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

• PASSaGE: Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2
  by Micheal Rosenberg and Corey Anderson
• RBrownie: an R package for testing hypotheses about rates of evolutionary change
  by Conrad Stack, Luke Harmon and Brian O’Meara
• MOTMOT: models of trait macroevolution on trees
  by Gavin Thomas and Rob Freckleton
• Python based GIS tools for landscape genetics: visualising genetic relatedness and measuring landscape connectivity
  by Thomas Etherington

Molecular ecology, phylogeny and evolution

• Discriminating plant species in a local temperate flora using the rbcL plus matK DNA barcode
  by Kevin Burgess, Aron Fazekas, Prasad Kesanakurti, Sean Graham, Brian Husband, Steven Newmaster, Diana Percy, Mehrdad Hajibabaei and Spencer Barrett
• Threshold choice and the analysis of protein marking data in long-distance dispersal studies
  by Frances Sivakoff, Jay Rosenheim and James Hagler
• Measuring the temporal structure in serially sampled phylogenies
  by Rebecca Gray, Oliver Pybus and Marco Salemi
• A simple polytomy resolver for dated phylogenies
  by Tyler Kuhn, Arne Mooers and Gavin Thomas
• Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data
  by Jeff Powell

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!

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.

Related

• Developing a deeper understanding of animal movements and spatial dynamics through novel application of network analyses
  by David Jacoby, Edd Brooks, Darren Croft and David Sims
• Marine Biological Association of the UK
• University of Exeter
• Cape Eleuthera Institute
• University of Plymouth
• More Methods author videos and podcasts

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

Welcome on board Matt!

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.

Related

• Methods in Ecology and Evolution Issue 3.1
• Browse past covers in the Methods cover gallery

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:

• A video by Brett Favaro on TRAPCAM, an inexpensive camera system for studying deep-water animals.
• A tutorial by Jeff Powell on his molecular approach to species identification.

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!

Population monitoring and management

• Meta-analysis of transmitter effects on avian behaviour and ecology
  Douglas G. Barron, Jeffrey D. Brawn and Patrick J. Weatherhead
• The effects of geolocator drag and weight on the flight ranges of small migrants
  Melissa Bowlin, Per Henningsson, Florian Muijres, Roel Vleugels, Felix Liechti, Anders Hedenstrom
• Spatially explicit spreadsheet modelling for optimising the efficiency of reducing invasive animal density
  Clive McMahon, Barry Brook, Neil Collier and Corey Bradshaw

Climate change

• Featuring 10 phenological estimators using simulated data
  Jean-Pierre Moussus, Romain Julliard and Frédéric Jiguet

Evolutionary ecology and phylogenomics

• Parameter landscapes unveil the bias in allometric prediction
  Cang Hui, John S. Terblanche, Steven L. Chown and Melodie A. McGeoch
• Phylogenetic signal and linear regression on species data
  Liam J. Revell

Plant monitoring and modelling

• Comparison of seedling emergence and seed extraction techniques for estimating the composition of soil seed banks
  Jodi N. Price, Boyd R. Wright, Caroline L. Gross, Wal R. D. B. Whalley

Community ecology

• A new method for detecting and interpreting biodiversity and ecological community thresholds
  Matthew E. Baker, Ryan S. King
• Comparing measures of species diversity from incomplete inventories: an update
  Jan Beck, Wolfgang Schwanghart
• A novel approach to detecting a regime shift in a lake ecosystem
  Gideon Gal and William Anderson

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.

Methods in Ecology and Evolution will be receiving its first Impact Factor in summer 2012 and we are very impressed with how well our articles are being cited. For those of you who have been following Methods from the start, you will notice some papers that we have already mentioned last year in our top cited blog posts. These are still going strong! Over the next few days we’ll be highlighting our most cited papers across a broad range of fields – stay tuned on MethodsBlog.

Statistical methods in ecology & evolution

Tomorrow we will be posting part 2, where we’ll be showcasing our top cited papers in plant monitoring and modelling, stable isotope ecology and community ecology, and come back on Wednesday for part 3, when we’ll be revealing our top papers in population monitoring, climate change, evolutionary ecology and phylogenomics.

Robert M May Prize winner 2011, Tyler Kuhn

Each year our editors select the best paper published in Methods by a young researcher. We are delighted to announce that this year’s winner of the Robert M May Prize is Tyler Kuhn for his paper co-authored with Arne Ø. Mooers and Gavin H. Thomas A simple polytomy resolver for dated phylogenies published in vol. 2.5 of the journal.

Tyler and co-authors present a simple approach to polytomy resolution (polytomy, i.e. unresolved nodes in phylogenetic trees), using biologically relevant models of diversification using free available software, BEAST and R. The paper should be useful for many future analyses of the mammalian supertree.

Raised in a small town in Canada’s far north, Tyler has always had a passion for understanding the natural world. This passion led him to the University of Victoria, where he completed his B.Sc. Honours in Earth Sciences in 2004. It was there that he discovered the world of paleontology. He returned to academia after spending several years working as a geologist to pursue his M.Sc in Quaternary paleontology. He completed this degree in 2010, focussing on the use of aDNA to improve our understanding of imperilled northern species, and to help inform management practices. During this time, he and his supervisor, Arne Mooers, became involved in a “side project” aimed at improving the useability of incompletely resolved phylogenies in conservation decision making processes. This work has since expanded far beyond his M.Sc. thesis to include several published papers, including the Robert May Prize winning paper on resolving polytomies of dated supertrees. Tyler currently lives in Canada’s frigid north and works as a government biologist, paleontologist and independent researcher.