Methods in Ecology and Evolution 5th Anniversary Symposium: The Livestream

On Wednesday 22 April 2015, Methods in Ecology and Evolution will be celebrating its 5th Anniversary. Methods is the British Ecological Society’s youngest journal and over the past five years it has established itself as the leading publication for methodological advances for both the ecological and evolutionary academic communities.

For those of you who can’t make it to either the first half or the Symposium in London (Looking Forward to the Next Five Years) or the second half in Calgary (Next Generation Ecology and Evolution: Genomics Tools for the Study of Ecology, Evolution, and Biomonitoring) we will be livestreaming every presentation.

What You Need to Watch the Livestream

Our 5th Anniversary Symposium will be streamed though Livestream.com. This platform is optomised for all browsers as well as Android and iOS devices. So all that you need is a computer, tablet or smart phone and the ability to connect to the internet.

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Bat Appreciation Day: The Latest Methodological Advances

Post provided by Kate Jones and the Biodiversity Modelling Research Group

The Funnel-eared bat (Natalus stramineus)

The Funnel-eared bat (Natalus stramineus) – © Veronica Zamora-Gutierrez

Today (17 April) is Bat Appreciation Day! Yes I know, a whole day to appreciate bats. Although my biodiversity modelling research group at University College London would argue that 24 hours is just not enough time to appreciate these cool, yet misunderstood animals, we wanted to mark the day by giving MEE a round-up of the latest methodological advances in bat monitoring and what we hope to see in the next few years.

Bat Detectives and Machine Learning

oisin_pictureOisin Mac Aodha PostDoc – If you have ever tried to spot bats flying around at night you will know that it can be very difficult. However, bats leak information about themselves into the environment in the form of the sounds they make while navigating and feeding. These calls are often too high for us to hear, but we can use devices known as bat detectors to transform them into a form that we can record and listen to. Monitoring bat populations over wide areas or long periods can result in huge amounts of data which is difficult to analyse though. To address this problem, our group, along with Zooniverse, have setup a citizen science project called Bat Detective which asks members of the public help us find bat calls in audio recordings that have been collected from all over Europe (the infographic below gives a bit more information on this). We have had an amazing response to date and our detectives have already located several thousand bat calls. However, to scale up monitoring, we need more automated methods of detecting calls. Using the analysis provided by our Bat Detectives, we are currently working on building algorithms that can automatically tell us if a recording contains a bat call.

In this video we see a visual representation of an audio signal called a spectrogram that features several bat calls. On top you see the result of an automated method we have developed for detecting bat calls. The larger the value, the more certain the algorithm is that there is a bat call at that point in time. Continue reading

A Dog’s Nose Knows: The Science is in on Wildlife Sniffer Dogs

Below is a press release about the Methods paper, ‘An assessment of the effects of habitat structure on the scat finding performance of a wildlife detection dog, taken from Science for Wildlife:

Badger the Wildlife Sniffer Dog

Scientists have for the first time tested wildlife detection dogs to see how they perform in different habitats, and the results are very impressive.

Wildlife sniffer dogs are trained to find the scats (poo) or scent of hard to find wildlife species. As threatened species continue to drop in numbers, they become much harder to find and conserve. Detection dogs are a potential solution to that problem.

Despite their amazing skills the use of sniffer dogs by wildlife management agencies is still limited, partly because there are many factors that might impact the dogs’ performance. One well-toted theory states that dogs might not perform well in thicker vegetation, compared to open areas. The lead author of the new study, Dr Kellie Leigh from Science for Wildlife, explains “Scent is heavier than air so it pools and gets caught up in vegetation and depressions, rather than dispersing from its source. That means the dogs might have more trouble finding the scent in some areas.”

Working together with professional dog trainer Martin Dominick from K9-Centre Australia, Dr Leigh ran an experiment with Badger, an Australian Shepherd trained to find the scat of spotted-tailed quolls. The quolls are the largest marsupial predator on mainland Australia and are becoming very hard to find in some areas. Over 120 searches, Badger scoured for quoll scats in three different Australian habitats, from open grassland to thick vegetation, under both winter and summer conditions. Continue reading

Issue 6.4: Opportunities at the Interface Between Ecology and Statistics

Issue 6.4 is now online!

