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