Cover image gallery

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Issue 4.5

This cover image shows a female chacma baboon (Papio ursinus) in the Okavango Delta, Botswana. During floods, animals often have to cross inundated areas to reach small islands with high-valued food items, such as fig fruits. While some animals enjoy the fresh water, most are stressed by the possibility of encountering crocodiles. To assess how wildlife is affected by such events, metabolites of glucocorticoids (stress hormones) and other hormones can be extracted and measured from faeces. Although a powerful and non-invasive method to answer questions regarding endocrinological processes in free-ranging animals, the long-term storage of hormone samples at remote field sites is of concern.
The article linked to the picture assesses variation in hormones extracted from baboon faeces and stored under different conditions for a period of one year. The results underscore the strengths and weaknesses of different storage methods that can be performed at remote field stations.
Image credited to: Urs Kalbitzer.

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Long-term storage effects in steroid metabolite extracts from baboon (Papio sp.) faeces – a comparison of three commonly applied storage methods
Urs Kalbitzer and Michael Heistermann

Issue 4.4

Whilst volunteer data collection programs provide an opportunity to address the challenge of studying biodiversity across large spatial scales, issues regarding the quality of the data collected in this manner must be addressed. Volunteer survey protocols are typically less standardised than their professional equivalents and in “Comparing diversity data collected using a protocol designed for volunteers with results from a professional alternative” Holt et al. consider the implications of this for marine fish diversity studies. The image of a SCUBA diver was taken at Hin Muang pinnacle in South Andaman Sea.
Photo © jimcatlinphotography.com.

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Comparing diversity data collected using a protocol designed for volunteers with results from a professional alternative
Ben G. Holt, Rodolfo Rioja-Nieto, M. Aaron MacNeil, Jan Lupton and Carsten Rahbek

Issue 4.3

Long-term demographic studies that use individually identified animals offer invaluable views of ecological processes. Photo-id is a powerful tool for studying wild animals, particularly as there is no need to handle animals – a good image is all that is required to “capture” individuals for life. ExtractCompare is the latest version of a freely-available semi-automated photo-id system that allows standardized comparison of natural patterns. Crucially, the new software takes into account some of the complications that arise with data of this type which had been overlooked previously.
Although female grey seals (Halichoerus grypus) are distinctively and laterally asymmetrically patterned, they pose a challenging problem for automated photo-id because of the impossibility of controlling the camera distance and angle to the subject (seals swimming offshore, and only partly visible as pictured, or lying on the shore) and the wide range of body postures they display. This work uses an extensive photo-id database of an intensively studied breeding colony, North Rona, to consider the problems of individuals generating multiple encounter histories through the risk of false rejection of matches or being captured from a single side. Survival, abundance and preference can be estimated now using patterns from different body areas by measuring and allowing for the risk of false rejection.
The research has confirmed that apparent annual survival of female seals at North Rona is lower than expected, something that is reflected in the declining number of seal pups born there. Pup production at the island has fallen from over 2000 in the 1970s to around 500 at present, whereas other colonies have increased.
Image by Paddy Pomeroy.

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Analysis of photo-id data allowing for missed matches and individuals identified from opposite sides
Lex Hiby, William D. Paterson, Paula Redman, John Watkins, Sean D. Twiss, and Patrick Pomeroy

Issue 4.2

The image shows the Yorkshire Dales National Park (YDNP), UK, above the village of Malham after brief, heavy snowfall. It was taken during an April transect survey of curlew (Numenius arquata) and other wader species.  Within large areas, such as the YDNP, variables at multiple spatial scales can influence the distribution of bird species. When modelling the distribution of a species, the identification of the important variables, at the correct spatial scales, is important in developing the most reliable models. Models can be complicated by the large number of landscape-scale variables, problems with spatial autocorrelation and the fact that the same variable may influence a species at more than one spatial scale.  In "Identifying appropriate spatial scales of predictors in species distribution models with the random forest algorithm" the authors investigated a novel computational method to identify appropriate variables and their spatial scales for predicting population distributions. Analyses of simulated species distributions demonstrated that the technique facilitated the evaluation of multiple spatial scales of multiple variables against each other. This approach was then applied to a real dataset on curlew collected during the field survey mentioned above.
Image by Ute Bradter.

