Issue 8.2

Issue 8.2 is now online!

The February issue of Methods is now online!

This issue contains four(!) Applications articles and two Open Access articles. These six papers are freely available to everyone – no subscription required.

 Earth Mover’s Distance: The Earth Mover’s Distance (or EMD) is a method commonly used in image retrieval applications. The authors of this paper propose its use to calculate similarity in space use in the framework of movement ecology. This will be helpful for many questions regarding behavioural ecology, wildlife management and conservation.

 warbleR: The R package warbleR is a new package for the analysis of animal acoustic signal structure. It offers functions for downloading avian vocalisations from the open-access online repository Xeno-Canto, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals or importing detected signals from other software, and much more.

– meteR: The open-source R package, meteR directly calculates all of Maximum entropy theory of ecology’s (METE’s) predictions from a variety of data formats; automatically handles approximations and other technical details; and provides high-level plotting and model comparison functions to explore and interrogate models.

– Noise Egg: The Noise Egg is a device that can produce a low-frequency sound, which can be used as an experimental source of noise both in aquaria and in the field. It was developed to study the effects of noise on communication and behaviour in small aquatic animals; however, it could be used for other purposes, such as testing the propagation of certain frequencies in shallow-water habitats.

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Issue 8.1

Issue 8.1 is now online!

The January issue of Methods is now online!

All of the articles in this month’s issue of Methods in Ecology and Evolution are free for the whole year. You will not need a subscription to access or download any of them throughout 2017.

Our first issue of this year contains three Applications articles and two Open Access articles. These five papers will be freely available permanently.

– CDMetaPOP: Cost–Distance Meta-POPulation provides a novel tool for questions in landscape genetics by incorporating population viability analysis, while linking directly to conservation applications.

– Rphylopars: An R implementation of PhyloPars, a tool for phylogenetic imputation of missing data and estimation of trait covariance across species (phylogenetic covariance) and within species (phenotypic covariance). Rphylopars provides expanded capabilities over the original PhyloPars interface including a fast linear-time algorithm, thus allowing for extremely large data sets (which were previously computationally infeasible) to be analysed in seconds or minutes rather than hours.

– ggtree: An R package that provides programmable visualisation and annotation of phylogenetic trees. ggtree can read more tree file formats than other software and allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion.

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Why Do We Need Digital Elevation Models to Infer the Local Adaptation of Alpine Plants?

Post provided by Kevin Leempoel

dsc_4214-crest-flight-27-06-11It’s not easy to characterise the local environment of species living in mountains because these habitats are highly heterogeneous. At a large scale, we typically assume that temperature varies with altitude, but at a local scale, we understand that exposure to wind or being in the shade has a great influence on climatic conditions. If you go from the south-facing to the north-facing side of a mountain, it can be easily 5°C colder. If we can feel that, so can the organisms that live up there. Plants in particular are submitted to tremendous climatic variations over a year. What we want to know is: how did they adapt to these climatic variations and how localised is their adaptation?

Overcoming the Challenges of Measuring Local Adaptation

We don’t know much about how organisms adapt locally because it’s so difficult to measure the environmental conditions that these plants are facing. Existing weather stations can’t capture micro-habitat conditions because they are few and far between. What we can do instead, is use topographic models of mountains to model their environment. After all, if orientation, slope or shade have an impact on climatic conditions, why couldn’t we use them to model local variations in temperature for example? Continue reading

Just snap it! Using Digital Cameras to Discover What Birds Eat

Post provided by Davide Gaglio and Richard Sherley

Digital photography has revolutionised the way we view ourselves, each other and our environment. The use of automated cameras (including camera traps) in particular has provided remarkable opportunities for biological research. Although mostly used for recreational purposes, the development of user-friendly, versatile auto-focus digital single lens reflex (DSLR) cameras allows researchers to collect large numbers of high quality images at relatively little cost.

These cameras can help to answer questions such as ‘What does that species feed its young?’ or ‘How big is this population?’, and can provide researchers with glimpses of rare events or previously unknown behaviours. We used these powerful research tools to develop a non-invasive method to assess the diets of birds that bring visible prey (e.g. prey carried in the bill or feet) back to their chicks. Continue reading

Issue 7.12

Issue 7.12 is now online!

The final 2016 issue of Methods is now online!

This month’s issue contains four Applications articles and two Open Access articles, all of which are freely available.

– iNEXT: The R package iNEXT (iNterpolation/EXTrapolation) provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the Hill number family (species richness, Shannon diversity and Simpson diversity).

– camtrapR: A new toolbox for flexible and efficient management of data generated in camera trap-based wildlife studies. The package implements a complete workflow for processing camera trapping data.

– rotl: An R package to search and download data from the Open Tree of Life directly in R. It uses common data structures allowing researchers to take advantage of the rich set of tools and methods that are available in R to manipulate, analyse and visualize phylogenies.

– Fluctuating-temperature chamber: A design for economical, programmable fluctuating-temperature chambers based on a relatively small commercially manufactured constant temperature chamber modified with a customized, user-friendly microcontroller.

