Issue 6.7

Issue 6.7 is now online!

The July issue of Methods is now online!

This month’s issue contains two Applications article and one Open Access article, all of which are freely available.

fuzzySim: Binary similarity indices are widely used in ecology. This study proposes fuzzy versions of the binary similarity indices most commonly used in ecology, so that they can be directly applied to continuous (fuzzy) rather than binary occurrence values, producing more realistic similarity assessments. fuzzySim is an open source software package which is also available for R.

 Actave.net: A freely accessible, web-based analysis tool for complex activity data, actave.net provides cloud-based and automatic computation of daily aggregates of various activity parameters based on recorded immersion data. It provides maps and graphs for data exploration, download of processed data for modelling and statistical analysis, and tools for sharing results with other users.

Anna Sturrock et al. provide this month’s Open Access article. In ‘Quantifying physiological influences on otolith microchemistry‘ the authors test relationships between otolith chemistry and environmental and physiological variables. The influence of physiological factors on otolith composition was particularly evident in Sr/Ca ratios, the most widely used elemental marker in applied otolith microchemistry studies. This paper was reported on in the media recently. You can read more about it here.

Our July issue also features articles on Monitoring, Remote Sensing, Conservation, Genetics and three papers on Statistics. Continue reading

Issue 6.6

Issue 6.6 is now online!

The June issue of Methods is now online!

This month’s issue contains one Applications article and one Open Access article.

VirtualCom: A simple and readily usable tool that will help to resolve theoretical and methodological issues in community ecology. VirtualCom simulates the evolution of the pool of regionally occurring species, the process-based assembly of native communities and the invasion of novel species into native communities. One of the authors of this Application is the 2014 Robert May Young Investigator Prize Winner, Laure Gallien.

Calibrating animal-borne proximity loggers, this month’s only Open Access article, comes from Christian Rutz et al. The authors calibrated a recently developed digital proximity-logging system (‘Encounternet’) for deployment on a wild population of New Caledonian crows. They show that, using signal-strength information only, it is possible to assign crow encounters reliably to predefined distance classes, enabling powerful analyses of social dynamics. Their study demonstrates that well-calibrated proximity-logging systems can be used to chart social associations of free-ranging animals over a range of biologically meaningful distances.

Our June issue also features articles on Phylogenetic MethodsPhysiological Ecology, Biomonitoring and Conservation, Species Distribution Monitoring and Bioinformatics. Continue reading

Issue 6.5

Issue 6.5 is now online!

The May issue of Methods is now online!

We have two freely available articles this month: one Application and one Open Access Article.

rSPACE: An open-source R package for implementing a spatially based power analysis for designing monitoring programs. This method incorporates information on species biology and habitat to parameterize a spatially explicit population simulation.

Tim Lucas et al. provide this month’s Open Access article: A generalised random encounter model for estimating animal density with remote sensor data. The authors have developed a Generalised Random Encounter Model (gREM) to estimate absolute animal density from count data from both camera traps and acoustic detectors. They show that gREM produces accurate estimates of absolute animal density for all combinations of sensor detection widths and animal signal widths. This model is applicable for count data obtained in both marine and terrestrial environments, visually or acoustically. It could be used for big cats, sharks, birds, echolocating bats, cetaceans and much more. Continue reading

Issue 6.4: Opportunities at the Interface Between Ecology and Statistics

Issue 6.4 is now online!

© Chun-Huo Chiu and Ching-Wen Cheng

The April issue of Methods, which includes our latest Special Feature: “Opportunities at the Interface Between Ecology and Statistics” is now online!

Opportunities ar the Interface Between Ecology and Statistics is a collection of eight articles which arose from the Eco-Stats Symposium at the University of New South Wales (Australia) in July 2013.This Symposium was designed to be a collaborative forum for researchers with interests in ecology and statistics. It brought together internationally recognised leaders in these two fields (such as Jane Elith, Trevor Hastie, Anne Chao and Shirley Pledger) – many of whom have contributed articles to this Special Feature.

The Eco-Stats Symposium was arranged around five special topics, all of which are represented in this issue of Methods. Those five topics are:

In his Editorial for the Special Feature, Guest Editor David Warton suggests that one of the reasons for the success of Methods in Ecology and Evolution may be that it provides a forum for statisticians and ecologists to interact. The articles in this issue, and the conference that gave rise to them, show that these interactions can provide significant benefits for both groups.

There will be another Eco-Stats Symposium at the University of New South Wales in December of this year (8-10 December, 2015).
For more details on this, please click here.
Continue reading

Associate Editor Profile: LOUISE JOHNSON

Dr Louise Johnson, a population geneticist working on the evolution of genetic systems, has been an Associate Editor for Methods in Ecology and Evolution since October 2013. In that time she has handled a range of manuscripts falling within her areas of expertise (primarily molecular evolution, population genetics and genomes).