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Identifying appropriate spatial scales of predictors in species distribution models with the random forest algorithm
by Ute Bradter, William E. Kunin, John D. Altringham, Tim J. Thom, Tim G. Benton

Issue 4.1

There is a growing number of high-quality food-web datasets that are augmented with estimates of body mass and/or numerical abundance. In "Cheddar - analysis and visualisation of ecological communities in R" the authors present a new R package that provides a wide range of food-web and community-level analyses and plots, focussed on such enhanced data. The package allows a large range of commonly applied analyses and visualisations to be produced with just a few lines of R code. A rapidly emerging area of research examines how food-web patterns vary across environmental, spatial or temporal gradients. One of the datasets included with Cheddar describes ten naturally occurring stream communities sampled across a wide pH range. A number of food-web properties vary across this gradient, with diversity, linkage density and complexity all increasing with pH. The graphs shown on this cover image are from three different food webs, arranged in circles of radius proportional to the number of nodes in the web and with red lines representing trophic links. The lower two communities (Dargall Lane, right, and Old Lodge, left) are acidic. The top web is an aggregation of the ten regional webs, including data from base-rich sites with complex, species-rich communities.

Image by Murray Thompson.

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Cheddar: analysis and visualisation of ecological communities in R
by Lawrence N. Hudson, Rob Emerson, Gareth B. Jenkins, Katrin Layer, Mark E. Ledger, Doris E. Pichler, Murray S. A. Thompson, Eoin J. O'Gorman, Guy Woodward and Daniel C. Reuman

Issue 3.6

Networks of species interactions reflect ecologically important processes occurring at a range of timescales. Plant-pollinator interactions, for example, can be understood at very short time-scales corresponding to physical contacts, intermediate timescales reflecting seasonal or yearly associations, or long timescales reflecting co-evolutionary relationships. Here, for example, is a stingless bee, Tetragonisca jaty, interacting with a flower in Costa Rica. Understanding the different timescales in a system is necessary for correct inference using network methods. In 'Temporal dynamics and network analysis', Blonder et al. synthesize recent developments in network theory that are important when studying systems that change over time.

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Temporal dynamics and network analysis
by Benjamin Blonder, Tina W. Wey, Anna Dornhaus, Richard James and Andrew Sih

Issue 3.5

An important tool of animal population biology is the ability to recognize and follow individual animals over space and time. One non-invasive way to do this is through the use of photographic mark-recapture, wherein unique markings are used to recognize individual animals. In “A computer-assisted system for photographic mark–recapture analysis”, the authors present a new software tool, Wild-ID, that employs the SIFT algorithm to semi-automate the process of matching new digital images to those in an existing image database. They apply this technique to a population of Masai giraffe (Giraffa camelopardalis tippelskirchi) in and around Tarangire National Park in northern Tanzania. This image shows a pair of cropped giraffe images matched by Wild-ID. The red lines connect matching “SIFT features”, identified by white dots, in the two images. The green lines indicate where the features on the lower image “should” have been located based on the affine transform applied to the upper image.

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A computer-assisted system for photographic mark–recapture analysis
by Douglas T. Bolger, Thomas A. Morrison, Bennet Vance, Derek Lee and Hany Farid

Issue 3.4

Stable-isotope ratios measured in migrating animals have proven to be of great value in understanding migration. For example, when a dragonfly emerges from the water, the isotope signature in that water body is fixed in its wing tissues, which thus provide information about its geographic origin. In this study we compared the isotope value from dragonfly wings of known origin with spatially explicit isoscapes based on water isotopes in precipitation. The relationship was strong, confirming the value of the method to study dragonfly migration.

One of the species used in the analysis was Pachydiplax longipennis. This individual was photographed at Red Slough Wildlife Management Area, Oklahoma. Photo © Dennis Paulson.

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A dragonfly (δ2H) isoscape for North America: a new tool for determining natal origins of migratory aquatic emergent insects
by Keith Hobson et al.

Issue 3.3

Recently developed light-weighed tracking devices for positioning through light intensity pattern ('geolocation') have begun to greatly improve our knowledge of animal migration. However, the analysis of geolocator data is impeded by many factors potentially affecting light levels and thus, ultimately the determination of positions. Herein, weather and vegetation are major factors altering the light regime experienced by the animals. The picture shows a Common Rosefinch (Carpodactus erythrinus) featured with a 0.5 gram geolocator device.

