Category Archives: General

Virtually Trekking Across the Pond with the Newest Senior Editor: Aaron M. Ellison

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Post Provided by Aaron Ellison

I’m delighted to be the newest member of the diverse team of Senior and Associate Editors who have made Methods in Ecology and Evolution one of the premier journals in the field. After 15 years working on the lead editorial teams of Ecology and Ecological Monographs, I’m really looking forward to applying my editorial energies to the ESA’s friendly competitor on the other side of the ‘pond’.

My background includes:

  • an undergraduate degree in East Asian Philosophy
  • a PhD in evolutionary ecology
  • research and teaching on the natural history and population, community, and landscape ecology of plants and animals (mostly invertebrates) in the marine intertidal and subtidal, among salt marshes and mangroves, tropical and temperate forests, and carnivorous plant bogs
  • extensive forays into statistics, mathematics, and software engineering
  • increasing attention to the history and practice of art and architecture and their relationship to ecological theory
  • a quirky social-media persona
  • and more than two decades of work in editing and publishing journals with scientific societies.

All of these things contribute to my open, catholic approach to scientific research, teaching, and publishing, and their relationship to the broader world.

The editors of Methods are always interested in seeing papers on methodological advances and approaches that lead to new directions. We love reading about creative solutions for new challenges in ecological and evolutionary research and applications in the broadest sense. As a new Senior Editor, I’m especially hoping to encourage more papers in three areas: field methods (about which I’ve published two of my own papers in Methods), reproducibility, and science communication. Continue reading →

2017 Robert May Prize Winner: Jonathan Henshaw

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The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2017 winner is Jonathan Henshaw, for his article ‘A unified measure of linear and nonlinear selection on quantitative traits‘.

The standard approach to quantifying natural selection, developed by Lande and Arnold, does not allow for comparable metrics between linear (i.e. selection on the mean phenotype) and nonlinear (i.e. selection on all other aspects of the phenotypic distribution, including variance and the number of modes) selection gradients. Jonathan Henshaw’s winning submission provides the first integrated measure of the strength of selection that applies across qualitatively different selection regimes (e.g. directional, stabilizing or disruptive selection). Continue reading →

Bias, Role Models and Women in STEM

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Post provided by Lee Hsiang Liow

As the newest Senior Editor of Methods in Ecology and Evolution – and someone who happens to have two X chromosomes – I’ve been asked to write a blog post to mark the International Day of Women and Girls in Science.

After being a postdoc for almost ten years, I landed a permanent academic job in the city I wanted to live and raise my daughter in. I have great colleagues and I love my job as a researcher and teacher. I feel incredibly lucky: I am a female scientist and I “made it”.

When I showed the previous paragraph to a close friend and fellow “scientist who made it” he reminded me that a male colleague could easily have written exactly the same thing, only replacing “female” with “male”. Although I agree with his observation, I was deeply frustrated by what could be implied by his response.

His response illustrates a problem: some people may think it’s “all fine” now or that the issue of gender inequality has been solved. They cite the numerous measures in place at different levels to help women enter STEM fields and to ensure female scientists get an equal chance at staying in the game. It might be close to “all fine” in Scandinavia – a region known for long periods of parental leave and ingrained culture to put children and families above work – but it’s not all chocolate mousse and cheesecake everywhere in the world. Continue reading →

Ending the Terror of R Errors

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Post provided by Paul Mensink

Last year, I introduced R to petrified first-year biology students in a set of tutorials. I quickly realised that students were getting bogged down in error messages (even on very simple tasks), so most of my time was spent jumping between students like a wayward Markov chain. I would often find a desperate face at the end of a raised hand looking hopelessly towards their R console muttering some version of “What the $%# does this mean?”. I instantly morphed from teacher to translator and our class progress was slower than a for-loop caught in the second Circle.

Error messages are often not very helpful

Error messages are often not very helpful

Fast forward to Ecology Across Borders last December in Ghent, where rOpenSci and special interest groups from the BES, GfÖ and NecoV  and Methods in Ecology and Evolution  co-hosted a pre-conference R hackathon. I was elated to see that one of the challenges was focused on translating R error messages into “Plain English” (thanks to @DanMcGlinn for the original suggestion!). Continue reading →

New Associate Editor: Chris Sutherland

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Today, we are pleased to welcome the latest new member of the Methods in Ecology and Evolution Associate Editor Board. Chris Sutherland joins us from the University of Massachusetts, USA and you can find out a little more about him below.

Chris Sutherland

“I’m an applied ecologist with a focus on spatial population ecology. I am particularly interested in understanding how spatial processes such as movement, dispersal and connectivity, influence the dynamics of spatially structured populations. Most of my research involves the development and application of spatially realistic hierarchical models for observations of individuals, populations and metapopulations.”

