The July issue of Methods is now online! 
This month’s issue features articles on evaluating biodiversity offsetting, managing remotely-collected data, quantifying log decay and much more.
Senior Editor Aaron Ellison has selected six featured articles this month – find out about them below. We also have three Applications and seven articles that are freely available to everyone – no subscription required!
落红不是无情物，化作春泥更护花。 –龚自珍(清)
“The fallen petals are not as cruel as they seem; they fertilize those in full bloom instead.” – Gong Zizhen (Qing Dynasty)
A decaying Douglas fir log
This picture shows a decomposing log of Douglas fir, Pseudotsuga menziesii (Mirb.) Franco, in Schovenhorst, The Netherlands, which is one of the deadwood incubation sites of the LOGLIFE “tree cemetery” project. 25 angiosperm and gymnosperm species covering a diverse range of functional traits were selected and incubated in the “common garden experiment”. This project was founded in 2012, aiming to disentangle the effects of different species’ wood traits and site-related environmental drivers on decomposition dynamics of wood, and its associated diversity of microbial and invertebrate communities.
Installing scientific instruments in the marine environment comes with many challenges. Equipment has to withstand the physical forces of tides, currents and storms. Researchers have to take into account the effects of biofouling, corrosion and human activities. Even access to the study site can pose its difficulties, as diving is limited by depth and weather conditions. Practical deployment mechanisms are therefore needed to sustain consistent data flows.
Acoustic telemetry enables the observation of animal movements in aquatic environments. Individual animals are fitted with a transmitter, relaying a signal that can be picked up by acoustic receivers. To facilitate a convenient installation of these instruments, we developed and tested a new design, mounting a receiver with an acoustic release on a tripod frame. This frame enables the recovery of all equipment and better yet, improves the quality of the data.
One of the unifying themes in ecology may be the acknowledgement that we live in a world of finite resources, and so we also live in a world of tradeoffs. A diverse range of research questions can be distilled into a question about tradeoffs. For example, how should an animal forage in the presence of predation? Which selective forces determine the life history of a flowering perennial? How should we manage a population to maximize the sustainable harvest rate?
Questions as varied as these can all be addressed using the same method of stochastic programming[1] (SDP) (see McNamara and Houston, 1986; Rees et al. 1999; and Runge and Johnson, 2002, respectively). SDP has been used extensively to study optimal tradeoffs in a wide range of applications in ecology, evolutionary biology, and management. It is a flexible and powerful modelling framework that allows for simultaneous consideration of an individual’s state, how an optimal decision might explicitly depend on time, and for a probabilistic landscape of risks and rewards.
The June issue of Methods is now online!
This month’s issue features articles on designing camera trap studies, measuring coral growth rates, quantifying carbon assimilation by marine calcifiers and much more.
Senior Editor Rob Freckleton has selected six featured articles this month – find out about them below. We’ve also got three Applications and a Practical Tools article which are freely available to everyone – no subscription required!
The May issue of Methods is now online!
As well as four Application and two Practical Tools articles, the latest issue of Methods in Ecology and Evolution includes six Featured Articles handpicked by our editors – you can find out more about them below.
Featured Articles
Tree-based inference of species interaction networks from abundance data
To be relevant, any network inference methodology needs to handle count data and to account for possible environmental effects. It also needs to distinguish between direct interactions and indirect associations, and graphical models provide a convenient framework for this purpose. A new method from Momal et al. meets these requirements and compares well with state-of-the-art approaches, even when the underlying graph strongly differs from a tree.
Modifying twisted nematic LCD screens to create dichromatic visual stimuli with LEDs – Practical Tools
Didion et al. present a cost-effective way of modifying a twisted nematic LCD screen that utilises coloured LEDs, that allows measuring animals’ sensitivity to, and discrimination between, wavelengths of light. It has the benefit of not requiring a-priori knowledge of animals’ photoreceptor classes. This technique overcomes many of the limitations of RGB-based LCD screens in a cost-effective way, and allows more accurate testing of the role of colour in visually guided behaviours.
moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in r – Application – Available Open Access
moveVis automates the processing of movement and environmental data to turn them into an animation. This includes (a) the regularisation of movement trajectories enforcing uniform time instances and intervals across all trajectories, (b) the frame-wise mapping of movement trajectories onto temporally static or dynamic environmental layers, (c) the addition of customisations, for example, map elements or colour scales and (d) the rendering of frames into an animation encoded as GIF or video file.
A simple, reliable method for long-term, in-stream data logger installation using rock-climbing software – Practical Tools
Long-term deployment of in-stream data loggers provides valuable information about stream conditions, particularly in times when streams are difficult to sample manually. Fogg et al. present a method for data logger installation in streams using rock-climbing hardware that is simple to assemble, economical and minimally invasive.
Exploring density- and frequency-dependent interactions experimentally: An r program for generating hexagonal fan designs – Application
Species interactions and diversity are strongly impacted by local processes, with both the density of a focal species and its frequency in the community being important. Hexagonal fan designs can include a range of both densities and frequencies in a single plot, providing large economies in space and material. Rozins et al. present an R program whereby the user can rapidly view a variety of designs and determine the configurations that work best with their space and material constraints.
Multi-species occupancy models as robust estimators of community richness Understanding patterns of diversity is central to ecology and conservation, yet estimates of diversity are often biased by imperfect detection. Tingley et al. use both simulations and an empirical dataset to evaluate bias, precision, accuracy and coverage of estimates of N from multi-species occupancy models compared to the widely applied iChao2 non-parametric estimator.
