Recently accepted articles

We have been very busy in the past couple of weeks and we have a whole range of recently accepted articles:

  • A novel digital telemetry system for tracking wild animals: a field test for studying mate choice in a lekking tropical bird
    Dan Mennill, Stéphanie Doucet, Kara-Anne Ward, Dugan Maynard, Brian Otis and John Burt
  • A general theory of multimetric indices and their properties
    Donald Schoolmaster, James Grace and E. Schweiger
  • Beyond sensitivity: nonlinear perturbation analysis of transient dynamics
    Iain Stott, Dave Hodgson, and Stuart Townley
  • A two-phase sampling design for increasing detection of rare species in occupancy surveys
    Krishna Pacifici, Robert Dorazio and Michael Conroy
  • Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
    Douglas Yu, Yingiu Ji, Brent Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang and Zhaoli Ding
  • How to measure and test phylogenetic signal
    Tamara Münkemüller, Sébastien Lavergne, Bruno Bzeznik, Stéphane Dray, Thibaut Jombart, Katja Schiffers and Wilfried Thuiller
  • Statistical evaluation of parameters estimating autocorrelation and individual heterogeneity in longitudinal studies
    Sandra Hamel, Nigel Yoccoz and Jean-Michel Gaillard
  • jPopGen Suite: population genetics analysis of DNA polymorphism from nucleotide sequences with errors
    Xiaoming Liu

They will be soon available on Early View.

Latest papers online

In the past week, MEE has been at the ITN Speciation conference in Jyväskylä. As a result, journal updates have been slower than usual. So here is a quick overview of the new papers available online during the past week:

Research papers:
Movement ecology of human resource users: using net squared displacement, biased random bridges and resource utilization functions to quantify hunter and gatherer behaviour
Sarah K. Papworth, Nils Bunnefeld, Katie Slocombe and E. J. Milner-Gulland
This paper is accompanied by a podcast. Follow this link if you use a Mac to access the podcast.

Modelling dispersal: an eco-evolutionary framework incorporating emigration, movement, settlement behaviour and the multiple costs involved
Justin M. J. Travis, Karen Mustin, Kamil A. Bartoń, Tim G. Benton, Jean Clobert, Maria M. Delgado, Calvin Dytham, Thomas Hovestadt, Stephen C. F. Palmer, Hans Van Dyck and Dries Bonte

Designing a benthic monitoring programme with multiple conflicting objectives
Allert I. Bijleveld, Jan A. van Gils, Jaap van der Meer, Anne Dekinga, Casper Kraan, Henk W. van der Veer and Theunis Piersma

Application – as you know, all our applications are free:
mvabund– an R package for model-based analysis of multivariate abundance data
Yi Wang, Ulrike Naumann, Stephen T. Wright and David I. Warton

Top 10 speciation and evolution papers

Methods will be attending the next ITN Speciation conference 2012 in Jyväskylä, Finland and to mark the occasion, the editorial team has put together a list of some our most relevant work in speciation and evolution.

Applications – concise papers describing new software, equipment, or other practical tools:

Molecular ecology, phylogeny and evolution

If you are going there, stop by to talk to me, Graziella Iossa, journal coordinator. See you on 26-28 February, 2012, at the University of Jyväskylä, Finland!

Network analyses of animal movement

Determining how animals move within their environment is a fundamental knowledge that contributes to effective management and conservation.

In our latest video, David Jacoby and Edd Brooks explain how their paper brings together two disparate and rapid advancing fields: biotelemetry and social networking analyses.

In a paper recently published in Methods, David, Edd and colleagues Darren Croft and David Sims, demonstrate some of the descriptive and quantitative approaches for determining how an animal’s movement interconnects home range habitats. David and colleagues describe the novel application of network analyses to electronic tag data whereby nodes represent locations and edges between nodes, the movements of individuals. They consider both local and global network properties from an
animal movement perspective and simulate the effects of node disruption as a proxy for habitat disturbance.

Network theory is a well-established theoretical framework and its integration into the fast
developing field of animal movement and telemetry might improve significantly how we interpret animal space use from electronically recorded data.


New associate editor

Methods is pleased to announce that Matthew Spencer has become the newest member of its editorial board, taking up the role of Associate Editor. Matt is a quantitative biologist at the University of Liverpool and is interested in using stochastic models to understand community dynamics and molecular evolution:

In particular, I want to work with models that are simple, flexible, and can be applied to real data sets.

Welcome on board Matt!

