Issue 3.2

Aerial photograph of a forest

Cover image for issue 3.2
© Getzin & Wiegand – Biodiversity Exploratories

About the issue

With topics ranging from phylogenetic analysis to statistics and distribution modelling, conservation, citizen science, surveys, genetic and demographic models to avian biology, our issue 3.2 should be of interest to most ecologists and evolutionary biologists. The issue also contains 5 free applications.

About the cover

This very high-resolution image of a beech-dominated forest in central Germany was taken by an unmanned aerial vehicle (UAV) at 250 meter above ground. In this photograph one can clearly recognize individual tree crowns and even smallest gaps. UAVs are increasingly used for ecological surveys because they provide extremely fine resolutions and thus allow the identification of previously undetected object details. Furthermore, UAVs can be considered as very cost-effective tools for the acquisition of data that can be used also very flexibly.

In Assessing biodiversity in forests using very high-resolution images and unmanned aerial vehicles Getzin, Wiegand and Schöning tested the hypothesis that gap-structural information on aerial images can be principally used for the ecological assessment of understorey plant diversity in forests. The authors demonstrate that spatially implicit information on gap shape metrics is indeed sufficient to reveal strong dependency between gap patterns as a filter for incoming light and plant biodiversity. The study highlights that understorey biodiversity can be actively controlled by the spatial quality, and not just quantity, of tree removal. Thus, even under the same quota of tree harvesting, the promotion of complex and irregularly shaped gaps may be beneficial to foster biodiversity in forests.



Our latest video is a must-see for all researchers interested in aging:

Fernando Colchero, Owen Jones and Maren Rebke, Max Plank Institute for Demographic Research, present BaSTA – Bayesian Survival Trajectory Analysis. The authors have put together this beautiful video exploring research on ageing and and how to deal with incomplete data.

Starring Tim Coulson, Imperial College, Fernando Colchero, Owen Jones, Maren Rebke and James Vaupel, Max Plank Institute for Demographic Research, Annette Baudisch, MPIRG for Modeling the evolution of aging, Saskia Hin, Laboratory of historical demography, MPIDR.

It also shows special cuts at the end!

BaSTA is a free application.


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

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!

Recently accepted articles

We have been very busy this week and we have a whole range of recently accepted articles:

  • Bats as bioindicators – The need of a standardized method for acoustic bat activity surveys
    Peter Stahlschmidt and Carsten Brühl
  • Developing a deeper understanding of animal movements and spatial dynamics through novel application of network analyses
    David Jacoby, Edward Brooks, Darren Croft and David Sims
  • BaSTA: an R package for Bayesian estimation of age-specific survival from incomplete mark-recapture/recovery data with covariates
    Fernando Colchero, Owen Jones and Maren Rebke
  • Designing a benthic monitoring programme with multiple conflicting objectives
    Allert Bijleveld, Jan van Gils, Jaap van der Meer, Anne Dekinga, Casper Kraan, Henk van der Veer and Theunis Piersma
  • Category count models for resource management
    Paul Fackler
  • mvabund – an R package for model-based analysis of multivariate abundance data
    David Warton, Yi Wang, Ulrike Naumann, and Stephen Wright
  • Movement ecology of human resource users: using net squared displacement, biased random bridges and resource utilisation functions to quantify hunter and gatherer behaviour
    Sarah Papworth, Nils Bunnefeld, Katie Slocombe and E.J. Milner-Gulland

Issue 2.6

Our last issue for 2011 is out. Issue 2.6 is packed with the latest methodological developments.

We have four new articles on monitoring: from positional accuracy in the field by Mike Dodd to distance sampling butterflies by Nick Isaac and colleagues, to how to account for non-independent detection of individuals by Julien Martin and collaborators and, finally, to a class of spatial capture-recapture models for ‘search-encounter’ data by Andrew Royle, Marc Kéry and Jérôme Guélat.

