Latest issue and other articles

A dragonfly

Cover image for issue 3.4 © Dennis Paulson.

Issue 3.4

Our latest issue covers an impressive array of subjects: from metabarcoding (with associated presentation), to population genetics and population monitoring (with video explaining a microphone array system). Modelling and monitoring dispersal also features heavily with four articles, one of which is accompanied by a video for a novel telemetry system to track wild animals. Articles also include topics such as transient dynamics, a review on hormone assay, phylogenetic comparative analysis, stable isotopes (featuring our cover article), plant physiology and finally, statistical methods.

About the cover

Stable-isotope ratios measured in migrating animals have proven to be of great value in understanding migration. For example, when a dragonfly emerges from the water, the isotope signature in that water body is fixed in its wing tissues, which thus provide information about its geographic origin. In A dragonfly (δ2H) isoscape for North America: a new tool for determining natal origins of migratory aquatic emergent insects,  Keith Hobson, David Soto, Dennis Paulson, Leonard Wassenaar and John Matthews compared the isotope value from dragonfly wings of known origin with spatially explicit isoscapes based on water isotopes in precipitation. The relationship was strong, confirming the value of the method to study dragonfly migration.

One of the species used in the analysis was Pachydiplax longipennis. This individual was photographed at Red Slough Wildlife Management Area, Oklahoma. Photo © Dennis Paulson.

Early View articles

Also, these recently accepted articles have appeared on Early View:

Rapid determination of comparative drought tolerance traits: using an osmometer to predict turgor loss point by Megan K. Bartlett, Christine Scoffoni, Rico Ardy, Ya Zhang, Shanwen Sun, Kunfang Cao and Lawren Sack

Free application: taxonstand: An r package for species names standardisation in vegetation databases by Luis Cayuela, Íñigo Granzow-de la Cerda, Fabio S. Albuquerque and Duncan J. Golicher

Projecting species’ range expansion dynamics: sources of systematic biases when scaling up patterns and processes by Greta Bocedi, Guy Pe’er, Risto K. Heikkinen, Yiannis Matsinos and Justin M. J. Travis

Review: Temporal dynamics and network analysis by Benjamin Blonder, Tina W. Wey, Anna Dornhaus, Richard James and Andrew Sih

Related

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.

Related

Recently accepted articles

We have been very busy in the past couple of weeks and we have a whole range of recently accepted articles:

  • A novel digital telemetry system for tracking wild animals: a field test for studying mate choice in a lekking tropical bird
    Dan Mennill, Stéphanie Doucet, Kara-Anne Ward, Dugan Maynard, Brian Otis and John Burt
  • A general theory of multimetric indices and their properties
    Donald Schoolmaster, James Grace and E. Schweiger
  • Beyond sensitivity: nonlinear perturbation analysis of transient dynamics
    Iain Stott, Dave Hodgson, and Stuart Townley
  • A two-phase sampling design for increasing detection of rare species in occupancy surveys
    Krishna Pacifici, Robert Dorazio and Michael Conroy
  • Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
    Douglas Yu, Yingiu Ji, Brent Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang and Zhaoli Ding
  • How to measure and test phylogenetic signal
    Tamara Münkemüller, Sébastien Lavergne, Bruno Bzeznik, Stéphane Dray, Thibaut Jombart, Katja Schiffers and Wilfried Thuiller
  • Statistical evaluation of parameters estimating autocorrelation and individual heterogeneity in longitudinal studies
    Sandra Hamel, Nigel Yoccoz and Jean-Michel Gaillard
  • jPopGen Suite: population genetics analysis of DNA polymorphism from nucleotide sequences with errors
    Xiaoming Liu

They will be soon available on Early View.

New associate editor

Methods is pleased to announce that Nick Isaac has become the newest member of its editorial board, taking up the role of Associate Editor. Nick is a macroecologist at the Centre for Ecology and Hydrology interested in questions about the abundance, distributions, diversity and extinction risk of species:

My research generally involves data that are structured in space, time and/or phylogenetically. I started out using the traditional approach in macroecology of ‘one value per species’, but increasingly I use multilevel models to explore patterns along multiple axes (space, time, species) and at a range of scales. Much of my work has involved developing new methods and/or comparing their statistical properties with existing approaches. Historically I used data on mammals and other vertebrates, but these days I work mostly on insects.

Welcome on board Nick!

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!

Robert May Prize 2011

Tyler Kuhn

Robert 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 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.

Biodiversity estimates from DNA sequences

The complexity of new methodologies can present a challenging barrier towards their uptake. Recognising this, Jeff Powell,  author of Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data, has put together an excellent tutorial to guide people through the implementation of his objective, theory-based method for predicting species boundaries, which explicitly incorporates uncertainty in the classification system into biodiversity estimation.

The tutorial is available to view and download from Slideshare, and the relevant R code can be found as supplementary material on Wiley Online Library.

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Watch the CEE meeting, Integrating ecology into macroevolutionary research

By way of an introduction to this blog post, watch this!

Back in March the Centre for Ecology and Evolution in London organised a meeting that brought together top researchers in macroevolution. The idea of the meeting was to highlight how advances in the study of macroevolution could be made by a closer integration with ecology, and the incoroporation of ecological ideas and ecological models.

The meeting had a terrific line-up of speakers, and a synthesis of the science is now available in Biology Letters.

As with any meeting of course, a limitation was that you had to be in London and free on the days of the symposium: I couldn’t make it as I was in the other side of the country and committed for the whole two days. However, in what is an innovation for evolutionary and ecological research, the organisers of the symposium recorded the talks and have now made them available to watch online. MEE, via our publishers Wiley-Blackwell, we were glad to sponsor the costs of making the talks available online. Not least as it meant that I could watch them!

Having now watched all of the talks, some highlights for me are:

However, all the talks are excellent and really worth watching.

I think this is an excellent resource for the evolutionary community: the videos have been professionally recorded and edited, and are easy and effective to watch. Given the modest costs of doing this, I hope that more meeting organisers will follow this lead.

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.

New addition to the editorial board

We’re pleased to announce that Luke Harmon has become the newest member of the Methods in Ecology and Evolution editorial board, taking up the role of Associate Editor. Luke is an Assistant Professor at the University of Idaho, whose research interests focus on  developing new comparative methods and applying them to large phylogenetic datasets:

Ongoing progress in building the tree of life provides a rare opportunity to learn about the dynamics of diversification through time and across clades. Current projects in my lab are focused on testing hypotheses about trait evolution, diversification, and adaptive radiation using statitical comparative methods. I am also interested in the interface between quantitative genetics and comparative methods.