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Smoothies and Sinusoids: Why Fourier Analysis is a Great Tool for Tropical Phenology

Post provided by Emma R. Bush and Nils Bunnefeld

What is Fourier Analysis?

Strictly speaking, Fourier analysis is the decomposition of any mathematical function into a series of sine and cosine waves (sinusoids). But let’s not talk about maths – how about food instead?

The Fourier transform is like a special set of sieves that helps you find out all the ingredients in your favourite smoothie ©VICUSCHKA/

The Fourier transform is like a special set of sieves that helps you find out all the ingredients in your favourite smoothie ©VICUSCHKA/

Imagine you’ve just bought a delicious smoothie from your local café. You like the smoothie so much that you want to know the recipe so that you can make it again at home whenever you want. You’re too shy to ask at the café, so you pour the smoothie through a series of special sieves that separate out each of the ingredients and you write down the recipe – 100ml orange juice, 50ml mango juice, 50ml banana purée and a handful of hipster kale (we haven’t tried this recipe, but we’re sure it would be lovely). You’re quite keen to keep drinking the smoothie, so you mix all the separated ingredients back together again, and the smoothie is just as delicious as before. Continue reading

Senior Editor Vacancy at Methods in Ecology and Evolution

Issue 6.7_Kakadu FloodplainsThe British Ecological Society (BES) is a thriving learned society established in 1913 whose vision is a world inspired, informed and influenced by ecology. It publishes five successful journals, and a quarterly newsletter, the Bulletin, that is distributed to its 5,000 members worldwide. At present, the BES is seeking an outstanding ecologist to join the team of Senior Editors on Methods in Ecology and Evolution.

Methods in Ecology and Evolution (MEE) is a high-profile broad-scope journal which promotes the development of new methods in ecology and evolution and facilitates their dissemination and uptake by the research community. It brings together papers from previously disparate sub-disciplines to provide a single forum for tracking methodological developments in all areas. The journal has excellent citation metrics including a current Impact Factor of 6.34 and an active social media presence.

Submissions to MEE are growing and we are seeking an Senior Editor to strengthen and complement the editorial team and to continue raising the journal’s profile worldwide. The journal’s editorial team currently consists of three Senior Editors who are supported by an international board of around 60 Associate Editors and dedicated editorial office personnel. The Editors work together to determine journal strategy and to increase the reputation and quality of the journal, in addition to making decisions on around 800 manuscripts submitted each year. Further details about the Journal and its current editorial team can be found at Continue reading

What is Methods in Ecology and Evolution?

In a new Methods in Ecology and Evolution podcast, the Senior Editors – Rob Freckleton, Bob O’Hara and Jana Vamosi – discuss the past, present and future of the journal. They talk about what sets it apart from other journals, their favourite articles and the kinds of papers that they would like to see more of. If you’re thinking about submitting to Methods in Ecology and Evolution, they have some advice for you as well.

Articles Mentioned by the Editors:

To find out more about Methods in Ecology and Evolution, read our Aims and Scope and Author Guidelines

Issue 7.11

Issue 7.11 is now online!

The November issue of Methods is now online!

This month’s issue contains four Applications articles and two Open Access articles, all of which are freely available.

– moveHMM: This R package allows ecologists to process GPS tracking data into series of step lengths and turning angles, and to fit a hidden Markov model to these data, allowing, in particular, for the incorporation of environmental covariates.

– BORIS: An open-source and multiplatform standalone program that allows a user-specific coding environment to be set for a computer-based review of previously recorded videos or live observations. Being open to user-specific settings, the program allows a project-based ethogram to be defined that can then be shared with collaborators, or can be imported or modified.

– inbreedR: An R package that provides functions to measure variance in inbreeding – through the strength of correlation in heterozygosity across marker loci – based on microsatellite and SNP markers with associated P-values and confidence intervals. Within the framework of Heterozygosity–fitness correlation theory, inbreedR also estimates the impact of inbreeding on marker heterozygosity and fitness.

– Terrestrial Precipitation Analysis: This package is comprised of the Precipitation Trends (P-Trend), Precipitation Attributes (P-Att) and Precipitation Manipulation (P-Man) tools. Combined, these web tools allow researchers to easily calculate fundamental precipitation statistics for past, present and projected future precipitation regimes for any terrestrial location in the world.

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Scat Collection Protocols for Dietary DNA Metabarcoding

DNA dietary analysis is a non-invasive tool used to identify the food consumed by vertebrates. The method relies on identifying prey DNA in the target animals’ scats. It’s especially useful for marine animals such as seals and seabirds as it is difficult to watch their feeding events.

In the video below, Julie McInnes describes scat collection protocols that she (along with Rachael Alderman, Bruce Deagle, Mary-Anne Lea, Ben Raymond and Simon Jarman) developed to optimise the detection of food DNA in vertebrate scat samples. The authors use the shy albatross to demonstrate their new methods.

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