Author Archives: India Stephenson

Methods in the press

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Two articles have been recently highlighted in the press.

Iain Stott, Dave Hodgson and Stuart Townley, University of Exeter, have developed Popdemo, a new software tool for helping prioritise efforts in species conservation. As well as determining which species need our help, it will also be useful in pest control and sustainable harvesting. The University press release was picked up by a variety of websites, including Phys.org and eScienceNews.

 

Batrachochytrium dendrobatidis

Batrachochytrium dendrobatidis. Source: Johnson/Speare, Public Domain

Science Daily, yesterday reported that preserved frogs hold clue to deadly pathogen. Katy Richards-Hrdlicka, University of Yale, and author of an article just appeared in Methods in Ecology and Evolution said:

“I have long proposed that the millions of amphibians maintained in natural-history collections around the world are just waiting to be sampled”

Katy developed a new method for charting the history of Batrachochytrium dendrobatidis, or Bd, an infectious pathogen driving many species to extinction.

Related

popdemo: an R package for population demography using projection matrix analysis
by Iain Stott, Dave Hodgson and Stuart Townley

Extracting the amphibian chytrid fungus from formalin-fixed specimens
by Katy Richards-Hrdlicka

Issue 3.3

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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.

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Recent content and new video

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Lots of exciting content has recently gone online.

Firstly, two interesting new applications (as always free): simapse, simulation maps for ecological niche modelling in Python and nadiv, an R package for estimating non-additive genetic variances in animal models.

Also, two research articles. In the first, Julien Beguin and colleagues introduce an alternative procedure for fitting Bayesian hierarchical spatial models (BHSM) with quite general spatial covariance structures. This procedure uses integrated nested Laplace approximations (INLA) as an alternative to MCMC. In the second, Martin Lavoie, Jen Owens and Dave Risk present a new method for real-time monitoring of soil CO2 efflux.This is attractive because of its low cost and low power consumption compared to traditional methods.

Lastly, Dan Mennill and co-authors show us an affordable, portable, wireless microphone array for spatial monitoring of animal ecology and behaviour. They accompany their article with a nice short video:

MEE article featured in Faculty of 1000

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Great recognition for one of our recent articles: Distance-based multivariate analyses confound location and dispersion effects by David Warton, Stephen Wright and Yi Wang, on multivariate analysis in ecology.

Warton and colleagues’ article has recently been highlighted on Faculty of 1000, a platform providing post-publication peer-review and selecting only the most important articles in biology and medicine. Just 2% of published articles are highlighted on Faculty of 1000 each month.

Ferdinando Boero and Stanislao Bevilacqua, Faculty of 1000 reviewers, said of Warton and colleagues’ article:

We strongly recommend reading this article because, beyond technical issues, it stimulates reflections on our consciousness of limits of statistical tools, which is often overwhelmed by our addiction to their routine application.

The article is also accompanied by a free application and a really great video:

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New associate editors

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Busy month at Methods, we are very pleased to announce that five new associated editors have just joined our journal: Olivier Gimenez, CNRS, France, Luca Giuggoli, University of Bristol, UK, Darren Kriticos, CSIRO, Australia, Jessica Metcalf, University of Oxford, UK,  and Helene Muller-Landau, Smithsonian Tropical Research Institute, Panama.

Olivier is a population biologist with a background in biostatistics studying animal demography in wild populations.

Luca is a physicist with an interest in animal foraging processes and the formation of territorial and home range patterns, as well as many other processes where individual agents move and interact collectively.

Darren is an ecological modeller with interests centred on theoretical and applied invasion ecology, especially invasive pests.

Jessica is an evolutionary ecologist at the Department of Zoology with an interest in disease, human demography and parasite evolution.

Finally, Helene is a plant ecologist with an interest in plant community and ecosystem ecology, especially of tropical forests.

Welcome on board Olivier, Luca, Jessica, Darren and Helene, we look forward to working with you!

Issue 3.2

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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.

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BaSTA

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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.

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New podcast and video

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In case you haven’t seen them, this month we have published a new podcast and video so far.

In our latest video, David Warton, The University of New South Wales, Australia, presents his ‘mvabund’ package on multivariate analysis. What makes this software different from other ones on multivariate analysis, is that it’s all about models that you can fit to your data. David explains how to look at the properties of your data and the common pitfalls in modelling multivariate data. He also goes through how to fit generalised linear models to your data. Do check David’s dancing!

Mvabund is a free application.

Movement ecology and habitat selection in human resource users

In their podcast with slideshow, Sarah Papworth and Nils Bunnefeld, Imperial College London, applied ecological methods and principles to GPS data on human movement to investigate the differences in movement ecology and habitat selection in human hunters and non hunters who return to a central place. Please note this is an mp4 file, to listen or download the mp3 file of the podcast click here.

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Recently accepted articles

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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.

Latest papers online

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In the past week, MEE has been at the ITN Speciation conference in Jyväskylä. As a result, journal updates have been slower than usual. So here is a quick overview of the new papers available online during the past week:

Research papers:
Movement ecology of human resource users: using net squared displacement, biased random bridges and resource utilization functions to quantify hunter and gatherer behaviour
Sarah K. Papworth, Nils Bunnefeld, Katie Slocombe and E. J. Milner-Gulland
This paper is accompanied by a podcast. Follow this link if you use a Mac to access the podcast.

Modelling dispersal: an eco-evolutionary framework incorporating emigration, movement, settlement behaviour and the multiple costs involved
Justin M. J. Travis, Karen Mustin, Kamil A. Bartoń, Tim G. Benton, Jean Clobert, Maria M. Delgado, Calvin Dytham, Thomas Hovestadt, Stephen C. F. Palmer, Hans Van Dyck and Dries Bonte

Designing a benthic monitoring programme with multiple conflicting objectives
Allert I. Bijleveld, Jan A. van Gils, Jaap van der Meer, Anne Dekinga, Casper Kraan, Henk W. van der Veer and Theunis Piersma

Application – as you know, all our applications are free:
mvabund– an R package for model-based analysis of multivariate abundance data
Yi Wang, Ulrike Naumann, Stephen T. Wright and David I. Warton