Synthesis, 'How to...', Review and Commentary Papers

Synthesis papers

Synthesis papers are balanced, comprehensive and concise overviews of well-established field or laboratory study systems targeted at a broad ecological audience. These papers review the trajectory of these studies and their impact on our understanding of general ecological theory, in addition to highlighting potentially fruitful avenues for future research. For more details please see our Synthesis paper guidelines.

'How to...' papers

How To papers are instructional papers that aim to serve as a practical guide for animal ecologists in using a specific experimental or theoretical model or system. For more details please see our 'How to...' paper guidelines.

Review papers

The editors welcome short, synthetic review articles providing novel insight and synthesis on topical subjects of general interest to the readership. Please note that we are not looking to publish papers that simply review the literature; reviews still need to provide genuine advances in our ecological thinking.

Commentary papers

This section of the journal is designed to stimulate scientific debate. Contributions may be short articles presenting new ideas (without data), conceptual advance or opinions.

We welcome submissions of Synthesis, 'How to...',  Review and Commentary papers. Please contact the editorial office if you would like to discuss a submission. Please see the author guidelines for submission details for these paper types.

Synthesis papers

Novel insights on population and range edge dynamics using an unparalleled spatiotemporal record of species invasion
Kristine L. Grayson, Derek M. Johnson

The gypsy moth Slow the Spread programme has resulted in one of the most spatially and temporally detailed population datasets in existence. This paper reviews the profound opportunity this research has provided to the fields of population dynamics and invasion biology and appeals to a broad audience by showing the wide variety of research areas and ecological theory facilitated by a well‐known invasive species. This synthesis also highlights how important ecological questions can be answered by thinking more broadly about monitoring data.

Wildlife disease ecology from the individual to the population: Insights from a long-term study of a naturally infected European badger population
Jenni L. McDonald, Andrew Robertson, Matthew J. Silk

Understanding the dynamics of infectious diseases in wildlife relies on long‐term individual‐based datasets. A study of European badgers naturally infected with bovine tuberculosis has produced unique insights into a diverse range of epidemiological and ecological questions, advancing our understanding of disease ecology from individual heterogeneity right through to population‐level processes.

Using experimentation to understand the 10-year snowshoe hare cycle in the boreal forest of North America
Charles J. Krebs, Rudy Boonstra, Stan Boutin

The authors summarize 45 years of research on the classic snowshoe hare—Canada lynx cycle and provide a comprehensive explanation of hare demography and suggest what research is needed in the future.

Insights into population ecology from long-term studies of red grouse Lagopus lagopus scoticus
Jesus Martínez-Padilla, Steve M. Redpath, Mohammed Zeineddine, François Mougeot
Vol 83 Iss 1 pp 85–98

Long-term studies have been the backbone of population ecology. This paper reviews the trajectory and impact of red grouse studies in this field. The authors highlight the impact of parasites on red grouse population dynamics, the role of intrinsic mechanisms in cyclic dynamics, and the need to consider multiple, interacting mechanisms.

'How to...' papers

A practical guide for inferring reliable dominance hierarchies and estimating their uncertainty
Alfredo Sánchez‐Tójar, Julia Schroeder, Damien R. Farine

Dominance hierarchies are widespread in nature. However, there are no clear guidelines about the sampling effort necessary for inferring reliable hierarchies, nor are there established tools for quantifying their uncertainty. The authors fill this gap of knowledge and provide researchers with an easy step-by-step guide on how to analyse dominance hierarchies.

When to choose dynamic versus static social network analysis
Damien R. Farine

Dynamic networks represent the substrate underpinning all evolutionary processes. While their importance is regularly touted, there is widespread confusion over their use and little guidance is available. This paper represents the first steps at establishing guidelines for when increased quality of predictions warrant accepting greater analytical complexity. The paper provides an important complement to a previous “How to…” by Farine and Whitehead.

