforward. The ability to achieve robust biological inference requires that practitioners know how and when to apply these tools. Here, we provide a general overview of current methods for the application of LMMs to biological data, and highlight the typical pitfalls that can be encountered in the statistical modelling process. We tackle several issues regarding methods of model selection, with particular reference to the use of information theory and multi-model inference in ecology. We offer practical solutions and direct the reader to key references that provide further technical detail for those seeking a deeper understanding. This overview should serve as a widely accessible code of best practice for applying LMMs to complex biological problems and model structures, and in doing so improve the robustness of conclusions drawn from studies investigating ecological and evolutionary questions.

A brief introduction to mixed effects modelling and multi-model inference in ecology.

Summary

1. Body condition is a major concept in ecology addressed in countless studies, and a variety of non-destructive methods are used to estimate the condition of individuals based on the relationship between body mass M and measures of length L. There is currently no consensus about the most appropriate condition index (CI) method, and various traditions have been established within subdisciplines in which ecologists tend to apply that method used previously by their peers.



2. Here, we present a reappraisal of six conventional CI methods: Fulton’s index (K = M/L3), Quetelet’s index (BMI = M/L2), Relative condition (Kn, computed as the observed individual mass divided by the predicted mass Mi* = a Lib where a and b are determined by ordinary least squares (OLS) regression of M against L), Relative mass (Wr, where a and b above are determined from a reference population), the Residual index (Ri, the residuals from an OLS regression of M against L) and ancova. We compare the performance of these methods with that of the Scaled mass index, a novel method which was previously shown to perform better than Ri as a predictor of fat and other body components [J. Peig & A.J. Green (2009) Oikos, 118, 1883].



3. To be reliable, a CI method must successfully account for the changing relationship between M and L as body size changes and growth occurs (i.e. for the scaling relationship between M and L). Using data from three species of small mammals we show that, unlike the Scaled mass index, all six conventional methods fail to do this, and as a result they consistently lead to significant differences in CIs between age classes and sex that are a mere consequence of changes in body size. The Scaled mass index was also particularly successful at detecting changes in CI resulting from high levels of contaminants.

https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1365-2435.2010.01751.x

The paradigm of body condition: a critical reappraisal of current methods based on mass and length

Environmental parasitology deals with the interactions between parasites and pollutants in the environment. Their sensitivity to pollutants and environmental disturbances makes many parasite taxa useful indicators of environmental health and anthropogenic impact. Over the last 20 years, three main research directions have been shown to be highly promising and relevant, namely parasites as accumulation indicators for selected pollutants, parasites as effect indicators, and the role of parasites interacting with established bioindicators. The current paper focuses on the potential use of parasites as indicators of environmental pollution and the interactions with their hosts. By reviewing some of the most recent findings in the field of environmental parasitology, we summarize the current state of the art and try to identify promising ideas for future research directions. In detail, we address the suitability of parasites as accumulation indicators and their possible application to demonstrate biological availability of pollutants; the role of parasites as pollutant sinks; the interaction between parasites and biomarkers focusing on combined effects of parasitism and pollution on the health of their hosts; and the use of parasites as indicators of contaminants and ecosystem health. Therefore, this review highlights the application of parasites as indicators at different biological scales, from the organismal to the ecosystem.

/pdf/parasite-responses-to-pollution-what-we-know-and-where-we-go-2aebi8pkno.pdf

Parasite responses to pollution: what we know and where we go in ‘Environmental Parasitology’

