What About Winter? Accounting for the Snow Season When We Simulate Climate Warming

Post provided by Rebecca Sanders-DeMott and Pamela Templer

Processes that occur in winter are a significant component of annual carbon and nutrient cycles. ©Travel Stock Photos

Processes that occur in winter are a significant component of annual carbon and nutrient cycles. ©Travel Stock Photos

The climate is changing throughout the globe with consequences for the biogeochemical processes and ecological relationships that drive ecosystems. Scientists have been conducting manipulative experiments to determine the effect of climate warming on ecosystems for several decades. These experiments allow us to observe ecosystem responses before the climate changes occur and have yielded invaluable insight that has expanded our understanding of the natural world.

There is a wide range of creative approaches to mimicking climate warming that have been used, for example open-topped chambers which passively heat small areas of soil and small stature plants (like the ITEX global network), burying heating cables in the soil to directly increase soil temperatures (e.g. Harvard Forest experiments), infrared heating lamps (like Jasper Ridge), or even large scale chambers that can encompass taller stature plants like trees and actively warm the air (like the SPRUCE experiment). The focus of much of these inquiries has been on changes that occur during the growing season, when biological activity is at its peak. Continue reading

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The BES Quantitative Ecology SIG: Who We Are, What We Do and What to Look Out for at #EAB2017

Post provided by Susan Jarvis and Laura Graham

Ecologists are increasingly in need of quantitative skills and the British Ecological Society Quantitative Ecology Special Interest Group (QE SIG) aims to support skills development, sharing of good practice and highlighting novel methods development within quantitative ecology. We run events throughout the year, as well as contributing to the Annual Meeting and providing a mailing list to share events, jobs and quantitative news.

Ecology Hackathon

The run up to the Ecology Across Borders joint Annual Meeting in Ghent this month is an exciting time for the SIG as we look forward to catching up with existing members as well as hopefully meeting some new recruits! Several of our SIG committee members will be in attendance and if you’ve been lucky enough to get a place at the Hackathon on the Monday you’ll meet most of us there. The Hackathon has been jointly developed by us and two of our allied groups; the GfÖ Computational Ecology Working Group and the NecoV Ecological Informatics SIG and is being sponsored by Methods in Ecology and Evolution. We’ll be challenging participants to work together to produce R packages suggested by the ecological community. You can see the list of package suggestions here. If you weren’t able to book a place at the Hackathon, but are interested in writing your own packages, you may be interested in the new Guide to Reproducible Code from the BES. Continue reading

Making YOUR Code Reproducible: Tips and Tricks

When we were putting together the British Ecological Society’s Guide to Reproducible Code we asked the community to send us their advice on how to make code reproducible. We got a lot of excellent responses and we tried to fit as many as we could into the Guide. Unfortunately, we ran out of space and there were a few that we couldn’t include.

Luckily, we have a blog where we can post all of those tips and tricks so that you don’t miss out. A massive thanks to everyone who contributed their tips and tricks for making code reproducible – we really appreciate it. Without further ado, here’s the advice that we were sent about making code reproducible that we couldn’t squeeze into the Guide:

Organising Code

©Leejiah Dorward

“Don’t overwrite data files. If data files change, create a new file. At the top of an analysis file define paths to all data files (even if they are not read in until later in the script).” – Tim Lucas, University of Oxford

“Keep one copy of all code files, and keep this copy under revision management.” – April Wright, Iowa State University

“Learn how to write simple functions – they save your ctrl c & v keys from getting worn out.” – Bob O’Hara, NTNU

For complex figures, it can make sense to pre-compute the items to be plotted as its own intermediate output data structure. The code to do the calculation then only needs to be adjusted if an analysis changes, while the things to be plotted can be reused any number of times while you tweak how the figure looks.” – Hao Ye, UC San Diego Continue reading

A Guide to Reproducible Code in Ecology and Evolution

Post provided by Natalie Cooper and Pen-Yuan Hsing

Cover image by David J. Bird

The way we do science is changing — data are getting bigger, analyses are getting more complex, and governments, funding agencies and the scientific method itself demand more transparency and accountability in research. One way to deal with these changes is to make our research more reproducible, especially our code.

Although most of us now write code to perform our analyses, it’s often not very reproducible. We’ve all come back to a piece of work we haven’t looked at for a while and had no idea what our code was doing or which of the many “final_analysis” scripts truly was the final analysis! Unfortunately, the number of tools for reproducibility and all the jargon can leave new users feeling overwhelmed, with no idea how to start making their code more reproducible. So, we’ve put together the Guide to Reproducible Code in Ecology and Evolution to help. Continue reading

Scales, Slime and Dragon(fly) Wings? Investigating the Surfaces of Organisms

Post provided by Dylan Wainwright

Our recent Methods in Ecology and Evolution paper – ‘Imaging biological surface topography in situ and in vivo shows how to use gel-based profilometry to image various biological surfaces. To start you need to press a gel into a surface of interest. The bottom surface of the gel is coated in a paint to create an impression of the surface that has standard optical properties (not clear, shiny, or coloured). Then lights are shone on the gel at different angles and photographs are taken at six different lighting angles. These photographs allow us to study the surface in incredible detail. The following images give more information on how we can do this and the benefits of it.

To find out more, read our Methods in Ecology and Evolution article ‘Imaging biological surface topography in situ and in vivo’. And to find out more about Dylan’s research, visit his website.