© Chun-Huo Chiu and Ching-Wen Cheng

The April issue of Methods, which includes our latest Special Feature: “Opportunities at the Interface Between Ecology and Statistics” is now online!

Opportunities ar the Interface Between Ecology and Statistics is a collection of eight articles which arose from the Eco-Stats Symposium at the University of New South Wales (Australia) in July 2013.This Symposium was designed to be a collaborative forum for researchers with interests in ecology and statistics. It brought together internationally recognised leaders in these two fields (such as Jane Elith, Trevor Hastie, Anne Chao and Shirley Pledger) – many of whom have contributed articles to this Special Feature.

The Eco-Stats Symposium was arranged around five special topics, all of which are represented in this issue of Methods. Those five topics are:

In his Editorial for the Special Feature, Guest Editor David Warton suggests that one of the reasons for the success of Methods in Ecology and Evolution may be that it provides a forum for statisticians and ecologists to interact. The articles in this issue, and the conference that gave rise to them, show that these interactions can provide significant benefits for both groups.

There will be another Eco-Stats Symposium at the University of New South Wales in December of this year (8-10 December, 2015).
For more details on this, please click here.
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2014 Robert May Prize Winner: Laure Gallien

The Robert May Prize is awarded annually for the best paper published in Methods by a young author at the start of their research career. We’re delighted to announce that the 2014 winner is Laure Gallien, for her article ‘Identifying the signal of environmental filtering and competition in invasion patterns – a contest of approaches from community ecology.

Today, biological invasions are of major concern for maintaining biodiversity. However, understanding what drives the success of invasive species at the scale of the community remains a challenge. Two processes have been described as main drivers of the coexistence between invasive and native species: environmental filtering and competitive interactions. However, recent reviews have shown that competitive interactions are rarely detected, and thus their importance as drivers of invasion success placed under question. But can this be due to pure methodological issues? Using a simulation model of community assembly, Laure and co-authors (Marta Carboni and Tamara Münkemüller) show that the infrequent detection of competition can arise from three important methodological shortcomings, and provide guidelines for future studies of invasion drivers at the scale of the community.

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Associate Editor Profile: LOUISE JOHNSON

Dr Louise Johnson, a population geneticist working on the evolution of genetic systems, has been an Associate Editor for Methods in Ecology and Evolution since October 2013. In that time she has handled a range of manuscripts falling within her areas of expertise (primarily molecular evolution, population genetics and genomes).

Louise Johnson

Dr Louise Johnson

Louise began her academic career with a degree in Genetics at the University of Edinburgh. She then moved south to complete her PhD on the evolution of mating systems in yeast at Imperial College London under the supervision of Professor Austin Burt. Following her successful time in London, she took up post-doctorate positions at the University of Nottingham (working on transposable elements with Professor John Brookfield) and across the Atlantic at the University of Virginia (looking at genome defences with Professor Janis Antonovics and Professor Michael Hood). Louise returned to the UK in 2006 to take up an RCUK Fellowship at the University of Reading and has been there ever since.

As part of our series of Editor Profiles, we asked Louise to tell us about some of her current research:

There are three projects which I am currently working on that I would like to outline. I’ll be discussing the cancer project – or at least the story so far – at the Methods in Ecology and Evolution 5th Anniversary Symposium later this month. Do check out the programme, and I hope to see you there! The whole point of a methods journal is to help each other do our research as well and easily as possible, so there’s a built-in community spirit about MEE, which bodes well for a fun and useful meeting. Before I start I should also say that I’m lucky to have amazing collaborators at Reading and beyond: for the projects below, credit is particularly due to my colleagues Rob Jackson and Tiffany Taylor, who had a huge input, and to Mike Brockhurst at York. Continue reading

Towards a More Reproducible Ecology

The following post has been provided by Dr Nick Isaac. Nick is organising the OpenData and Reproducibility Workshop at Charles Darwin House, London on 21 April 2015 (more information below). He is also an Associate Editor for Methods in Ecology and Evolution.

Macro_finalThe open science movement has been a major force for change in how research is conducted and communicated. Reproducibility lies at the heart of the open science agenda. It’s a broad topic, covering how data are shared, interpreted and reported.