In Geolocation by light: accuracy and precision affected by environmental factors Simeon Lisovski and colleagues demonstrated the effect of weather, topography and vegetation on the measurement of day/night length, time of solar midnight/noon and the resulting position estimates using light measurements from stationary geolocators at known places and from geolocators mounted on birds.

Photo © Germán Garcia - Creative Commons Attribution 2.0 Generic.

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Geolocation by light: accuracy and precision affected by environmental factors
by Simeon Lisovski et al.

Issue 3.2

This very high-resolution image of a beech-dominated forest in central Germany was taken by an unmanned aerial vehicle (UAV) at 250 meter above ground. In this photograph one can clearly recognize individual tree crowns and even smallest gaps. UAVs are increasingly used for ecological surveys because they provide extremely fine resolutions and thus allow the identification of previously undetected object details. Furthermore, UAVs can be considered as very cost-effective tools for the acquisition of data that can be used also very flexibly.

In Assessing biodiversity in forests using very high-resolution images and unmanned aerial vehicles Getzin, Wiegand and Schöning tested the hypothesis that gap-structural information on aerial images can be principally used for the ecological assessment of understorey plant diversity in forests. The authors demonstrate that spatially implicit information on gap shape metrics is indeed sufficient to reveal strong dependency between gap patterns as a filter for incoming light and plant biodiversity. The study highlights that understorey biodiversity can be actively controlled by the spatial quality, and not just quantity, of tree removal. Thus, even under the same quota of tree harvesting, the promotion of complex and irregularly shaped gaps may be beneficial to foster biodiversity in forests.

Photo © Getzin & Wiegand - Biodiversity Exploratories.

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Assessing biodiversity in forests using very high-resolution images and unmanned aerial vehicles
by Stephan Getzin, Kerstin Wiegand and Ingo Schöning

Issue 3.1

The African dwarf crocodile (Osteolaemus tetraspis) is endemic to closed-canopy forests of Central and West Africa and is the smallest of the world's true crocodiles. The species is difficult to study in the wild and therefore poorly known, but likely plays an important ecological role as a top aquatic predator in cool water forest systems. The dwarf crocodile is also a major food and economic resource to local people and, as a result, is threatened with overhunting for the bushmeat trade. The image depicts a collection of young dwarf crocodiles, possibly representing three cohorts, measured in a capture-recapture study in Loango National Park, Gabon.

The article linked to the image is On thinning of chains in MCMC by William Link and Mitchell Eaton. In the article, the authors caution against the routine practice of thinning chains in Markov chain Monte Carlo (MCMC) simulations. Many analysts, recognizing that MCMC precision decreases as the autocorrelation of the chains increases, routinely thin (sub-sample) their chains. Thinning reduces autocorrelation, but the associated gains in precision are more than offset by the reduction in chain length. Thinning of chains is therefore wasteful, though occasionally justified under circumstances discussed in the article.

The young dwarf crocodiles were photographed by Mitchell Eaton in 2004.

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On thinning of chains in MCMC
by William Link and Mitchell Eaton

Issue 2.6

Biological soil crusts (BSCs) are communities composed by mosses, lichens, liveworths fungi and bacteria that are prevalent in drylands worldwide. Lichen-dominated BSCs affect multiple ecosystem functions in those habitats where they are present, including carbon and nitrogen cycling, soil stabilization, and water infiltration and runoff.

In Randomization tests for quantifying species importance to ecosystem function, Nicholas Gotelli, Werner Ulrich and Fernando Maestre introduce randomization tests for evaluating the effect of individual species on ecosystem variables measured in multiple plots. This approach is tested using data on ecosystem functioning in lichen-dominated BSC assemblages from central Spain, and further validated using an independent microcosm experiment. The method proposed in this article provides a simple index and statistical test of species importance that can form the basis for additional hypothesis tests and experimental studies of species occurrence and ecosystem functioning.

This BSC-forming lichen community was photographed by Fernando T. Maestre in gypsum outcrops from Sax (SE Spain).

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Randomization tests for quantifying species importance to ecosystem function
by Nicholas J. Gotelli, Werner Ulrich and Fernando T. Maestre

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Impact – a FORTRAN program for gradient analysis.

