Issue 9.2

Issue 9.2 is now online!

The February issue of Methods is now online!

This double-size issue contains six Applications articles (one of which is Open Access) and two Open Access research articles. These eight papers are freely available to everyone, no subscription required.

 Temperature Manipulation: Welshofer et al. present a modified International Tundra Experiment (ITEX) chamber design for year-round outdoor use in warming taller-stature plant communities up to 1.5 m tall.This design is a valuable tool for examining the effects of in situ warming on understudied taller-stature plant communities

 ZoonThe disjointed nature of the current species distribution modelling (SDM) research environment hinders evaluation of new methods, synthesis of current knowledge and the dissemination of new methods to SDM users. The zoon R package aims to overcome these problems by providing a modular framework for constructing reproducible SDM workflows.

 BEIN R Package: The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data. The bien r package allows users to access the multiple types of data in the BIEN database. This represents a significant achievement in biological data integration, cleaning and standardisation.

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Why Simpler Models are Better

(this is the first in a possibly irregular series of posts about papers that catch my eye. I don’t intend to only cover MEE papers, but I had to start somewhere)

ResearchBlogging.orgA perennial worry for anyone building models for the real world is whether they actually represent the real world. If the whole process of finding and fitting a model has been done well, the model will represent the data. But the data is only part of the real world. How can we be sure our model will extrapolated beyond the data?
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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.


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.

Modelling static and dynamic variables

Jessica Stanton discusses the problem of accounting for both static and dynamic variables in designing species distribution models under climate change in our newest author video.


New species distribution modelling survey

SDM survey, c. Microsoft Research Cambridge 2011Researchers from the Computational Ecology and Environmental Sciences  division of Microsoft Research Cambridge are carrying out a survey to help improve the way in which we develop software for species distribution modelling, and as part of wider research into how the software available to researchers affects the advancement of knowledge. It should take about 15 minutes of your time, and you don’t have to use SDM for your feedback to be useful.

It’s important that they get as many diverse responses as possible, so if you’ve used SDM at all then please do get involved. The survey closes on the 1st of July, so get your skates on! Visit the survey homepage to learn more, and take part in the survey.


  • Listen to one of the survey’s authors, Greg McInerny, talk about species distribuion modelling in this Methods podcast

Some things are not the average

Issue 2.3 of Methods in Ecology and Evolution will be officially published online later this week, but in the meantime we’ve got a great new podcast accompanying one of the papers.

Greg McInerny, of Microsoft Research, discusses the content of his recently co-authored paper addressing the issue of adequately accounting for inter-cell environmental variation when constructing species distribution models.

The paper, Fine-scale environmental variation in species distribution modelling: regression dilution, latent variables and neighbourly advice, by Greg McInerny and Drew Purves, is currently available on Early View but will be formally published in issue 2.3 later this week.

Download the podcast

Fine-scale environmental variation in species distribution modelling


Methods digest – update

A round up of recent methods-relevant research published recently: it is ages since we did this, largely because the journal has been so busy with papers coming in and being published. Do send through links to any new methods papers to me or to the journal, or post a comment below.

In Evolution, Werthelm & Sanderson look at how estimates of diversification rates are influenced by improved estimates of divergence times; Robert Lanfear introduces a new method for comparing rates of molecular evolution on trees.

In Systematic Biology Eric Stone has an extremely interesting article on why common comparative methods are robust to tree misspecification. Martin Linder et al. evaluate Bayesian models of substitution rate evoluton, whist Chung & Ané compare Bayesian methods for gene and species tree reconstructions. Simon Ho et al. have a short paper on Bayesian estimation of substitution rates from ancient DNA sequences.  Leaché & Rannala compare the accuracy of species tree estimation under different methods. Anne Kupczok explores the consequences of different null models for shape bias of supertree methods. John Huelsenbeck et al. compare phylogenetic models with the ‘No Common Mechanisms Model’.

In the Journal of Animal Ecology Andrew Jackson & co. have a paper on a new R package (SIBER) for comparing isotopic niche widths.

Sophie Smout et al. look at how heterogeneity of detection and mark loss affect estimates of survival in grey seals in Journal of Applied Ecology. Issue 1 of 2011 has a special profile introduced by Julia Jones on monitoring species abundance.

Eve McDonald-Madden et al. have a paper in Ecological Applications on how to allocate conservation resources when the persistence of a species in not certain. Mary Beth Rew and colleagues look at the problem of how many genetic markers should be used to tag an individual in the presence of close relatives.

A paper by Adam Algar et al. in Ecology looks at how it is possible to quantify the roles of trait-based filters in determining local and regional species composition. Florent Bled, Andy Royle & Emmanuelle Cam have a paper on testing hypotheses about nesting site dynamics by combining population and fitness data.

In Oikos, Sofia Berg et al. have a paper on the use of sensitivity analysis to identify keystones in foodwebs.

Finally for this update, in Ecography Simon Linke and co look at how multivariate analysis can produce conservation planning that addresses the needs of practitioners. Steinar Engen et al. describe a new approach to measuring the similarity of communities and Canrain Liu et al. have a paper on measuring the accuracy of species distribution models using presence absence data.

I’ll try to do another update in the next couple of weeks to cover some of the journals I have missed in this one.

Methods digest – June 2010

Here is the methods digest update for June 2010 – do let me know if there is anything that you think I should feature.

In Oikos Novak & Wooton have a paper on using indices to quantify the effects of comeptition and Landau & Ryan present new ‘null model tests for presence-absence data’ (NMTPAs).

A paper in Conservation Letters by Michael Kearney et al. evaluates species distribution models by comparing the output of correlative and mechanistic models.

In the Journal of Ecology the debate about how to measure the intensity and importance of competition continues to rage. Walker et al. also review the use of chronosequences in studies of succession. Hautier et al. look at how to model the growth of parasitic plants (see also the editorial commentary by Mark Rees).

In the current issue of Systematic Biology, Susana Magallón applies a method using fossils to break long branches to molecular dating of the angiosperm phylogeny. Carstens & Dewey have a new method for species delimitation. Haartman et al. have a paper on sampling trees from evolutionary models.Towsend & Lopez-Giraldez look at the optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships.

Salvador Pueyo et al. in Ecology Letters look at the problem of testing for criticality in ecosystem dynamics. Kuhnert et al. review the use of expert knowledge in Bayesian modelling.

In the latest issue of Ecology Bailey et al. look at estimation in multistate models with unobservable states. Mérigot et al. look at goodness of fit measures for dendrogram analyses.

Hines et al in Ecological Applications present a new approach for occupancy modelling for cluster sampling. In the same issue Waddle et al. present a new approach for estimating co-occurrence of interacting species.

Finally, in the American Naturalist Hamilton et al. look at the problem of estimating the uncertainty in estimates of species richness, and Solow & Smith look at how to estimate abundance from occupancy.