Accounting for genetic differences among unknown parents in microevolutionary studies: how to include genetic groups in quantitative genetic animal models
Matthew E. Wolak & Jane M. Reid
Vol 86 Iss 1 pp 7–20

Quantitative genetic ‘animal models’ are central to studies of adaptive evolution in wild populations. The authors show that unknown parents are ubiquitous in wild population pedigrees and can substantially bias animal model parameter estimates. The authors comprehensively demonstrate ‘how to’ implement ‘genetic group’ methods, which minimize bias and estimate key biological parameters.

Constructing, conducting and interpreting animal social network analysis
Damien R. Farine & Hal Whitehead
Vol 84 Iss 5 pp 1144–1163

This practical guide covers principles for collecting data from social animals, constructing social networks, and interpret network measures. It explains how to conduct hypothesis testing using null models with common statistical tests, and how to estimate power and precision. It includes examples and tutorials for doing animal social network analysis using R.

Read the Virtual Issue on social network analysis featuring this paper here.

On the variety of methods for calculating confidence intervals by bootstrapping
Marie-Therese Puth, Markus Neuhäuser & Graeme D. Ruxton
Vol 84 Iss 4 pp 892–897

Many scientists use bootstrapping as a method to generate confidence intervals around statistics that they calculate. But several different bootstrapping methods are available. The authors highlight that they can give quite different results, and offer advice on which to chose and how best to implement them.

Building integral projection models: a user's guide
Mark Rees, Dylan Z. Childs & Stephen P. Ellner
Vol 83 Iss 3 pp 528–545

Recent advances in the construction and analysis of integral projection models (IPMs) mean they offer a remarkably powerful tool to study ecological and evolutionary dynamics. Part of their appeal is that they can be parameterised using data frequently collected by ecologists. Here, Rees and colleagues provide a detailed description of the steps involved in constructing an IPM, explaining how to: (i) translate one’s study system into an IPM; (ii) implement an IPM; and (iii) diagnose potential problems with an IPM. The authors emphasize how the study organism's life cycle, and the timing of censuses, together determine the structure of the IPM kernel and important aspects of the statistical analysis used to parameterise an IPM using data on marked individuals.

Quantifying individual variation in behaviour: mixed-effect modelling approaches
Niels J. Dingemanse & Ned A. Dochtermann
Vol 82 Iss 1 pp 39-54

Growing interest in proximate and ultimate causes and consequences of between- and within-individual variation in labile components of the phenotype – such as behaviour or physiology – characterizes current research in evolutionary ecology. Here, in this 'How to' paper, Dingemanse and Dochtermann explain how to use mixed-effect models to partition variation in, and correlations among, phenotypic attributes into between- and within-individual variance components. The authors detail optimal sampling schemes to accurately estimate (with sufficient power) a wide range of repeatabilities and key (co)variance components, such as between- and within-individual correlations.

An ecologist's guide to the animal model
Alastair J. Wilson, Denis Réale, Michelle N. Clements, Michael M. Morrissey, Erik Postma, Craig A. Walling, Loeske E. B. Kruuk & Daniel H. Nussey
Vol 79 Iss 1 pp 13-26

In one of our first 'how to' papers Wilson and colleagues provide a user's guide for researchers planning on using the Animal Model. The review outlines key concepts in quantitative genetics and how an animal model estimates relevant quantitative genetic parameters, such as heritabilities or genetic correlations. Using example tutorials, some basic applications of the animal model are explored and the important statistical issues relating to best practice when fitting different kinds of mixed models are discussed. The authors also touch on more complex applications of the animal model, and highlight key pitfalls and dangers for the researcher wanting to begin using quantitative genetic tools to address ecological and evolutionary questions.

Review papers

A computer vision for animal ecology
Ben Weinstein

Ecologists are increasingly using image capture to bolster data collection. However, reviewing these images remains a bottleneck. Computer vision can increase the accuracy and efficiency of image review. The author outlines the goals, tools and applications of ecological computer vision to animal ecology.

