Open Access Week 2014

2014 OA VI - coverOnce more Open Access Week has rolled around.

At MEE we operate a hybrid model: although we are a subscription journal, authors can choose to make their papers open access (for a price – sorry). Over the past year, 21 papers have been published as open access (listed here). They span the range of topics we cover, including citizen science, using cell phones, and asking people nicely to not vandalise your equipment.

There are several models for open access, and the Gold route – making the final version freely available – may not be for everyone. But we also let authors put pre-prints on the web (details here); this is an excellent way of getting more feedback on your manuscripts before a final version (there are other green OA models, but personally I think the preprint version has more advantages).

So, enjoy these papers, and next time you have a paper accepted by MEE – or indeed any other journal with a hybrid model – consider making it open access for all to read. You might be surprised: someone might read it.

Bob, Senior Editor

Graybill/ENVR 2014 – highlights, current trends and what’s next

In this video David Warton interviews the organisers of the “Modern Statistical Methods for Ecology” Graybill/ENVR Conference (Sept 7-10 2014, Fort Collins) – Alix Gitelman, Geof Givens, and Janine Illian.  They discuss highlights of the conference, current trends in statistical ecology, and where the Graybill conference series (organised at Colorado State every year) is going next.

Noisy SCUBA bubbles scare fish(shh!)

SCUBA

Flickr (CC BY-SA 2.0)

A new Methods paper comparing SCUBA diving to bubble-free diving suggests that fish are deterred by the sound of SCUBA bubbles, particularly in heavily fished areas, which can result in potentially biased fish counts and research conclusions.

Steven Lindfield and colleagues from the University of Western Australia studied coral reef fish populations in Guam using two diving systems: the commonly used SCUBA equipment that produces bubbles, and a silent closed-circuit rebreather (CCR) that doesn’t produce bubbles.

To carry out the studies all divers used an underwater stereo-video system, and the footage was later used to figure out the number of fish present in the area, fish length and weight, and the minimum distance fish would allow a diver to approach before fleeing.

The findings show that within protected areas of water where no fishing occurs, fish surveys carried out by SCUBA divers and bubble-free divers produced similar results. However, in areas of water where fishing occurs, the bubble-free divers recorded 48% more species and up to 260% greater fish abundance, suggesting that they were able to sneak up on fish that usually shy away from SCUBA divers.

In their paper the authors state: “These results highlight the general importance of identifying all major sources of error associated with sampling populations in such variable environments. More specifically, it indicates how such errors can result in erroneous conclusions being drawn on the impacts of fishing and the effectiveness of marine protected areas (MPAs)”.

The paper can be found here: Lindfield, S. J., Harvey, E. S., McIlwain, J. L., Halford, A. R. (2014), Silent fish surveys: bubble-free diving highlights inaccuracies associated with SCUBA-based surveys in heavily fished areas. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.12262

Issue 5.9

mee-5-9-coverlargeIssue 5.9 is now available online, including articles on telemetry and sensors, markers and sequences, modelling and model assessment, and extending current data. In addition there are 2 freely available applications: MeCa, a toolbox for the calculation of metabolism in heterogeneous streams and Rphylip: an R interface for PHYLIP

About the cover: This month we have a Cape gannet (Morus capensis) at its nest on Bird Island, Algoa Bay, South Africa. Cape gannets are colonially-breeding seabirds, foraging as top predators of commercially-important epipelagic fish resources. In “An automated approach towards measuring time-activity budgets in colonial seabirds”, the authors demonstrate an unobtrusive, simple, long-term method for remotely recording nest attendance of colonial seabirds using advancements in VHF transmitter technology. Time spent away from the nest (foraging trip duration) was shown to be a reliable proxy for foraging effort. These time-activity budget data can potentially be used to interpret the real-time state of local marine conditions or provide a mechanism for ecological hypothesis testing using the fine-scale data generated. This has applicability for several colonial animal species.
Photo © David B. Green.

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be included in forthcoming issues.

New Associate Editors

We’d like to welcome Jason Matthiopoulos (from the University of Glasgow), Oscar Gaggiotti (from the University of St Andrews), and Greg McInerny (from the University of Oxford) to our Editorial Board team!

Jason Mathiopoulos

Jason Matthiopoulos

Jason is interested in modelling the patterns and mechanisms that characterise spatial and population ecology. Much of his work has focused on building theory by translating biological hypotheses to mathematical models, using modern inference to fit these models to population, demographic, behavioural and physiological data, and applying the conclusions to wildlife conservation, natural resource management and risk assessment.

Oscar Gaggiotti

Oscar Gaggiotti

Oscar’s research focuses on the study of spatial patterns of genetic diversity to better understand the evolutionary and ecological processes responsible for their origin and maintenance. He develops ecologically realistic population genetics theory and statistical methods using the metapopulation paradigm and Bayesian statistics, and applies these methods to two research problems: (i) statistical inference of demographic history and ecology of populations and, (ii) study of local adaptation to understand the molecular bases of phenotypic variation.

Greg McInerny

Greg McInerny

Greg has joined as an Applications Editor and will be handling a lot our Applications papers. His research is a blend of science, software and visualisation. Most scientific questions require some level of methodological advance. Those methods are frequently instantiated in code or software. And finally, the results need to be explored and communicated to a variety of users. Fusing these different aspects of science is demanding, but worthwhile. Alongside Greg’s interests in the regulation and generation of biodiversity, he has a special interest in the usability of software and how usability can increase software functionality and quality. Usability isn’t just about GUIs!