New associate editor

Methods is pleased to announce that Nick Isaac has become the newest member of its editorial board, taking up the role of Associate Editor. Nick is a macroecologist at the Centre for Ecology and Hydrology interested in questions about the abundance, distributions, diversity and extinction risk of species:

My research generally involves data that are structured in space, time and/or phylogenetically. I started out using the traditional approach in macroecology of ‘one value per species’, but increasingly I use multilevel models to explore patterns along multiple axes (space, time, species) and at a range of scales. Much of my work has involved developing new methods and/or comparing their statistical properties with existing approaches. Historically I used data on mammals and other vertebrates, but these days I work mostly on insects.

Welcome on board Nick!

Explaining the cover image for issue 3.1

African dwarf crocodiles

Cover image for issue 3.1

The African dwarf crocodile (Osteolaemus tetraspis) is endemic to closed-canopy forests of Central and West Africa and is the smallest of the world’s true crocodiles. The species is difficult to study in the wild and therefore poorly known, but likely plays an important ecological role as a top aquatic predator in cool water forest systems.  The dwarf crocodile is also a major food and economic resource to local people and, as a result, is threatened with overhunting for the bushmeat trade.  The image depicts a collection of young dwarf crocodiles, possibly representing three cohorts, measured in a capture-recapture study in Loango National Park, Gabon.

The article linked to the image is On thinning of chains in MCMC by William Link and Mitchell Eaton. In the article, the authors caution against the routine practice of thinning chains in Markov chain Monte Carlo  (MCMC) simulations. Many analysts, recognizing that MCMC precision decreases as the autocorrelation of the chains increases, routinely thin (sub-sample) their chains. Thinning reduces autocorrelation, but the associated gains in precision are more than offset by the reduction in chain length. Thinning of chains is therefore wasteful, though occasionally justified under circumstances discussed in the article.

To illustrate, the authors refer to a recent application (Eaton and Link 2011, Ecological Applications) in which they applied Bayesian multimodel inference to evaluate two growth models used to estimate individual dwarf crocodile age from capture-recapture data.  They demonstrate analytically that thinning their model-selection chains would have decreased autocorrelation but would also decrease the precision with which posterior model probabilities were approximated.

The young dwarf crocodiles were photographed by Mitchell Eaton in 2004.


Volume 3 Issue 1: Now online

It seems that from the number of submissions we receive at the journal, Methods in Ecology and Evolution has filled an important niche. As our editor-in-chief, Rob Freckleton, wrote to introduce our second volume: “those doing science need to be kept up to date on new approaches, and those developing new methods need a place to publish, as well as be supported in getting their methods used”. The journal appears to have done just that: not only have we published some very popular articles (see our recent posts on 2011 top cited papers part 1, part 2 and part 3) but we have also seen a keen interest from our authors in utilising the online extras that we offer to disseminate their work.

As always, in issue 3.1 we cover a very broad range of articles – the scope includes everything from statistics, to ecophysiology and stable isotope methods. The applications of the methods are as varied as reconstructing snow depth surfaces, tracking migratory songbirds, estimating immigration in neutral communities and assessing the effects of watershed and reach characteristics on riverine assemblages. Being the first issue of the year all content is free to access.

One of our big aims is to promote the uptake of methods. On our video and podcast page, we have support for the papers in this issue, including:

Our first Open Access article by Erica Spotswood and colleagues, How safe is mist netting? Evaluating the risk of injury and mortality to birds, attracted a lot media attention. You can read the press coverage for this article on our News and Highlights page.

This issue also contains a free phylogenetic application: MOTMOT, a model of trait macroevolution on trees by Gavin Thomas and Rob Freckleton. Check out our Applications page describing the latest software tools. It’s worth remembering that all Applications are free.

Finally, Mitch Eaton and William Link provided the catchy photograph that make this issue’s front cover. You can read more about the cover on a separate post, available tomorrow!

We hope you enjoy reading this issue!

2011 top cited papers – part 3

Welcome to part 3 of our review of the most highly cited papers published by Methods in Ecology and Evolution in 2011. In case you missed them, here are part 1 and part 2 of this series.

Population monitoring and management

Climate change

Evolutionary ecology and phylogenomics

2011 top cited papers – part 2

Today we look at part 2 of our most cited papers in Methods in Ecology and Evolution in 2011.

Plant monitoring and modelling

Stable isotope ecology

Community ecology

Our most cited papers on statistical methods in ecology and evolution, modelling species and the environment, and physiological ecology were covered in part 1 – and finally tomorrow we’ll look at our top papers in population monitoring, climate change, evolutionary ecology and phylogenomics.