Dynamic, spatial models of parasite transmission in wildlife: their structure, applications, and remaining challenges
Lauren A. White, James D. Forester, Meggan E. Craft

This paper provides a comprehensive overview of dynamic, spatial models and how they have contributed to understanding pathogen transmission in wildlife. It highlights patterns in the literature, possible integration with other ecological disciplines, and shows how spatial models can contribute to understanding changes in transmission patterns resulting from anthropogenic activity.

An evolutionary framework outlining the integration of individual social and spatial ecology
Quinn M.R. Webber, Eric Vander Wal

The authors integrate the ecological and evolutionary implications of individual social and spatial behaviour as the 'socioecological environment'. They discuss the role of animal personality, nice theory, quantitative genetics, and eco-evolutionary dynamics through the lens of the 'socioecological environment'.

Allee effects in social species
Elena Angulo, Gloria M. Luque, Stephen D. Gregory, John W. Wenzel, Carmen Bessa‐Gomes, Ludek Berec, Franck Courchamp

In social species, individuals form groups to optimise their fitness. When group size is small, extinctions are more likely, a demographic process called Allee effect. The authors review evidence for Allee effects in different taxa and they model the role of demographic and behavioural factors that may combine to strengthen Allee effects.

The many faces of fear: a synthesis of the methodological variation in characterizing predation risk
Remington J. Moll, Kyle M. Redilla, Tutilo Mudumba, Arthur B. Muneza, Steven M. Gray, Leandro Abade, Matt W. Hayward, Joshua J. Millspaugh, Robert A. Montgomery
Vol 86 Iss 4 pp 749–765

Predators strongly influence prey behaviour via the risk of death, but ‘risk’ can be characterized in many ways. The authors quantify variation in how researchers define, measure, model and interpret ‘risk’, discuss why this variation is important and suggest how risk‐related research can be improved.

Does primary productivity modulate the indirect effects of large herbivores? A global meta-analysis
Joshua H. Daskin and Robert M. Pringle
Vol 85 Iss 4 pp 857–868

The authors show that the strength of the effects of large mammalian herbivores (deer, antelope, elephants, etc.) on the abundance of other animals is greatest in the least productive ecosystems. Where climate change reduces primary productivity, the impacts of ongoing herbivore population declines and irruptions may be greatest.

COMADRE: a global data base of animal demography
Roberto Salguero-Gómez, Owen R. Jones, C. Ruth Archer et al.
Vol 85 Iss 2 pp 371-384

Population ecologists have developed and published thousands of matrix population models for animals ranging from C. elegans to corals, sheep, lions or even humans, but these data were dispersed in the literature. The authors introduce the COMADRE Animal Matrix Database, an open-data repository with high-resolution demographic information for animals world-wide.

Can habitat selection predict abundance?
Mark S. Boyce, Chris J. Johnson, Evelyn H. Merrill, Scott E. Nielsen, Erling J. Solberg and Bram Van Moorter
Vol 85 Iss 1 pp 11-20

Habitat is fundamental to the distribution and abundance of animals. The authors show how habitat selection models can be linked to population size thereby creating a direct link between habitats and population ecology.

Relationship between growth and standard metabolic rate: measurement artefacts and implications for habitat use and life-history adaptation in salmonids
Jordan Rosenfeld, Travis Van Leeuwen, Jeffrey Richards & David Allen
Vol 84 Iss 1 pp 4-20

Mass-specific standard metabolic rate (SMR, or maintenance metabolism) varies greatly among individuals. Metabolism is particularly sensitive to variation in food consumption and growth creating the potential for significant bias in measured SMR for animals that are growing (e.g. juveniles) or of uncertain nutritional status. Consequently, interpreting individual variation in metabolism requires a sound understanding of the potentially confounding role of growth and the relative importance of fixed (genetic) vs. environmental drivers of SMR variation. This review clarifies some of the mechanisms that drive variation in metabolic state among individuals or through ontogeny, and highlights how they relate to variation in capacity for growth, and how they may arise from fundamental ecological tradeoffs that influence anatomical design.