Reproducibility has been advanced by a coalition of publishers (who have been embarrassed by a series of high-profile retractions), funding agencies keen that data should be re-useable after the life of a grant, and young researchers taking a more collaborative attitude than previous generations.

There is now a vast range of tools and platforms to help scientists share data and other materials (e.g. Dryad, Github, Figshare) and to create efficient and reproducible workflows (e.g. Sweave, Markdown, Git and, of course, R). There’s even a MOOC (Massive Open Online Course) in Reproducible Research, run out of Johns Hopkins University.

Ecology has lagged behind wet-lab biology and other disciplines in the adoption of reproducibility concepts and there are few examples of ecological studies that are truly reproducible. To address this, we’re running a one-day workshop at Charles Darwin House, London on Tuesday 21 April entitled OpenData & Reproducibility Workshop: the Good Scientist in the Open Science era. Continue reading

Understanding and Presenting YOUR Data

A Beginner’s Guide to Data Exploration and Visualisation with R
by Elena N. Ieno and Alain F. Zuur

A Beginner's Guide to Data ExplorationIn 2010 Alain Zuur, Elena Ieno and Chris Elphick published a paper in Methods in Ecology and Evolution entitled ‘A protocol for data exploration to avoid common statistical problems‘ (Volume 1, Issue 1). Little did they know at the time that this paper would become one of the journal’s all-time top downloaded and top cited papers, with a total of 22,472 downloads between 2010 and 2014.

Based on this success they decided to extend the material in the paper into a book.

Zuur and his colleagues at Highland Statistics ltd. give about 25 five-day statistics courses per year. Their typical audience consists of biological scientists at the post-graduate and post-doctoral levels. Early on in each course they have the following conversation with the participants:

Speaker: “Do you review submitted manuscripts for journals?”
Audience: “Yes.”
Speaker: “Do you like the statistical part of these manuscripts?”
Audience: “No!”
Speaker: “Do you understand the statistical part?”
Audience: “Not always.”

What if there were ways you could make reviewing your paper easier and more enjoyable for reviewers? What if making your manuscript easier to understand and nicer to read would increase the likelihood of your work being published?

A Beginner’s Guide to Data Exploration and Visualisation with R explains how you can do exactly that! Alain Zuur and Elena Ieno use ecological datasets to discuss the data exploration and visualisation tools you can use to make your paper simpler for readers and reviewers to understand. The authors also explain how to visualise the results of statistical models, an important aspect of scientific papers. Continue reading

Issue 6.3

Issue 6.3 is now online!

The March issue of Methods is now online!

We have three freely available Applications articles in this issue. Anyone can access these with no subscription required and no charge to download.

TR8: This R package was built to provide plant scientists with a simple tool for retrieving plant functional traits from freely accessible online traitbases.

StereoMorph: A new R package for the rapid and accurate collection of 3D landmarks and curves using two standard digital cameras.

MotionMeerkat: A new standalone program that identifies motion events from a video stream. This tool reduces the time needed to review videos and accommodates a variety of inputs.

This month we have a total of FIVE Open Access articles. That makes eight articles in this issue of Methods in Ecology and Evolution that you can read for free!

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My Career in Science (and Elsewhere)

The following is a piece written by Jane Elith, the author highlighted in our first International Women’s Day article. Dr Elith also won the Recognition of Achievement for a Research Paper award for Methods in Ecology and Evolution in 2014 (you can read her full paper here).

 We asked Jane: what drew you to a career in science?

Jane Elith MEE Recognition of Achievement for a Research Paper Award Winner

Dr Jane Elith

I’ve always loved nature, and at school found I was better at science than other subjects. Obvious choices for university would have been Quantitative Ecology or Conservation Biology, but back in the early 1970s such courses didn’t exist in Melbourne. I decided on a Bachelor of Science (Forestry) – science, but focused on trees. However that wasn’t to be – the Head of Forestry advised me that there was no future for women in Forestry. By memory, his reasoning was that there were no facilities for women in the field and entrenched attitudes amongst foresters would make it impossible to get a job. I can’t quite believe, looking back, that I accepted that and changed tracks. But I did.

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