New Applications Editors

We would like to welcome 4 new Applications Editors to our editorial board: Rich Fitzjohn from Macquarie University, Australia, Ruth King from the University of St Andrews, Scotland, Brian O’Meara from the University of Tennessee, Knoxville, and Timothée Poisot from the University of Canterbury, New Zealand.

Rich, Ruth, Brian and Tim are the first of a new group of Associate Editors who will deal solely with our Applications papers, (citable descriptions of new software, equipment, or other practical tools) while considering the implementation of methods as computational tools.

Rich Fitzjohn

Rich Fitzjohn

Rich investigates why some groups of species are far more diverse than others, and the contribution of differences in species traits to coexistence. He uses phylogenetic and trait data to develop new statistical approaches to describe variation in diversity. Current research uses mathematical and simulation modeling to understand how trait variation allows for species co-existence. He’s also interested in developing tools to make science more open and reproducible.

Ruth King

Ruth King

Ruth’s research interests primarily lie within the area of statistical ecology. In particular she is interested in the development of novel statistical methodology for analysing complex ecological, and associated, data. Areas of interest include the analysis of capture-recapture-recovery data, state-space/hidden Markov models, integrated population modelling, incorporating covariate information and/or individual heterogeneity (including dealing with associated missing data) and associated Bayesian and classical model-fitting tools.

Brian O'Meara

Brian O’Meara

Brian works on developing and applying phylogenetic methods to address key questions in evolution and, to a lesser extent, ecology. His work largely focuses on comparative methods, including methods for heterogeneity in continuous and discrete characters, but he also works on phylogeography, species delimitation, protein evolution, diversification, and more.

Tim Poisot

Timothée Poisot

Tim is interested in the spatial and temporal dynamics of species interactions at the community level. His research seeks to develop predictive models to forecast the structure of communities when observations about species interactions are scarce, understanding the relevance of variability in community structure on emerging ecosystem properties, and the evolutionary dynamics of multi-species assemblages. He explores these questions using computational approaches, from standard models of population dynamics to graph-theoretical approaches.

Issue 5.8

mee-5-8-coverlargeIssue 5.8 includes articles on lidar & radar in ecology, occurrence data analysis, ecological networks, measuring habitats, life history variation, dispersal, biodiversity–productivity and monitoring populations, along with the freely available application article: ‘a simple numerical tool to infer whether a species is extinct‘.

There’s an associated video this month in which Phillip Stepanian and colleagues talk about the background and motivation behind their paper: ‘an introduction to radar image processing in ecology‘, followed by a short tutorial.

About the cover: This issue’s cover image shows a bull African elephant (Loxodonta africana), called B1177 ‘Obama’, moving through Samburu National Reserve in Kenya. Positional data collected using GPS tracking is increasingly used to study the movement ecology of a wide variety of species and can also be used for applied conservation as in our elephant program in Kenya. Space-use estimators are often needed to model an individual’s utilization of its environment based on sampled positional data. In the associated article we present a new space-use estimator called the Elliptical Time-Density (ETD) model that is ideally suited to frequently sampled GPS locations. Unlike other methods, this approach is based on empirically derived parameters that are biologically interpretable.
Photo© George Wittemyer.

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be included in forthcoming issues.

Are your analyses too fancy?

In this video David Warton interviews Ben Bolker, Professor in Theoretical and Statistical Ecology at McMaster University and maintainer of the lmer package, and Mark Brewer, Principal Consultant for Ecology and Environmental Science at BioSS, Scotland. They discuss the tendency to develop and use big fancy analyses that are in some applications unnecessarily complex, why it happens, and what can be done about it. Look out for a cameo from one of our Editors!

Ecology in China

ChinaEcology_Advert2At MEE we are looking to publish the best methodological papers. It is no surprise, then, that we are able to contribute several papers to this ‘Ecology in China’ Virtual Issue. The topics covered range from an elegant new way of using very old technology (Zhao et al.) to methods based on next generation sequencing to investigate biodiversity (for example Liu et al.). It is a pleasure to see the range of work being both submitted to MEE from China, and then to see that so much of it is going on to be published by us. Clearly, Chinese researchers are finding themselves at the forefront of ecological research, especially in the application of DNA-based methods, and so are finding themselves having to develop new methods for these new technologies. It is a pleasure to be a part of this Virtual Issue, where we can showcase how Chinese ecology is developing, and the methods that are being developed in China which will help researchers all over the world advance the science of ecology.

Bob O’Hara, Senior Editor

Click here to read this Virtual issue.

Kinect connects for mangroves research

Here is a video and press release about the recent Methods paper, ‘Investigating three-dimensional meso-scale habitat complexity and its ecological implications using low-cost RGB-D sensor technology‘, taken from Griffith University:


Motion sensing technology, best known in computer games, is vastly improving Queensland scientists’ ability to quantify habitat complexity in mangroves.

The Kinect line of devices developed by Microsoft for Xbox consoles and Windows PCs is marrying gaming technology with ecological research to deliver precise three-dimensional data in greater efficiency and at a fraction of the cost of current imaging techniques.

At Griffith University’s Australian Rivers Institute (ARI) on the Gold Coast, Professor Joe Lee, Dr Jan Warnken and Higher Degree Research student Ms Shafagh Kamal have been Continue reading