Chris has had a couple of articles published in Methods in Ecology and Evolution in recent years. In his 2015 article ‘Modelling non-Euclidean movement and landscape connectivity in highly structured ecological networks‘ Chris and his co-authors (Angela K. Fuller and J. Andrew Royle) evaluated the consequences of not accounting for movement heterogeneity when estimating abundance in highly structured landscapes, and demonstrated the value of this approach for estimating biologically realistic space-use patterns and landscape connectivity.

‘A multiregion community model for inference about geographic variation in species richness‘ by Chris, Mattia Brambilla, Paolo Pedrini and Simone Tenan was published in the journal in 2016. This paper reported on a new approach that provided a mechanism for testing hypotheses about why and how species richness varies across space.

Last year, Chris was also involved in ‘Quantifying spatial variation in the size and structure of ecologically stratified communities‘, which was published in the August issue of Methods. In this article, the authors provided a novel hierarchical multi-region community model for direct modelling of trait-based patterns of species richness along environmental gradients by splitting communities into ecologically relevant strata.

Chris currently has a number of ongoing projects including a long term (20 year) metapopulation study on water voles in North West Scotland with the objectives of better understanding the spatial drivers of colonisation-extinction dynamics and persistence of spatially structured populations. He is also working on monitoring and density estimation of a recovering population of American marten using photographic capture-recapture using a novel camera trapping design.

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

A Guide to Reproducible Code in Ecology and Evolution

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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 →

New Associate Editor: Edward Codling

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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.

New Associate Editor: David Soto

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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.

Solving YOUR Ecology Challenges with R: Ecology Hackathon in Ghent

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©2016 The R Foundation

Scientific software is an increasingly important part of scientific research, and ecologists have been at the forefront of developing open source tools for ecological research. Much of this software is distributed via R packages – there are over 200 R packages for ecology and evolution on CRAN alone. Methods regularly publishes Application articles introducing R packages (and other software) that enable ecological research, and we’re always looking for new ways to enable even more and better ecological software.

This December, we will be teaming up with rOpenSci and special interest groups from BES, GfÖ and NecoV to hold our first Ecology Hackathon at the Ecology Across Borders conference in Ghent. The hackathon will be held as a one-day pre-conference workshop on Monday 11th December. Together, the attendees will identify some challenges for ecological research, and team up to build R packages that help solve them.

We’ve started compiling potential topics for new R packages in a collaborative document, but we need more. Are you having any difficulties in your research that could be solved with an R package? Is there a package that you wish existed but have never been able to find? If so, WE WANT TO HEAR FROM YOU!

Please take a look at our current list of challenges and add your suggestions!

Two More New Associate Editors

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Today we are welcoming two more Associate Editors to the Methods in Ecology and Evolution who were invited to work with the journal following our open call earlier this year. Jessica Royles joins from the University of Cambridge, UK and Simon Blomberg is coming to us from the University of Queensland, Australia. You can find out more about both of them below.

Simon Blomberg

“I am a statistician who started out as a lizard demographer. I am interested in all applications of statistics in evolutionary biology and systematics. It is my passion to see that good science gets done by everybody, and sound statistical methods are essential to reach that goal. My research involves the application of stochastic process models (predominantly Itoh diffusions) to the macroevolution of quantitative traits. I believe that evolution can be described by beautiful mathematics but theory must be tested with data. I have published widely on phylogenetic comparative methods. I use Bayesian methods, data augmentation, regularisation and other modern and traditional statistical methods. I am interested in how to treat missing data. I still like lizards. Also jazz.”

Simon has been working on stochastic process models for a couple of years. His most recent article ‘Beyond Brownian motion and the Ornstein-Uhlenbeck process: Stochastic diffusion models for the evolution of quantitative characters‘ is now available on BioRxiv and he would welcome comments on it from the Methods community.

Jessica Royles

“I am interested in the impact of climate change on plant physiology and specialise in using stable isotopes as environmental markers. Having worked in Antarctica I have strong interests in polar biology, high latitude peatlands and fieldwork techniques. My current work focusses on  temperate bryophytes and I am interested in using techniques including gas exchange and chlorophyll fluorescence at different spatial scales to link the leaf level to the ecosystem level.”

Jessica’s most recently published article – ‘Widespread Biological Response to Rapid Warming on the Antarctic Peninsula‘ – describes how she and her co-authors used moss cores to study Antarctic warming due to climate change. The article builds on her previous paper ‘Plants and Soil Microbes Respond to Recent Warming on the Antarctic Peninsula‘. Jessica is currently working on a Moss Ecophysiology project which aims to investigate the value of mosses as tools to understand past climate.

We are thrilled to welcome Simon and Jessica to the Associate Editor Board and we look forward to working with them over the coming years.