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.

Working from Home, Isolation and Staying Sane

Post provided by Graziella Iossa

Since I’ve been working from home and self-isolating for health reasons since the end of last summer, I thought that a post around the strategies that have helped me during this time might be useful.

Maslow’s Hierarchy of Needs

If you cant go to work to do the science,
the science comes home with you!
©Chloe Robinson

So, first and foremost, your mental health. It’s really hard to concentrate on anything work-related if you’re not in the right mental state. Of course, these are not ordinary times, so making sure that family, friends and those we care about are doing well, would be my first step. When I feel anxious about the times ahead, the single most important thing that helps me to deal with anxiety is having those who I care for the most, close by. If that’s not possible because they’re self-isolating, keeping in touch remotely regularly is the next best thing. Developmental psychologists recognise that human motivation is linked to a hierarchy of needs: if the most basic needs are not met, more complex needs cannot be fulfilled. In a pandemic, it’s likely that our priorities will change and we need to adapt to them, this might take a while and that’s to be expected.

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Standardising Methods in Climate Change Experiments: A Community Effort

Post provided by AUD HALBRITTER

CHINESE TRANSLATION PROVIDED BY HUI TANG

這篇博客文章也有中文版

Climate change is threatening biodiversity and ecosystems around the world. We urgently need to better understand how species and ecosystems respond to these changes. There are already thousands of climate change experiments and observational studies out there that could be used to synthesise findings across systems and regions. But it turns out that making meaningful syntheses isn‘t always so straightforward!

The Need for Standardised Methods and Reporting

There are two major challenges (and some minor ones too) for synthesising data across different experiments. First, the data are not always available. This problem arises because key study information – such as metadata, covariates or methodological details – are often not adequately or consistently reported across studies.

The second problem is that scientists use different protocols. This leads to a diversity of ways of measuring and quantifying the same variables. Different protocols may measure or report the same variables in slightly different ways, so the data are not compatible. Consistency in measurements and protocols is one reason why working in large networks – such as ITEX, Herbivory, or NutNet – to name only a few, is so powerful. In these networks, experiments and observations are repeated across large regions or worldwide using strict protocols for experimental design and measurements. Continue reading

Issue 10.12: Statistical Ecology, UAVs, Invasive Species and More

The December issue of Methods is now online!

The final 2019 issue of Methods in Ecology and Evolution is online now.

To close out another brilliant year, we’ve got papers on invasive species, convolutional neural networks, rapid spatial risk modelling, species distribution models and much more.

You can find out more about our Featured Articles (selected by the Senior Editor) below. We also discuss this month’s Open Access and freely available papers we’ve published in our latest issue (Practical Tools and Applications articles are always free to access, whether you have a subscription or not) .

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Thank You to All of Our Reviewers: Peer Review Week 2019

As many of you will already know, this week is Peer Review Week (16-20 September). Peer Review Week is a global event celebrating the vital work that is done by reviewers in all disciplines. Throughout the week, we’ve been looking back at some of the peer review advice and guidance that we’ve published on the blog.

The theme for this year’s Peer Review Week is quality in review. So we thought that the best way to end the week would be to thank to everyone who has reviewed for us. Without the hard work and expertise of the people who voluntarily review papers for us, Methods in Ecology and Evolution would not be the successful journal that it is today. We are incredibly grateful for all of the time and effort that reviewers put into reading and commenting on the manuscripts that we send to them.

We’d like to send a HUGE THANK YOU to everyone who has ever reviewed for Methods in Ecology and Evolution – whether you’ve worked on one paper or twenty – we really appreciate your time and effort.

You can see the names of everyone who has reviewed for us so far in 2019 on our website.

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Could We Be Treating Invertebrates More Ethically?

Post provided by ELEANOR DRINKWATER

©Joaquim Alves Gaspar

For ecology to stay ethical and maintain public support, we need to revisit invertebrate ethics in research.  With our recent advances in understanding invertebrate cognition and shifts in public opinion, an ethical re-examination of currently used methodologies is needed. In our article – ‘Keeping invertebrate research ethical in a landscape of shifting public opinion’ – that’s exactly what we aim to do.

Invertebrate Cognition

Recent work, particularly on lobsters, has raised questions about whether invertebrates can experience suffering. In lobsters for example, noxious stimuli can induce long term changes in behaviour, and these changes can be inhibited by adding analgesic. While these findings can be interpreted as evidence for pain perception in crustaceans, the question of invertebrate suffering is still hotly debated, and a firm consensus is still to be reached. But these studies, coupled with recent public concern about the ethics of large-scale sampling projects, highlight the need for discussion on invertebrate ethics in ecology research. Continue reading

Analysing Big Datasets while Answering Big Ecological Questions: #BESQuantMove2019

Post provided by LAURA GRAHAM and THEONI PHOTOPOULOU

Last week we heard about the importance of small conferences from Natalie Cooper. Hopefully she inspired you to look into smaller meetings going on this summer. If so, how about joining the Quantitative and Movement Special Interest Groups in Sheffield on 9 and 10 July for our back-to-back annual meetings?

This joint meeting will take advantage of shared strengths as well as shared challenges between the two groups and foster links between them. Both days will be a mix of keynotes, short contributed talks, poster sessions and discussion. Plus lots of all-important networking.

The meeting will be along the common theme of analysing big datasets while answering big ecological questions and the challenges associated with it. We welcome submissions of talks and posters. There will also be discussions on general issues with computation; integrating different datasets; and propagating uncertainty in ecological analyses.

The registration deadline is FRIDAY 7 JUNE – just three days away at the time of posting! Attendees will have the opportunity to attend one, or both annual meetings. A quick insider tip for registration: it’s cheaper to join the BES as a member and register for a BES member ticket, than to register for the non-BES member ticket. Continue reading