Virtual Issue: Evolution 2013

Edited by Rob Freckleton and Bob O'Hara
June 2013

Now in our fourth year, Methods in Ecology and Evolution (MEE) has published some 300 papers. One of the main objectives when launching the journal was to bring together research in ecology and evolution, as well as to try to create a unique platform for authors developing new methods. Timed for Evolution 2013, this Virtual Issue highlights some of the papers with an evolutionary theme published in the preceding year.

Uniquely in ecology and evolution, we publish ‘applications’ papers that describe new tools for research. The aim is to give creators of important resources, such as code and software, the opportunity to create publishable (and citeable!) outputs, and hence gain the full academic credit for their work. For readers, this is an important source of information and background on the tools they use. These have been extremely popular, and in this Virtual Issue we have highlighted 5 of the Applications papers published over the past year which implement methods as diverse as (phylogenetic) tree harvesting, analysing phylogenetic data and a tool for choosing markers in population genetics. We would like to emphasise that, although most Applications papers submitted have described software and code, we are open to considering Applications that describe any type of tool that a researcher might use on a computer, in the lab or in the field. All Applications papers are free to access.

The link between ecology and evolution is important to MEE: the research papers we have highlighted include excellent examples of these such as modelling dispersal, testing for niche conservatism. Barcoding methods are included, which increasingly are used in an ecological context; the Applications and research papers include a high proportion of papers that describe methods for comparative analyses, which underpin both ecological and evolutionary studies. This selection therefore showcases the excellent range of research that we have published spanning both ecology and evolution.


Treebase: an R package for discovery, access and manipulation of online phylogenies
Carl Boettiger and Duncan Temple Lang

EasyABC: performing efficient approximate Bayesian computation sampling schemes using R
Franck Jabot, Thierry Faure and Nicolas Dumoulin

Sample Planning Optimization Tool for conservation and population Genetics (SPOTG): a software for choosing the appropriate number of markers and samples
Sean Hoban, Oscar Gaggiotti and ConGRESS Consortium and Giorgio Bertorelle

Diversitree: comparative phylogenetic analyses of diversification in R
Richard G. FitzJohn

paleotree: an R package for paleontological and phylogenetic analyses of evolution
David W. Bapst

Standard papers

SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion
Travis Ingram and D.Luke Mahler

On the practical usage of genetic algorithms in ecology and evolution
Steven Hamblin

Null model tests for niche conservatism, phylogenetic assortment and habitat filtering
Werner Ulrich, Marcin Piwczyński, Fernando T. Maestre and Nicholas J. Gotelli

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

How to measure and test phylogenetic signal
Tamara Münkemüller, Sébastien Lavergne, Bruno Bzeznik, Stéphane Dray, Thibaut Jombart, Katja Schiffers and Wilfried Thuiller

Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification
Rupert A. Collins, Laura M. Boykin, Robert H. Cruickshank and Karen F. Armstrong


Cover image credited to: Steve Hodgson, licensed under Creative Commons Attribution 2.0 Generic.

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