New Associate Editors

Over the next few weeks we will be welcoming three new Associate Editors to Methods in Ecology and Evolution. Susan Johnston (University of Edinburgh, UK) became a member of the Associate Editor Board on Monday 5 October. She will be joined on 19 October by Natalie Cooper (Natural History Museum, London, UK) and finally by Luísa Carvalheiro (University of Brasília, Brazil) on 2 November. You can find out more about all three of our new Associate Editors below.

Susan Johnston

Susan Johnston“My research focuses on using genomic information to understand evolution in natural populations. I adapt mixed model approaches to determine the genetic architecture of interesting traits (e.g. estimating heritability, genome-wide association studies, outlier analyses) to examine its relationship with fitness or importance in local adaptation. I am interested in the potential of affordable genomics to answer evolutionary and ecological questions in wild systems, and how to deal with various statistical issues arising from such studies in small and/or structured populations.”

Susan’s most recently published article is ‘Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population‘, co-authored with T. Aykanat, P. Orell, E. Niemelä, J. Erkinaro and C.R. Primmer. The findings suggest that different evolutionary processes affect sub-populations of Atlantic salmon and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence. This article was published in Molecular Ecology.

Natalie Cooper

Natalie Cooper“I am an evolutionary biologist, focusing mainly on macroevolution and macroecology. My interests include phylogenetic comparative methods, morphological evolution, using museum specimens in research, and integrating neontological and palaeontological data and approaches for understanding broad-scale patterns of biodiversity.”

Natalie has recently been published in Molecular Phylogenetics and Evolution (‘Effects of missing data on topological inference using a Total Evidence approach‘ with T. Guillerme) and in Evolution (‘Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)‘ with C.L. Nunn). She was also a speaker at the Methods in Ecology and Evolution 5th Anniversary Symposium. Her presentation, ‘Limitations of Phylogenetic Comparative Methods‘, is freely available on YouTube.

Luísa Carvalheiro

Luisa Carvalheiro“My research focuses on community ecology & conservation. I have particular interest in the study of dynamics of biodiversity through time and space; and on the evaluation of how such biotic changes affect ecosystem functioning and ecosystem services, considering how the complex network of ecological interactions in which species are integrated mediates such changes.”

Earlier this year Luísa’s article ‘Susceptibility of pollinators to ongoing landscape changes depends on landscape history‘ (with J. Aguirre-Gutiérrez, J.C. Biesmeijer, E.E. van Loon, M. Reemer, and M.F. Wallis De Vries) was published in Diversity and Distributions. The article emphasizes the limited value of a one-size-fits-all biodiversity conservation measures and highlights the importance of considering landscape history when planning biodiversity conservation actions. This article is Open Access. Luísa was also the lead author of ‘The potential for indirect effects between co-flowering plants via shared pollinators depends on resource abundance, accessibility and relatedness‘ an Open Access article published in Ecology Letters last year.

We are thrilled to welcome Susan, Natalie and Luísa to the Associate Editor Board and we look forward to working with them over the coming years.

International Day for Biological Diversity 2015

Happy International Day for Biological Diversity everyone!

As you may know, today (Friday 22 May) is the United Nations Day for Biodiversity and we are celebrating by highlighting some of the best papers that have been published on biodiversity in Methods in Ecology and Evolution. This is by no means an exhaustive list and you can find many more articles on similar topics on the Wiley Online Library (remember, if you are a member of the BES, you can access all Methods articles free of charge).

If you would like to learn more about the International Day for Biological Diversity, you may wish to visit the Convention on Biological Diversity website, follow them on Twitter or check out today’s hashtag: #IBD2015.

Without further ado though, here are a few of the best Methods papers on Biological Diversity:

Methods Cover - August 2012Biodiversity Soup

We begin with an Open Access article from one of our Associate Editors, Douglas Yu (et al.). This article was published in the August issue of 2012 and focuses on the metabarcoding of arthropods. The authors present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. They also demonstrate that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information.

Continue reading

Issue 6.3

Issue 6.3 is now online!

The March issue of Methods is now online!

We have three freely available Applications articles in this issue. Anyone can access these with no subscription required and no charge to download.

TR8: This R package was built to provide plant scientists with a simple tool for retrieving plant functional traits from freely accessible online traitbases.

StereoMorph: A new R package for the rapid and accurate collection of 3D landmarks and curves using two standard digital cameras.

MotionMeerkat: A new standalone program that identifies motion events from a video stream. This tool reduces the time needed to review videos and accommodates a variety of inputs.

This month we have a total of FIVE Open Access articles. That makes eight articles in this issue of Methods in Ecology and Evolution that you can read for free!

Continue reading

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


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.


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.