Issue 8.1

Issue 8.1 is now online!

The January issue of Methods is now online!

All of the articles in this month’s issue of Methods in Ecology and Evolution are free for the whole year. You will not need a subscription to access or download any of them throughout 2017.

Our first issue of this year contains three Applications articles and two Open Access articles. These five papers will be freely available permanently.

– CDMetaPOP: Cost–Distance Meta-POPulation provides a novel tool for questions in landscape genetics by incorporating population viability analysis, while linking directly to conservation applications.

– Rphylopars: An R implementation of PhyloPars, a tool for phylogenetic imputation of missing data and estimation of trait covariance across species (phylogenetic covariance) and within species (phenotypic covariance). Rphylopars provides expanded capabilities over the original PhyloPars interface including a fast linear-time algorithm, thus allowing for extremely large data sets (which were previously computationally infeasible) to be analysed in seconds or minutes rather than hours.

– ggtree: An R package that provides programmable visualisation and annotation of phylogenetic trees. ggtree can read more tree file formats than other software and allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion.

Continue reading

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Choosing Where to Submit: Is Your Manuscript Right for MEE?

You’ve spent months, or even years, working on a project. You’ve finalised your manuscript and you’re ready to submit. But which journal should you send your paper to?

@ Colin (click image to see original)

@ Colin (click image to see original)

In recent years, this question has only gotten harder. As more and more journals enter the market, the decision of where to send your paper is becoming increasingly confusing. With predatory journals muddying the waters and an increasing pressure to publish, deciding where to submit can be a daunting task for even seasoned academics.

Is Methods in Ecology and Evolution the right journal for your manuscript? Is your manuscript right for Methods? Hopefully this blog post will give you a set of tools to make that decision a little easier. Most of these can be applied to other journals too (although some may need to be tweaked a little). Continue reading

Ten Top Tips for Reviewing Statistics: A Guide for Ecologists

post provided by Dr Mark Brewer.

Mark is a statistician with Biomathematics & Statistics Scotland, based in Aberdeen. His main statistical research interests are Species Distribution Modelling, Compositional Data Analysis, Bayesian Mixture Modelling and Bayesian Ordinal Regression. Mark was one of the presenters at the UK half of the Methods in Ecology and Evolution 5th Anniversary Symposium in April. You can watch his talk, ‘Model Selection and the Cult of AIC’ here.

The level of statistical analysis in ecology journals is far higher than in most other disciplines. Ecological journals lead the way in the development of statistical methodology, necessitated by challenging practical problems involving complex data sets. As a statistician, publishing also in hydrology, soil science, social science and forensic science journals, I’ve found papers in those areas are much more likely to only use well-established methods than papers in ecology.

Here’s the big question though: why then do I have the most difficulty with ecological journals when it comes to statistical analyses? Let’s be clear here: when I say “difficulty”, I mean I receive reviews which are just plain wrong. Most statisticians I’ve spoken to who work in ecology have anecdotes from reviews which demonstrate a lack of understanding by the non-statistician reviewer (including the all-too-frequent “perhaps you should consult a statistician”). So, why the apparent disconnect?

The difference seems to be in how non-statisticians in different disciplines treat the statistics in a paper. In many subject areas, reviewers are almost deferential to the statistical analysis; in ecology, reviewers can be forthright in their condemnation, often without justification. Reviewers have every right to question the statistical analysis in a paper, but the authors have the exact same right to expect a high quality review from a genuine expert in the field. Has ecology become blasé about statistics? Continue reading

Issue 6.1

Issue 6.1 is now online!

Our first issue of 2015 is now online!

This month we include one freely available Applications article:

A biochemical approach for identifying plastics exposure in live wildlife

We also have two wonderful Open Access papers, ‘Evaluation and management implications of uncertainty in a multispecies size-structured model of population and community responses to fishing‘ by Robert B. Thorpe, Will J. F. Le Quesne, Fay Luxford, Jeremy S. Collie and Simon Jennings and ‘Split diversity in constrained conservation prioritization using integer linear programming‘ by Olga Chernomor, Bui Quang Minh, Félix Forest, Steffen Klaere, Travis Ingram, Monika Henzinger and Arndt von Haeseler.

This month’s cover image shows more than 170 plastic pieces that were found in the digestive system of a single deceased seabird. Plastic items this seabird ate included industrial pellets (‘nurdles’) that are just a few millimeters long, drink bottle lids, ties used for helium balloons, a plastic doll’s arm and numerous other plastic pieces, some more than 55 mm in length. We can necropsy deceased birds to find out what they have eaten as they forage in the open ocean. However, to understand the pervasiveness of plastics in the marine environment and the potential impacts to wildlife, non-destructive sampling is key.

There is a new method to assess the ubiquity of plastics ingestion in seabirds. A simple swabbing technique, coupled with gas-chromatography/mass spectrometry, can be used to identify phthalate plasticizers that have been adsorbed into the preening oil of seabirds.The approach is quick, simple and can be used on live, wild-caught individuals without harm, serving as an effective tool to help manage declining, threatened or endangered species.

You can read more about this swabbing technique in Hardesty et al.’s ‘A biochemical approach for identifying plastics exposure in live wildlife‘, which is available free of charge.
Photo © Britta Denise Hardesty, CSIRO.

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be included in forthcoming issues.

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 3.3

Rosefinch with geolocator tag

Cover image for issue 3.3
© Germán Garcia – CC Attribution 2.0 Generic

About the issue

Issue 3.3 contains an amazing number of extra features: three videos, one podcast and one Powerpoint presentation. The topics in the issue range from DNA barcoding, surveys, measuring diversity, population and movement modelling and includes five free applications.

About the cover

Recently developed light-weighed tracking devices for positioning through light intensity pattern (‘geolocation’) have begun to greatly improve our knowledge of animal migration. However, the analysis of geolocator data is impeded by many factors potentially affecting light levels and thus, ultimately the determination of positions. Herein, weather and vegetation are major factors altering the light regime experienced by the animals. The picture shows a Common Rosefinch (Carpodactus erythrinus) featured with a 0.5 gram geolocator device.

In Geolocation by light: accuracy and precision affected by environmental factors Simeon Lisovski and colleagues demonstrated the effect of weather, topography and vegetation on the measurement of day/night length, time of solar midnight/noon and the resulting position estimates using light measurements from stationary geolocators at known places and from geolocators mounted on birds.

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

BaSTA

Our latest video is a must-see for all researchers interested in aging:

Fernando Colchero, Owen Jones and Maren Rebke, Max Plank Institute for Demographic Research, present BaSTA – Bayesian Survival Trajectory Analysis. The authors have put together this beautiful video exploring research on ageing and and how to deal with incomplete data.

Starring Tim Coulson, Imperial College, Fernando Colchero, Owen Jones, Maren Rebke and James Vaupel, Max Plank Institute for Demographic Research, Annette Baudisch, MPIRG for Modeling the evolution of aging, Saskia Hin, Laboratory of historical demography, MPIDR.

It also shows special cuts at the end!

BaSTA is a free application.

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.

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!