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.

• 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

In the first video of the new year, Gary Powney and Tom Oliver show how long-term monitoring data on the Speckled Wood butterfly (Pararge aegeria) from the UK monitoring butterfly scheme can be used to assess functional connectivity of the landscape.

In a paper recently published in Methods, Gary Powney, Tom Oliver and colleagues use synchrony between population counts as a new empirical method to assess functional connectivity – the permeability of landscapes given species dispersal attributes. Functional connectivity is important because well-connected metapopulations are expected to be more resistant to stochastic events causing extinction. They use long-term monitoring data on the Speckled Wood butterfly and find that population synchrony is positively correlated with landscape suitability, suggesting that synchrony might be used to measure functional connectivity.

A key finding is that relatively close populations may exchange sufficient migrants for synchronisation, regardless of the matrix suitability. In contrast, more separate populations are synchronised only where the landscape permits functional connectivity, most likely through dispersal between intermediate stepping-stone populations.

This technique might be used to test and prioritise the effectiveness of land management for conservation of species and to mitigate the effects of climate change.

Related

• Measuring functional connectivity using long-term monitoring data
  by Gary Powney, David Roy, Daniel Chapman, Tom Brereton and Tom Oliver
• Centre for Ecology and Hydrology
• Imperial College London
• UKBMS
• More Methods author videos and podcasts

Cover image for issue 2.6

The cover image for the last issue of the year of Methods in Ecology and Evolution is a biological soil crust (BSC), a community which may be composed by mosses, lichens, liveworths fungi and bacteria that are prevalent in drylands worldwide.

Lichen-dominated BSCs (like the one in the image) affect multiple ecosystem functions in those habitats where they are present, including carbon and nitrogen cycling, soil stabilization, and water infiltration and runoff.

The article linked to the image is Randomization tests for quantifying species importance to ecosystem function by Nicholas Gotelli, Werner Ulrich and Fernando Maestre. In the article the authors introduce randomization tests for evaluating the effect of individual species on ecosystem variables measured in multiple plots. This approach is tested using data on ecosystem functioning in lichen-dominated BSC assemblages from central Spain, and further validated using an independent microcosm experiment. The method proposed in this article provides a simple index and statistical test of species importance that can form the basis for additional hypothesis tests and experimental studies of species occurrence and ecosystem functioning.

This BSC-forming lichen community was photographed by Fernando T. Maestre in gypsum outcrops from Sax (South East Spain).

Related

• Methods in Ecology and Evolution Issue 2.6
• Browse past covers in the Methods cover gallery

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.

For its first year of publication, Methods was made freely available online, while this year libraries have been able to opt-in to receive free, institution-wide access in perpetuity to the first two volumes of the journal and BES members have enjoyed free individual access. However, from January 2012 onwards, Methods will join the four other Society journals and be available on a subscription basis only. BES members will be able to access reduced-rate individual subscriptions.

Methods will still be made available to institutions in developing countries, through the AGORA, OARE and INASP philanthropic initiatives, and the journal will still be able to support authors keen to make their work even more widely available through Open Access publishing. The journal will also be continuing to provide free access to its Application papers – concise, practical descriptions of new software, equipment or other tools. And, of course, our videos, podcasts, and other enhancements designed to encourage and promote the easy dissemination of new advancements will also still be freely available to help promote and drive the development of new methods in ecology and evolution.

• Functional rarefaction for species abundance data
  Carlo Ricotta, Sandrine Pavoine, Giovanni Bacaro and Alicia Acosta
• Sampling period, size, and duration influences measures of bat species richness from acoustic surveys
  Samuel Skalak, Richard Sherwin and R. Brigham
• Barcoding’s next top model: an evaluation of nucleotide substitution models for specimen identification
  Rupert Collins, Laura Boykin, Robert Cruickshank and Karen Armstrong
• Asessing individual heterogeneity using model selection criteria: How many mixture components in capture-recapture models?
  Sarah Cubaynes, Christian Lavergne, Eric Marboutin and Olivier Gimenez

We’ve also accepted abc: an R package for Approximate Bayesian Computation (ABC), by Katalin Csilléry, Olivier Francois and Michael Blum, which will join our collection of free application papers.