Software Review Collaboration with rOpenSci

© The rOpenSci Project, 2017

The role of science journals is to publish papers about scientific research. We need to maintain some quality in what is published, so we use peer review, and ask experts in the subject of a paper to read it and check that it is correct, the arguments make sense etc.

One of the types of paper we publish is Applications, most of which describe software that will help ecologists and evolutionary biologists to do their research. Our focus is on the paper itself, but we also want to be confident that the software is well written, e.g. that it has no obvious bugs, and that it is written so that future versions will not break.

Of course, it takes a lot of time to thoroughly review software, and that is not the primary job of the journal’s peer review process. But we appreciate that this needs to be done, and indeed many of our reviewers and editors put a lot of time into doing just this, something we really appreciate. But can we do this better?

Fortunately, we were approached by the rOpenSci organisation, who wanted to collaborate with us to do this (a huge thanks to Scott Chamberlain for this initial approach and all of his hard work in putting this collaboration together). They are a group of coders, mainly in ecology, who have written a large number of open source R packages for a variety of tasks (e.g. importing data, visualisation). They also want to maintain good quality code, so they have implemented a variety of methods to do this.

One of these is code review. This is another form of peer review, but focused on the code, not the paper. This means the reviewer can concentrate on checking that the code works, that it is well written and documented (so other people can read the code and adapt it), and that it has the right sets of tests, so that if something changes, it is straightforward to check that it still works. Continue reading

New Associate Editor: Edward Codling

Today, we are pleased to be the latest new member of the Methods in Ecology and Evolution Associate Editor Board. Edward Codling joins us from the University of Essex, UK and you can find out a little more about him below.

Edward Codling

“My research is focused on using new mathematical and computational techniques to study problems in biology and ecology. In particular, I’m interested in movement ecology, and specifically the development of theoretical models and empirical analysis tools that give insights into animal movement and behaviour. I am also interested in spatial population dynamics and the application of modelling and analysis tools to marine fisheries and other natural resource management questions.”

Edward is currently working on a range of problems within the rapidly growing field of movement ecology. This includes a recent theoretical study of animal navigation using random walk theory and an empirical study into coral reef fish larval settlement patterns. An ongoing project is exploring how analysis of dairy cow movement and behaviour could be used as part of a farm monitoring and management system to improve cow health and welfare. He is also continuing to work on new tools and methods for the assessment and management of fisheries, particularly in the case where data is limited.

We are thrilled to welcome Edward as a new Associate Editor and we look forward to working with him on the journal.

How Can We Quantify the Strength of Migratory Connectivity?

Technological advancements in the past 20 years or so have spurred rapid growth in the study of migratory connectivity (the linkage of individuals and populations between seasons of the annual cycle). A new article in Methods in Ecology and Evolution provides methods to help make quantitative comparisons of migratory connectivity across studies, data types, and taxa to better understand the causes and consequences of the seasonal distributions of populations.

In a new video, Emily Cohen, Jeffrey Hostetler and Michael Hallworth explain what migratory connectivity is and how the methods in their new article – ‘Quantifying the strength of migratory connectivity‘ – can help you to study it. They also introduce and give a quick tutorial on their new R package MigConnectivity.

This video is based on the article ‘Quantifying the strength of migratory connectivity by Cohen et al.

New Associate Editor: David Soto

Today, we are pleased to be the latest new member of the Methods in Ecology and Evolution Associate Editor Board. David Soto joins us from the University of Leuven in Belgium and you can find out a little more about him below.

David Soto

“I am an isotope ecologist with interests in developing new stable isotope methods and techniques for tracing spatio-temporal changes in food webs, and understanding animal movement and large-scale migration. My current research focus is on aquatic food webs using isotopic tracers such as hydrogen isotopes, and on insect migration patterns predicting natal origins by combining isoscapes and likelihood-based geospatial assignment methods.”

David is currently working on isotopic methodologies to quantify the linkages and support of aquatic and terrestrial primary production sources into Afrotropical aquatic food webs. He recently developed a new method to distinguish dietary sources combining stable isotopes and trace metal accumulation data. Other recent published articles investigated the use of hydrogen isotopes to track fish provenance and to infer butterfly migration movements across the Sahara. He is also collaborating with the IsoriX core team to develop a new method and R package to infer spatial origins of migratory animals using mixed models.

We are thrilled to welcome David as a new Associate Editor and we look forward to working with him on the journal.

Improved and Harmless Demethylation Method for Ecological Epigenetic Experiments

In a new Methods in Ecology and Evolution video, Javier Puy outlines a new method of experimental plant DNA demethylation for ecological epigenetic experiments. While the traditionally-used approach causes underdeveloped root systems and high mortality of treated plants, this new one overcomes the unwanted effects while maintaining the demethylation efficiency. The authors demonstrate its application for ecological epigenetic experiments: testing transgenerational effects of plant–plant competition.

This novel method could be better suited for experimental studies seeking valuable insights into ecological epigenetics. As it’s based on periodical spraying of azacytidine on established plants, it’s suitable for clonal species reproducing asexually, and it opens the possibility of community-level experimental demethylation of plants.

This video is based on the article ‘Improved demethylation in ecological epigenetic experiments: Testing a simple and harmless foliar demethylation application by Puy et al.