Issue 11.9: Methods for individual bird recognition, zooplankton sampling and more!

The September issue of Methods is now online! 11.9 JPEG

We have a larger issue of 14 articles this month, featuring  methods for individual bird recognition, zooplankton sampling, coral health assessment and much more.

Senior Editor Lee Hsiang Liow has selected five featured articles – find out about them below. We also have three Applications, three Practical Tools articles and 11 articles that are freely available to everyone – no subscription required!

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Navigating the data-rich world of aquatic acoustic telemetry

Post provided by Kim Whoriskey

Early Career Researcher Kim Whoriskey takes us behind the Methods paper ‘Current and emerging statistical techniques for aquatic telemetry data: A guide to analysing spatially discrete animal detections’ which led to her being shortlisted for our Robert May Prize in 2019.

Understanding how aquatic animals move is becoming increasingly important for protecting them. Knowing where they migrate, how long they stay, and what they do when they travel through changing marine environments provides us with key information on movement corridors, habitat hotspots, and changing population distributions. This information can then be used to help manage and conserve many different aquatic species, from developing guidelines for recreational fishing practices to defining marine spatial planning measures.

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Our August Issue is OUT NOW

The August issue of Methods is now online!Cover JPEG

We have a larger issue of 14 articles this month, featuring tools for microbial evolution experiments, automatic biomass estimation of invertebrates, labeling biological samples and much more.

Senior Editor Bob O’Hara has selected five featured articles this month – find out about them below. We also have four Applications, one Practical Tools article and 10 articles that are freely available to everyone – no subscription required!

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Happy 10th Anniversary to us!

This year is our 10th Anniversary! To celebrate, we’ve made a timeline of highlights from the past decade, from the first paper ever submitted, to a top-cited article with 3,295 citations.

We’d like to give a big thanks our dedicated editors, plus all the authors and reviewers who are developing the fields of ecology and evolution with groundbreaking new methods. Here’s to 10 more years!

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Issue 11.7: Biodiversity offsetting, demersal fisheries & decaying logs

The July issue of Methods is now online! Cover JPEG

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!

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Methodology matters for comparing coarse wood and bark decay rates across tree species

Post provided by Chenhui Chang

 

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)

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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.

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The tripod frame: mooring acoustic receivers on the seabed

Post provided by Jolien Goossens

Jolien Goossens tells us about the challenges of installing acoustic receivers on the seabed and the tripod they designed to overcome them.

sea

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.

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Neo was right—The Matrix explains everything

Post provided by Jody Reimer

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?

Jody

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. 

[1] Also known as Markov Decision Processes

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Issue 11.6: goats, camera traps, coral imaging and more!

The June issue of Methods is now online!

June Cover

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!

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Issue 11.5: Our May issue is now online!

The May issue of Methods is now online!11.5 Cover jpeg

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 LEDsPractical 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.x

moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in rApplication – 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.

streamA simple, reliable method for long-term, in-stream data logger installation using rock-climbing softwarePractical 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 designsApplication
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:

GCM compareR: A web application to assess differences and assist in the selection of General Circulation Models for climate change researchice

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

11.5 Cover jpeg

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.