Species diversity and community similarity in fluctuating environments: parametric approaches using species abundance distributions
Bernt-Erik Sæther, Steinar Engen & Vidar Grøtan
Vol 82 Iss 4 pp 721–738

Characterizing and comparing communities are difficult challenges because processes involving species interactions as well as causing fluctuations in population size generally are unknown. The authors provide here the first comprehensive review of how to analyse community dynamics in space and time using parametric approaches utilizing the full distribution of abundances of species rather than some summary indices. They go on to suggest that such specific assumptions for the choice of species abundance model will facilitate more robust comparisons of changes in community structure in time and space.

Mechanistic models of animal migration behaviour – their diversity, structure and use
Silke Bauer & Marcel Klaassen
Vol 82 Iss 3 pp 498-508

Recently, migration research has been in the upswing with many new and more general insights being gained – mainly due to the development of new tracking and logging devices. Although modelling approaches have at the same time also proliferated, the application of these theoretical models has not kept pace with the recent rapid advances in empirical methods. In this review, the authors provide an overview of the existing approaches for studying migration, and characterise their general features, assumptions and limitations, but also their data requirements for parameterisation and scrutiny of model predictions. They also review the use of modelling approaches across 107 studies, characterising their use across taxa and research questions, highlighting the biases and resulting research opportunities, indicated above. Finally, they provide a summary of the model characteristics to assist in selecting candidate modelling approaches for future applications.

Female ornaments revisited – are they correlated with offspring quality?
Jarle T. Nordeide, Jukka Kekäläinen, Matti Janhunen & Raine Kortet
Vol 82 Iss 1 pp 26-38

Understanding the evolution of signalling and female ornaments remains a difficult challenge in evolutionary ecology. The direct selection hypothesis has been posited a general explanation for the evolution of ornaments in females, and is currently widely considered as a main mechanism accounting for the evolution of female ornaments. Here, Nordeide and colleagues challenge the generality of this view by reviewing the literature for empirical studies on mutually ornamented species with conventional sex roles, focusing on the association between female ornaments and quality of their offspring.

Evidence-based control of canine rabies: a critical review of population density reduction
Michelle K. Morters, Olivier Restif, Katie Hampson, Sarah Cleaveland, James L. N. Wood & Andrew J. K. Conlan
Vol 82 Iss 1 pp 6-14

Rabies persists in a diverse range of reservoir hosts and remains a major lethal zoonotic disease primarily in developing communities; most people are infected by dog bites. Despite the availability of effective vaccines, the control of rabies is often complicated by the use of methods that aim to reduce population density, including culling. However, recent evidence questions density-dependent transmission in domestic dogs and thus any role for culling domestic dogs as a means to control rabies. Here, a group of leading scientists critically review both empirical and theoretical evidence regarding the role of density in the transmission of rabies, and the clear distinction between wildlife and domestic dogs. Through reviewing, for the first time, the evidence regarding culling for canine rabies, this article raises serious practical and ethical implications of population density reduction.

Direct fitness of group living mammals varies with breeding strategy, climate and fitness estimates
Luis A. Ebensperger, Daniela S. Rivera & Loren D. Hayes
Vol 81 Iss 5 pp 1013-1023

This review is the first formal meta-analysis made to quantitatively test hypotheses that explain (predict) covariation between direct fitness and group living across social mammals. The authors show that group living had modest, yet positive effects on direct fitness. For instance, positive and significant effects characterized studies conducted on singular (highly skewed) as opposed to plural breeding (slightly skewed) societies, in tropical as opposed to temperate or arid climates, and carnivores and primates, but not rodents and other mammals. This review provides an important step towards understanding and predicting covariation between fitness and sociality and has a great potential to influence and stimulate subsequent studies on the subject. Image: Spotted Hyaena Crocuta crocuta taken by Claudia Amphlett.  The female spotted hyaena and cubs (two of which are her own) are members of the largest clan in Amboseli National Park, Kenya.