Human-altered environmental conditions affect many species at the global scale. An extreme form of anthropogenic alteration is the existence and rapid increase of urban areas. A key question, then, is how species cope with urbanization. It has been suggested that rural and urban conspecifics show differences in behaviour and personality. However, (i) a generalization of this phenomenon has never been made; and (ii) it is still unclear whether differences in personality traits between rural and urban conspecifics are the result of phenotypic plasticity or of intrinsic differences. In a literature review, we show that behavioural differences between rural and urban conspecifics are common and taxonomically widespread among animals, suggesting a significant ecological impact of urbanization on animal behaviour. In order to gain insight into the mechanisms leading to behavioural differences in urban individuals, we hand-raised and kept European blackbirds (Turdus merula) from a rural and a nearby urban area under common-garden conditions. Using these birds, we investigated individual variation in two behavioural responses to the presence of novel objects: approach to an object in a familiar area (here defined as neophilia), and avoidance of an object in a familiar foraging context (defined as neophobia). Neophilic and neophobic behaviours were mildly correlated and repeatable even across a time period of one year, indicating stable individual behavioural strategies. Blackbirds from the urban population were more neophobic and seasonally less neophilic than blackbirds from the nearby rural area. These intrinsic differences in personality traits are likely the result of microevolutionary changes, although we cannot fully exclude early developmental influences.

Urbanization and its effects on personality traits: a result of microevolution or phenotypic plasticity?

When vertebrate physiological ecologists use the terms ‘stress’ or ‘physiological stress’, they typically mean the level of hypothalamus–pituitary–adrenal (HPA-) axis activation. Measurements of stress hormone concentrations (e.g. glucocorticoids in blood, urine or faeces), leukocytes (e.g. the neutrophil–lymphocyte ratio or heterophil equivalent), immunofunction (e.g. innate, cell-mediated or humoral immunity measures) and regenerative anaemia (e.g. mean erythrocyte volume and red blood cell distribution width) have all been used to estimate HPA-axis activity in free-living vertebrates. Stress metrics have provided insights into aspects of autecology or population regulation that could not have been easily obtained using other indices of population wellbeing, such as body condition or relative abundance. However, short- and long-term stress (often problematically termed acute and chronic stress, respectively) can interact in unpredictable ways. When animals experience trapping and handling stress before blood, faeces and/or urine is sampled, the interaction of short- and long-term stress can confound interpretation of the data, a fact not always acknowledged in studies of stress in free-living vertebrates. This review examines how stress metrics can be confounded when estimates of HPA-axis activation are collected for free-living vertebrates and outlines some approaches that can be used to help circumvent the influence of potentially confounding factors.

Interpreting indices of physiological stress in free-living vertebrates

Body condition is assumed to influence an animal’s health and fitness. Various non-destructive methods based on body mass and a measure of body length have been used as condition indices (CIs), but the dominant method amongst ecologists is currently the calculation of residuals from an ordinary least squares (OLS) regression of body mass against length. Recent studies of energy reserves in small mammals and starlings claimed to validate this method, although we argue that they did not include the most appropriate tests since they compared the CI with the absolute size of energy reserves. We present a novel CI (the ‘scaled mass index’) based on the central principle of scaling, with important methodological, biological and conceptual advantages. Through a reanalysis of data from small mammals, starlings and snakes, we show that the scaled mass index is a better indicator of the relative size of energy reserves and other body components than OLS residuals, performing better in all seven species and in 19 out of 20 analyses. We also present an empirical and theoretical comparison of the scaled mass index and OLS residuals as CIs. We argue that the scaled mass index is a useful new tool for ecologists.

New perspectives for estimating body condition from mass/length data: the scaled mass index as an alternative method

Cadmium and lead concentrations in Skrjabinotaenia lobata (Cestoda: Catenotaeniidae) and in its host, Apodemus sylvaticus (Rodentia: Muridae) in the urban dumping site of Garraf (Spain)

Jordi Peig

Papers

New perspectives for estimating body condition from mass/length data: the scaled mass index as an alternative method

The paradigm of body condition: a critical reappraisal of current methods based on mass and length

Cadmium and lead concentrations in Skrjabinotaenia lobata (Cestoda: Catenotaeniidae) and in its host, Apodemus sylvaticus (Rodentia: Muridae) in the urban dumping site of Garraf (Spain)