Application and Practical Tools articles
We’ve got four Application and two Practical Tools articles in this month’s issue of Methods in Ecology and Evolution. Four of them have been covered in our Featured Articles above, so here are the other two:
Climate change research often relies on downscaled general circulation models (GCMs) to project future climate scenarios. As more than 35 GCMs are available at a resolution of 10km and finer, methods are needed to choose which GCM projection is appropriate to use for a region of interest. GCM compareR is a new open-source web app for comparing GCMs, allowing the informed selection from the range of available projections by researchers and policy makers.
AragoJ – A free, open-source software to aid single camera photogrammetry studies Close-range photogrammetry retrieves quantitative information about objects using photography. While software options for extracting information from 3D reconstructions exists, tools for 2D images are scarce, often tailored to specific applications. AragoJ is an open-source software, designed to integrate all steps in 2D close-range photogrammetry in a single program.
The flower on the cover
This issue’s cover shows an experimental array of Silene latifolia flowers, used to study the spread of the anther‐smut pathogen, Microbotryum lychnidis‐dioicae. The array contains a mixture of healthy and diseased flowers, where the influence of the pathogen is to replace the pollen with dark‐colored fungal spores that are conspicuous against the white flower background. Pollinators then pick up and distribute the spores during normal foraging visits.
In their article, Rozins et al. address the difficulty in designing experimental arrays that examine species interactions with a combination of density and frequency‐dependent effects. In addition to such vector‐borne disease transmission, local competition within plant communities are strongly influenced by density and frequency‐dependent responses to species composition and abundance. The authors demonstrate the merit of radial hexagonal fan designs over more traditional systematic grid arrays. To facilitate experimental studies and to ease implementation, they present an R program whereby the user can rapidly view a variety of designs and determine the configurations that work best with their space and material constraints. Photo credit: ©Michael E. Hood, Amherst College
To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be showing up in issues later this year.
Cover image for issue 3.4 © Dennis Paulson.
Our latest issue covers an impressive array of subjects: from metabarcoding (with associated presentation), to population genetics and population monitoring (with video explaining a microphone array system). Modelling and monitoring dispersal also features heavily with four articles, one of which is accompanied by a video for a novel telemetry system to track wild animals. Articles also include topics such as transient dynamics, a review on hormone assay, phylogenetic comparative analysis, stable isotopes (featuring our cover article), plant physiology and finally, statistical methods.
About the cover
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 A dragonfly (δ2H) isoscape for North America: a new tool for determining natal origins of migratory aquatic emergent insects, Keith Hobson, David Soto, Dennis Paulson, Leonard Wassenaar and John Matthews 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.
Also, these recently accepted articles have appeared on Early View:
Rapid determination of comparative drought tolerance traits: using an osmometer to predict turgor loss point by Megan K. Bartlett, Christine Scoffoni, Rico Ardy, Ya Zhang, Shanwen Sun, Kunfang Cao and Lawren Sack
Free application: taxonstand: An r package for species names standardisation in vegetation databases by Luis Cayuela, Íñigo Granzow-de la Cerda, Fabio S. Albuquerque and Duncan J. Golicher
Projecting species’ range expansion dynamics: sources of systematic biases when scaling up patterns and processes by Greta Bocedi, Guy Pe’er, Risto K. Heikkinen, Yiannis Matsinos and Justin M. J. Travis
Review: Temporal dynamics and network analysis by Benjamin Blonder, Tina W. Wey, Anna Dornhaus, Richard James and Andrew Sih
Related
Map of the United States, showing the study area
Another of our recent articles, Assessing transferability of ecological models: an underappreciated aspect of statistical validation, by Seth Wenger and Julian Olden, has recently been highlighted on Faculty of 1000. F1000 is a platform providing post-publication peer-review and selecting only the most important articles in biology and medicine. Just 2% of published articles are highlighted on Faculty of 1000 each month.
Ben Bolker and Michael McCoy, Faculty of 1000 reviewers, note of Wenger and Olden’s article:
The authors show that allowing for spatial variability can provide a better assessment of transferability (a form of out-of-sample accuracy).
This lesson, delivered with a good deal of common sense, reminds us more generally that model selection and assessment tools can never be magic bullets, but must be tempered with an awareness of the scope and limitations of the data.
Read more about this article in a previous post by Bob O’Hara.
Related:
Two articles have been recently highlighted in the press.
Iain Stott, Dave Hodgson and Stuart Townley, University of Exeter, have developed Popdemo, a new software tool for helping prioritise efforts in species conservation. As well as determining which species need our help, it will also be useful in pest control and sustainable harvesting. The University press release was picked up by a variety of websites, including Phys.org and eScienceNews.
Batrachochytrium dendrobatidis. Source: Johnson/Speare, Public Domain
Science Daily, yesterday reported that preserved frogs hold clue to deadly pathogen. Katy Richards-Hrdlicka, University of Yale, and author of an article just appeared in Methods in Ecology and Evolution said:
“I have long proposed that the millions of amphibians maintained in natural-history collections around the world are just waiting to be sampled”
Katy developed a new method for charting the history of Batrachochytrium dendrobatidis, or Bd, an infectious pathogen driving many species to extinction.
popdemo: an R package for population demography using projection matrix analysis
by Iain Stott, Dave Hodgson and Stuart Townley
Extracting the amphibian chytrid fungus from formalin-fixed specimens
by Katy Richards-Hrdlicka
Cover image for issue 3.3
© Germán Garcia – CC Attribution 2.0 Generic
About the issue
Issue 3.3 contains an amazing number of extra features: three videos, one podcast and one Powerpoint presentation. The topics in the issue range from DNA barcoding, surveys, measuring diversity, population and movement modelling and includes five free applications.
About the cover
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.
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