Louise Johnson

Dr Louise Johnson

Louise began her academic career with a degree in Genetics at the University of Edinburgh. She then moved south to complete her PhD on the evolution of mating systems in yeast at Imperial College London under the supervision of Professor Austin Burt. Following her successful time in London, she took up post-doctorate positions at the University of Nottingham (working on transposable elements with Professor John Brookfield) and across the Atlantic at the University of Virginia (looking at genome defences with Professor Janis Antonovics and Professor Michael Hood). Louise returned to the UK in 2006 to take up an RCUK Fellowship at the University of Reading and has been there ever since.

As part of our series of Editor Profiles, we asked Louise to tell us about some of her current research:

There are three projects which I am currently working on that I would like to outline. I’ll be discussing the cancer project – or at least the story so far – at the Methods in Ecology and Evolution 5th Anniversary Symposium later this month. Do check out the programme, and I hope to see you there! The whole point of a methods journal is to help each other do our research as well and easily as possible, so there’s a built-in community spirit about MEE, which bodes well for a fun and useful meeting. Before I start I should also say that I’m lucky to have amazing collaborators at Reading and beyond: for the projects below, credit is particularly due to my colleagues Rob Jackson and Tiffany Taylor, who had a huge input, and to Mike Brockhurst at York. 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

Our 5th Anniversary Symposium

Charles Darwin House, London, UK: 10:00 – 18:00 (GMT)

Alberta Room, Dining Centre, University of Calgary, Canada: 08:30 – 17:00 (MST)

22 April 2015

Symp ad w_bannerMethods in Ecology and Evolution, the British Ecological Society’s youngest journal, turns five this year. To celebrate we will be holding a joint Symposium – beginning in the UK and concluding in Canada.

We will be hearing what’s in store for the future from young, international researchers including the first winner of the Robert May Young Investigator’s Prize and some of the journal’s Associate Editors. Topics that will be discussed include model selection, data analysis, R and more.

You can find out more about the Symposium, including information on all of the talks on our website. If you have any questions that aren’t answered there, feel free to get in touch (coordinator@methodsinecologyandevolution.org).

If you haven’t registered to attend the Symposium yet, there is still time. Be quick though, our Early Bird prices are coming to an end on Friday 20 March.

You can register for our 5th Anniversary Symposium HERE.

We understand that for a lot of our dedicated readers, it simply won’t be possible to get to either Calgary or London. Therefore, we will be live streaming the whole event. Every speaker’s talk, from the UK and from Canada, will be available LIVE – online and free of charge. We will be releasing more information about the live stream closer to the date, so keep an eye out for it here and on our website (link above).

We hope that you will be able join us, in person or online, to celebrate five wonderful years of Methods in Ecology and Evolution.

 

Flawed Method puts Tiger Rise in Doubt

The following is a press release about the Methods paper ‘An examination of index-calibration experiments: counting tigers at macroecological scales‘ taken from the University of Oxford News and Events page:

Flaws in a method commonly used in censuses of tigers and other rare wildlife put the accuracy of such surveys in doubt, a new study suggests.

A team of scientists from theNH_QT_K2934024 University of Oxford, Indian Statistical Institute, and Wildlife Conservation Society exposes, for the first time, inherent shortcomings in the ‘index-calibration’ method that means it can produce inaccurate results. Amongst recent studies thought to be based on this method is India’s national tiger survey (January 2015) which claimed a surprising but welcome 30 percent rise in tiger numbers in just four years.

The team urges conservation practitioners to guard against these sources of error, which could mislead even the best conservation efforts, and suggests a constructive way forward using alternative methods of counting rare animals that avoid the pitfalls of the index-calibration approach.

A report of the research is published this week in the journal Methods in Ecology and Evolution.

Continue reading

Issue 6.2

Issue 6.2 is now online!

The February issue of Methods is now online!

This month we have two applications articles. Both are free to access, no subscription required.

– NLMpy: A PYTHON software package for the creation of neutral landscape models (there are also two videos associated to this paper on our Youtube channel)

BAT an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity

There are also two OnlineOpen articles in this month’s issue. Power analysis for generalized linear mixed models in ecology and evolution, by Paul C. D. Johnson,Sarah J. E. Barry, Heather M. Ferguson and Pie Müller, focuses on why and how we use power analysis for GLMMs using simulations more than we should.

Our second Open Access article is also the source of our cover image, which shows the ciliate protist Paramecium caudatum (about 0.25 mm long). Protist species like this are commonly found in aquatic habitats and offer a unique study system to test ecological and evolutionary concepts. The protist was isolated from a natural pond and subsequently used for microcosm experiments, which have a long tradition in order to test ecological and evolutionary concepts.

In the accompanying review paper, Florian Altermatt et al. describe a wide range of available techniques to use this and many other protists species to conduct microcosm experiments. The review paper gives detailed protocols of available techniques with a focus on modern, high-frequency and high-throughput measurements, and outlines how such microcosm experiments may be used to address a wide range of questions.

This comprehensive guide to using protist microcosms as a model system in ecology and evolution in ‘Big answers from small worlds‘, which is available free of charge.
Photo © Regula Illi and Florian Altermatt.

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.

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.