Two articles focus on modelling distributions. Darryl MacKenzie and colleagues present their work on modelling habitat and species distribution dynamics and Peter Wilson introduces an analytical framework applying a distance-based approach to the ordination and analysis of maps produced by species distribution modelling tools.

Kristen L. Granger and collaborators explain their extraction and assay methods on seed chemistry while Adam Davis et al look at seed predation rates.

Also, Joseph Chipperfield et al model dispersal kernels, Alexandre Bec and co-authors assess the reliability of fatty acid–specific stable isotope analysis for trophic studies. Jeroen Groot and Walter Rossing review recent developments in systems modelling which support learning by creating a salient diversity of management alternatives and by translating science-based results into stakeholder perspectives.

Nicholas J. Gotelli, Werner Ulrich and Fernando T. Maestre explore randomization tests for quantifying species importance to ecosystem function and their article takes the front cover.

Finally, the issue contains two free Application articles. In the first Conrad Stack, Luke Harmon and Brian O’Meara detail RBrownie, an R package for testing hypotheses about rates of evolutionary change. In the second, Stefan Prost and Christian Anderson present TempNet, a method to display statistical parsimony networks for heterochronous DNA sequence data.

Ask your librarian to get free access in perpetuity to the first two years of Methods in Ecology and Evolution by completing this request form or learn about how to access the journal in 2012.

Our twelfth application!

The publication of smatr 3 – an R package for estimation and inference about allometric lines, by David Warton, Remko Duursma, Daniel Falster and Sara Taskinen, marks our twelfth published application paper – and, like the first eleven, it’s available for free.

Methods in Ecology and Evolution’s applications are intended to provide a citable description of new methods and techniques in ecology and evolution, with the intention of promoting and maximising the uptake of these new approaches. The papers we’ve already published span a huge range of methodologies, providing new tools for testing the tempo of evolution in phylogenetic trees, assessing the effectiveness of forest carbon conservation, and performing a broad array of spatial statistical analyses – to name but a few.

You can view the full range of applications on the MEE website.

Methods blogging

Here’s a nice piece by Karthik Ram, of Inundata, about RNCEP, an application whose introduction we recently published on Early View.

RNCEP is a package of open-source R functions that make it easy to access and use two free, long-term, high-quality atmospheric data sets with global coverage, and comes highly recommended for anyone interested in climate data and questions related to global change!


Top papers for June

Open access research papers, freely available applications, and papers supported by podcasts continued to be our most popular publications for June.

Open papers How safe is mist netting? Evaluating the risk of injury and mortality to birds, by Spotswood et al., and A simple method for in situ-labelling with 15N and 13C of grassland plant species by foliar brushing, by Putz et al., both received a lot of downloads, with How safe is mist netting? – the first large-scale analysis of the risks involved in mist netting – being featured on the Guardian science blogs, and in Conservation and Birdwatch magazines.

Applications – all freely available – likewise continue to be highly downloaded, with several new arrivals just falling short of being among our most popular papers for this month.

Finally, as ever, papers accompanied by podcasts have continued to be popular, with Getting started with meta-analysis, The art of modelling range-shifting species, and Fine-scale environmental variation in species distribution modelling all featuring among the month’s top ten most downloaded.



Accessing Methods in Ecology and Evolution

Methods in Ecology and Evolution stopped being available to everyone at the start of this year, but that doesn’t mean you can’t still access it for free!

For starters, you can encourage your institutional librarian to sign up for free access to volumes 1 and 2, in perpetuity, by directing them to this opt-in form.  You can also get free access to Methods as a member of the British Ecological Society – please contact the journal coordinator for further details, or check earlier issues of the Bulletin.

In the meantime, our application papers remain free to access, and much of the software they describe is also free to download.  Methods should also be available via the GORA, OARE and INASP philanthropic initiatives.

Finally, if you’re keen to ensure that your work is openly available to all, please remember that Methods is a part of the Wiley Online Open programme.