Issue 2.5

Common or blue wildebeest (Connochaetes taurinus) can be found across the southern and eastern areas of Africa, grazing in areas of open savanna and grassland. This group were photographed in northern Tanzania by Thomas Morrison, Dartmouth College.

Over two and a half thousand such photographs of wildebeest were used to test a data-conditioning technique for overcoming misidentification error in capture-recapture studies, published in this issue of Methods in Ecology and Evolution.

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Estimating survival in photographic capture–recapture studies: overcoming misidentification error
by Thomas A. Morrison, Jun Yoshizaki, James D. Nichols and Douglas T. Bolger

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An illustration of "the challenging nature of individual wildebeest identification" undertaken during the course of this study.
 

Issue 2.4

Cane toads (Rhinella marina) are terrestrial amphibians native to Central and Southern America, and which were introduced to Australia in 1935 in an attempt to curb the spread of agricultural pests. Despite proving unsuccessful in this regard, cane toads have thrived and are now endemic in north-eastern Australia, and have had a noticable impact upon local biodiversity.

In Measuring amphibian immunocompetence: validation of the phytohemagglutinin skin-swelling assay in the cane toad, Rhinella marina, Brown, Shilton and Shine demonstrate that PHA injection offers a convenient assay to quantify immune function in frogs and toads, providing a convenient new tool with applications for assessing global amphibian declines.

This cane toad was photographed by conservation biologist Brian Gratwicke. Image licensed under Creative Commons Attribution 2.0 Generic (CC BY 2.0).

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Measuring amphibian immunocompetence: validation of the phytohemagglutinin skin-swelling assay in the cane toad, Rhinella marina
by Gregory P. Brown, Catherine M. Shilton and Richard Shine

Extra features

• View related papers published in other journals of the British Ecological Society
• View more of Brian Gratwicke's photographs

 

Issue 2.3

This striking cover image is an example of the graphical output of PASSaGE 2, an application providing a broad array of spatial statistical analyses not commonly found in other software packages or GIS software, documented in this edition of Methods in Ecology and Evolution. In this case, the image represents a colour-graded surface map of elevation data.

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PASSaGE: Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2
by Michael S. Rosenberg and Corey Devin Anderson

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Read more about our free application papers
 

Issue 2.2

A mixed-species group of coral reef fishes on Mangalonga Island, Solomon Islands. Coral reef fish communities are generally composed of a small number of subsets of coexisting species whose members often have a high degree of similarity in resource use. Given this similarity, the quantification of niche overlap in resource use is an important tool for investigating relative abundance distributions and species coexistence in coral reef fishes. Photo by Shane Geange.

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A unified analysis of niche overlap incorporating data of different types
by Shane Geange, Shirley Pledge, Kevin Burns and Jeffrey Shima

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Watch the demonstration of unified analysis with Shane Geange
 

Issue 2.1

Lepidochitona cinerea is a species of chiton: a form of marine mollsusc in the class Polyplacophora. Instead of solid shells, molluscs in this class posess eight interlocking aragonitic plates, allowing them to curl up and protect themselves when dislodged from the substrate. The polyplacophore fossil record stretches back for at leat 400 million years.

Gene sequencing of Lepidochitona cinerea has been used to provide a basis for the development of optimal gene selection protocols for future Polymerase Chain Reaction (PCR) multi-gene analyses, paving the way for the expansion of molecular-based reconstructions of deep molluscan phylogeny. The chitons' placement on a bivalve shell is, therefore, particularly appropriate. Photo credit: C. Kühne.

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Selecting ribosomal protein genes for invertebrate phylogenetic inferences: how many genes to resolve the Mollusca?
by Achim Meyer, Alexander Witek and Bernhard Lieb
 

Issue 1.4

Burrowing owls (Athene cunicularia) are found across both North and South America, where they nest in abandoned burrows such as those vacated by prairie dogs. Unusually for owls, they are frequently active by day, and include fruit and seeds in their varied diet. Data gathered from point-coordinate capture-recapture studies of burrowing owls has been used to develop new methods of estimating species population size in songbird and reptile species.

This female burrowing owl was photographed in Joshua Tree, California, and is believed to be one of a colony of up to twenty adult and juvenile owls. Photo credit: Kevin Cole, licensed under Creative Commons Attribution 2.0 Generic (CC BY 2.0).