Beyond phytohaemagglutinin: assessing vertebrate immune function across ecological contexts
Gregory E. Demas, Devin A. Zysling, Brianna R. Beechler, Michael P. Muehlenbein & Susannah S. French
Vol 80 Iss 4 pp 710-730

The focus of this review is to describe a wide range of eco-immunology techniques, from the simple to the sophisticated, with the goal of providing researchers with a range of options to consider incorporating in their own research programs.  By incorporating assessments of immune function into their specific research questions, animal ecologists will gain a more comprehensive understanding of organism–environment interactions.

Wildlife diseases: from individuals to ecosystems
Daniel M. Tompkins, Alison M. Dunn, Matthew J. Smith & Sandra Telfer
Vol 80 Iss 1 pp 19-38

The Authors review our ecological understanding of wildlife infectious diseases from the individual host to the ecosystem scale, highlighting where conceptual thinking lacks verification, discussing difficulties and challenges, and offering potential future research directions.  They look at cross-scale interactions associated with parasitism and how such interactions may offer key insights into bigger picture questions such as when and how different regulatory factors are important, when disease can cause species extinctions, and what characteristics are indicative of functionally resilient ecosystems.

Carry-over effects as drivers of fitness differences in animals
Xavier A. Harrison, Jonathan D. Blount, Richard Inger, D. Ryan Norris & Stuart Bearhop
Vol 80 Iss 1 pp 4-18

Carry over effects are likely to explain a significant amount of variation in life history traits, yet we have a very poor understanding of the ways in which they operate or how widespread they are. Here we review the evidence for carry over effects and suggest a number of priorities for future investigation.

Mechanisms driving change: altered species interactions and ecosystem function through global warming 
Lochran W. Traill, Matthew L. M. Lim, Navjot S. Sodhi & Corey J. A. Bradshaw
Vol 79 Iss 5 pp 937-947

Traill et al. review the mechanisms behind ecosystem functions, the processes that facilitate energy transfer along food webs, and the major processes that allow the cycling of carbon, oxygen and nitrogen, and use case studies to show how these have already been, and will continue to be, altered by global warming.

Maximal heat dissipation capacity and hyperthermia risk: neglected key factors in the ecology of endotherms
John R. Speakman & Elzbieta Król
Vol 79 Iss 4 pp 726-746

In their review Speakman and Krol suggest that capacity to dissipate heat is a major constraint on endotherm maximal metabolic rates and hence their ecology.

Analysis of variance with unbalanced data: an update for ecology & evolution
Andy Hector, Stefanie von Felten & Bernhard Schmid
Vol 79 Iss 2 pp 308-316

Facctorial analysis of variance (anova) with unbalanced (non-orthogonal) data is a commonplace but controversial and poorly understood topic in applied statistics. We summarize the main recent developments and emphasise the shift away from the search for the 'right' anova table in favour of presenting one or more models that best suit the objectives of the analysis.

Considering ecological dynamics in resource selection functions
Philip D. McLoughlin, Douglas W. Morris, Daniel Fortin, Eric Vander Wal & Adrienne L. Contasti
Vol 79 Iss 1 pp 4-12

We believe that there is a need for us to reacquaint ourselves with ecological theory when interpreting Resource Selection Function models. We outline a suite of factors likely to govern ecologically based variation in a Resource Selection Function.  Investigating the basis of ecological dynamics in a Resource Selection Function will allow us to develop more robust models when applied to forecasting the spatial distribution of animals. It may also further our understanding of the relative importance of ecological interactions on the distribution and abundance of species.

Ecological feedbacks and the evolution of resistance
Meghan A. Duffy & Samantha E. Forde
Vol 78 Iss 6 pp 1106-1112

The idea that parasites can affect host diversity is pervasive, and the possibility that parasites can increase host diversity is of particular interest. In this review, we focus on diversity in the resistance of hosts to their parasites, and on the different ways in which parasites can increase or decrease this resistance diversity.

Linking movement behaviour, dispersal and population processes: is individual variation a key?
Colin Hawkes
Vol 78 Iss 5 pp 894-906

Movement behaviour has become increasingly important in dispersal ecology and dispersal is central to the development of spatially explicit population ecology. The ways in which the elements have been brought together are reviewed with particular emphasis on dispersal distance distributions and the value of mechanistic models.  (It is with regret we announce that Colin Hawkes died suddenly in July 2009.  Our deepest sympathy goes to his son Tom and the rest of the family).