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Estimating population size using capture-recapture encounter histories created from point-coordinate locations of animals
By Jeffrey Manning and Caren Goldberg

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View more of Kevin Cole’s work.
 

Issue 1.3

The arctic fox (Vulpes lagopus) is one of the main predators of the arctic tundra ecosystem. It is an opportunistic, circumpolar species that samples all year round the terrestrial or marine food chains. It feeds preferentially on small rodents but also on food sources containing variable or higher amounts of lipids, such as eggs of birds nesting in the Arctic. When using stable isotope analysis and mixing models to reconstruct a diet, results can be strongly biased by variable lipid concentrations in food sources. We used the diet of the arctic fox as an example illustrating the effects of different lipid levels in food sources on the estimation of diet composition. The adult fox photographed here was observed on Bylot Island, Nunavut, in August 2008.

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Sensitivity of stable isotope mixing models to variation in isotopic ratios: evaluating consequences of lipid extraction by Arnaud Tarroux, Dorothée Ehrich, Nicolas Lecomte, Timothy D. Jardine, Joël Bêty and Dominique Berteaux

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Watch an interview with Arnaud Tarroux about this article.
 

Issue 1.2

Eastern hemlock (Tsuga canadensis) is a foundation tree species in over 6 million hectares of eastern North American forests. This species is now threatened in much of its range as an exotic insect, the hemlock woolly adelgid (Adelges tsugae) spreads rapidly and killing hemlock trees within 5-10 years of infestation. Pre-emptive salvage logging in advance of the adelgid is also reducing hemlock cover, especially in northeastern North America. These panoramic photographs illustrate hemlock stands before and after girdling to simulate adelgid attack (top pair), before and after a logging operation (middle pair), and an undisturbed hemlock control plot (bottom pair) in the Harvard Forest Hemlock Removal experiment. Individual photographs were taken with a 24-mm Nikon manual lens mounted on a Nikon D-3 digital camera operated in FX mode. Each panorama was assembled from 4-7 individual photographs using Canon's Photostich software, version 3.1. Post-processing, including minor color correction and cropping, was done using IrfanView version 4.23. Photo credit and image processing: Aaron M. Ellison.

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Experimentally testing the role of foundation species in forests: the Harvard Forest Hemlock Removal Experiment by Aaron M. Ellison, Audrey A. Barker-Plotkin, David R. Foster and David A. Orwig

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Watch an interivew with Aaron Ellison about this article.
 

Issue 1.1

Asian swamp buffalo (Bubalus bubalis) introduced to Australia in the early 19th Century now populate much of the tropical north and cause severe environmental disturbances to savanna and wetland ecosystems. Despite a broad-scale cull of hundreds of thousands of free-ranging buffalo occurring in the 1980s and 1990s to eradicate brucellosis and tuberculosis, the population is recovering and continuing to threaten protected areas such as Kakadu National Park. A small wild harvest of several thousand buffalo occurs each year in Arnhem Land where mustering is aided by helicopters and on-ground vehicles. The buffalo pictured are housed in temporary holding pens and then shipped for live export. Photo credit: Jesse Northfield (used with permission).

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Spatially explicit spreadsheet modelling for optimising the efficiency of reducing invasive animal density by Clive R. McMahon, Barry W. Brook, Neil Collier and Corey J. A. Bradshaw

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Watch an interview with Corey Bradshaw about this article.

Virtual Issues

Open Access

The cover for this cross-journal virtual issue reuses Open Access Week promotional material, licensed under Creative Commons Attribution 2.0 Generic. 

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BES Journals - Open Access

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Learn more about open access publishing with Methods in Ecology and Evolution

Forests and Global Change

The covers for the virtual issues compiled by Methods in Ecology and Evolution and the Journal of Applied Ecology are both derived from the same photograph of red and green autumnal leaves, chosen to reflect the issues' complementary qualities. Photo credit: Junichiro Aoyama, licensed under Creative Commons Attribution 2.0 Generic. Adapted by Elizabeth Horne.

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Methods in Ecology and Evolution - Forests and Global Change
Journal of Applied Ecology - Forests and Global Change

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View the original image
View more of Junichiro Aoyama's work

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