Cascading top-down effects of changing oceanic predator abundances
Julia K. Baum & Boris Worm
Vol 78 Iss 4 pp 699-714

Top-down control can be an important determinant of ecosystem structure and function, but in oceanic ecosystems, where cascading effects of predator depletions, recoveries, and invasions could be significant, such effects had rarely been demonstrated until recently.
Here we synthesize the evidence for oceanic top-down control that has emerged over the last decade, focusing on large, high trophic-level predators inhabiting continental shelves, seas, and the open ocean.

Ecological networks - beyond food webs
Thomas C. Ings, José M. Montoya, Jordi Bascompte, Nico Blüthgen, Lee Brown, Carsten F. Dormann, François Edwards, David Figueroa, Ute Jacob, J. Iwan Jones, Rasmus B. Lauridsen, Mark E. Ledger, Hannah M. Lewis, Jens M. Olesen, F.J. Frank Van Veen, Phil H. Warren & Guy Woodward
Vol 78 Iss 1 pp 253-269

Ecological networks can be subdivided into three broad types: 'traditional' food webs, mutualistic networks and host–parasitoid networks. There is a recent trend towards cross-comparisons among network types and also to take a more mechanistic, as opposed to phenomenological, perspective. For example, analysis of network configurations, such as compartments, allows us to explore the role of co-evolution in structuring mutualistic networks and host–parasitoid networks, and of body size in food webs.

A review of extinction in experimental populations
Authors: Blaine D. Griffen John M. Drake Vol 77 Iss 6 pp 1274-1287
Population extinction is a fundamental ecological process. Recent experimental work has begun to test the large body of theory that predicts how demographic, genetic and environmental factors influence extinction risk. We review empirical studies of extinction conducted under controlled laboratory conditions.  Our synthesis highlights four findings; highlighting the need to integrate community ecology into population theory, studies are needed that quantitatively compare observed and predicted extinction rates, need for more investigation into migration effects, laboratory experiments often conflict with field studies.

Commentary papers

Advancing research on animal‐transported subsidies by integrating animal movement and ecosystem modelling
Julia E. Earl, Patrick A. Zollner
Vol 86 Iss 5 pp 987–997

We synthesize relevant literature on active subsidies and movement ecology in order to propose a concept to predict active subsidy spatial distributions. We discuss innovative techniques to facilitate the integration of animal movement and ecosystem data.

Do animals exercise to keep fit?
Lewis G. Halsey
Vol 85 Iss 3 pp 614-620

We humans know we are not physically fit unless we do extra, voluntary exercise. Yet we have never asked whether the same is true for animals. If it is, then given that energy will be spent keeping fit this raises important issues about new energetic trade-offs, which have never been considered.

Tackling extremes: challenges for ecological and evolutionary research on extreme climatic events
Liam D. Bailey and Martijn van de Pol
Vol 85 Iss 1 pp 85-96

There has been growing ecological interest on the topic of extreme climatic events, yet there has been no critical discussion of current work. In this paper the authors discuss how to define an extreme event, potential future research questions, and methods to improve research quality.

British Ecological Society Presidential Address

Mosquito ecology and control of malaria
H. Charles J. Godfray
Vol 82 Iss 1 pp 15-25

Vector control is a crucial aspect of limiting the spread of malaria, and it relies of an understanding of Anopheles mosquito ecology and in particular population dynamics. In this article derived from his presidential address, former BES president Charles Godfray argues that a more explicitly ecological approach to mosquito biology may assist in the design of vector control programmes. He usese examples concerning the mosquitoes that transmit malaria in Africa, and provides a brief overview of Anopheles and Plasmodium biology and the main interventions available to reduce disease burden. He also describes some innovative ways it may be possible to control mosquitoes utilising modern molecular biology and finally considers the threats, opportunities and challenges to mosquito vector ecology.