Map of Chemicals in Jellyfish Could be the Future to Protecting UK Waters and Marine Life

Below is a press release about the Methods in Ecology and Evolution article ‘Spatial models of carbon, nitrogen and sulphur stable isotope distributions (isoscapes) across a shelf sea: An INLA approach‘ taken from the University of Southampton.

Jellyfish opportunistically caught in UK waters are used to map chemical variations across marine space. ©University of Southampton

Jellyfish opportunistically caught in UK waters are used to map chemical variations across marine space. ©University of Southampton

Scientists at the University of Southampton have developed maps of chemicals found in jellyfish which could offer a new tool for conservation in British waters and fisheries. The maps will also be able to detect fraudulently labelled food in retail outlets by helping to trace the origins of seafood.

The Southampton based research team including Dr Clive Trueman, Dr Katie St. John Glew and Dr Laura Graham, built maps of the chemical variations in jellyfish caught in an area of approximately 1 million km2 of the UK shelf seas. These chemical signals vary according to where the fish has been feeding due to differences in the marine environment’s chemistry, biology and physical processes. Continue reading

Issue 7.2: Demography Beyond the Population

Issue 7.2 is now online!

Sagebrush steppe in eastern Idaho, USA

© Brittany J. Teller

The February issue of Methods is now online! As you may have seen already, it includes the BES cross-journal Special Feature: “Demography Beyond the Population“. There are also eight other wonderful articles to read.

We have four articles in the Demography Beyond the Symposium Special Feature. You can read an overview of them by two of the Feature’s Guest Editor Sean McMahon and Jessica Metcalf here (Sean and Jessica are also Associate Editors of Methods).

If you’d like to find out more about each of the individual papers before downloading them, we have blog posts about each one. Daniel Falster and Rich Fitzjohn discuss the development of plant and provide some advice on creating simulation models in Key Technologies Used to Build the plant Package (and Maybe Soon Some Other Big Simulation Models in R). There is a look back at the evolution of Integral Projection Models from Mark Rees and Steve Ellner in How Did We Get Here From There? A Brief History of Evolving Integral Projection Models. In Inverse Modelling and IPMs: Estimating Processes from Incomplete Information Edgar González explains how you can estimate process that you can’t observe. And keep an eye out for Brittany Teller’s blog post coming next week!

Don’t wait too long to get the Demography Beyond the Population Special Feature papers though, they’re freely available for a limited time only

Continue reading

Issue 6.11

Issue 6.11 is now online!

The November issue of Methods is now online!

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

mvMORPH: A package of multivariate phylogenetic comparative methods for the R statistical environment which allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion. Its use can be extended to any biological data set with one or multiple covarying continuous traits.

Low-cost soil CO2 efflux and point concentration sensing systems: The authors use commercially available, low-cost and low-power non-dispersive infrared (NDIR) CO2 sensors to develop a soil CO2 efflux system and a point CO2 concentration system. Their methods enable terrestrial ecologists to substantially improve the characterization of CO2 fluxes and concentrations in heterogeneous environments.

This month’s Open Access article comes from Jolyon Troscianko and Martin Stevens. In ‘Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern‘ they introduce a toolbox that can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox is freely available as an addition to the open source ImageJ software and will considerably enhance the appropriate use of digital cameras across multiple areas of biology. In particular, researchers aiming to quantify animal and plant visual signals will find this useful. This article received some media attention upon Early View publication over the summer. You can read the Press Release about it here.

Our November issue also features articles on Population Genetics, Macroevolution, Modelling species turnover, Abundance modelling, Measuring stress and much more. Continue reading

Study Finds Black Bears in Yosemite Forage Primarily on Plants and Nuts

Below is a press release about the Methods paper ‘Measuring the realized niches of animals using stable isotopes: from rats to bears‘ taken from the University of California, San Diego:

©PLF73 (Click image to see original)

Animal proteins only make up a small part of a black bear’s diet. ©PLF73 (Click image to see original)

Black bears in Yosemite National Park that don’t seek out human foods subsist primarily on plants and nuts, according to a study conducted by biologists at UC San Diego who also found that ants and other sources of animal protein, such as mule deer, make up only a small fraction of the bears’ annual diet.

Their study, published in Methods in Ecology and Evolution, might surprise bear ecologists and conservationists who had long assumed that black bears in the Sierra Nevada rely on lots of protein from ants and other insects because their remains are frequently found in bear feces. Instead, the researchers believe that bears likely eat ants for nutrient balance. Continue reading

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!

2011 top cited papers – part 2

Today we look at part 2 of our most cited papers in Methods in Ecology and Evolution in 2011.

Plant monitoring and modelling

Stable isotope ecology

Community ecology

Our most cited papers on statistical methods in ecology and evolution, modelling species and the environment, and physiological ecology were covered in part 1 – and finally tomorrow we’ll look at our top papers in population monitoring, climate change, evolutionary ecology and phylogenomics.

Issue 2.6

Our last issue for 2011 is out. Issue 2.6 is packed with the latest methodological developments.

We have four new articles on monitoring: from positional accuracy in the field by Mike Dodd to distance sampling butterflies by Nick Isaac and colleagues, to how to account for non-independent detection of individuals by Julien Martin and collaborators and, finally, to a class of spatial capture-recapture models for ‘search-encounter’ data by Andrew Royle, Marc Kéry and Jérôme Guélat.

Two articles focus on modelling distributions. Darryl MacKenzie and colleagues present their work on modelling habitat and species distribution dynamics and Peter Wilson introduces an analytical framework applying a distance-based approach to the ordination and analysis of maps produced by species distribution modelling tools.

Kristen L. Granger and collaborators explain their extraction and assay methods on seed chemistry while Adam Davis et al look at seed predation rates.

Also, Joseph Chipperfield et al model dispersal kernels, Alexandre Bec and co-authors assess the reliability of fatty acid–specific stable isotope analysis for trophic studies. Jeroen Groot and Walter Rossing review recent developments in systems modelling which support learning by creating a salient diversity of management alternatives and by translating science-based results into stakeholder perspectives.

Nicholas J. Gotelli, Werner Ulrich and Fernando T. Maestre explore randomization tests for quantifying species importance to ecosystem function and their article takes the front cover.

Finally, the issue contains two free Application articles. In the first Conrad Stack, Luke Harmon and Brian O’Meara detail RBrownie, an R package for testing hypotheses about rates of evolutionary change. In the second, Stefan Prost and Christian Anderson present TempNet, a method to display statistical parsimony networks for heterochronous DNA sequence data.

Ask your librarian to get free access in perpetuity to the first two years of Methods in Ecology and Evolution by completing this request form or learn about how to access the journal in 2012.

Top cited papers – part 2

Here’s part 2 of our look at Methods in Ecology and Evolution’s most highly cited papers to date!

Plant monitoring and modelling

Stable isotope ecology

Community ecology

We covered statistical methods in ecology and evolution, modelling species and the environment, and physiological ecology in part 1 of our look at our most popular papers so far – and on Monday we’ll be rounding off with our top papers in population monitoring, climate change, evolutionary ecology and phylogenetics.

Methods in Ecology and Evolution – news

I hope that you have had an enjoyable and productive summer – this is just to update on a few bits of news from Methods in Ecology and Evolution.

First, Issue 3 has appeared – there are articles on topics including:

  • Evolutionary Ecology
  • Stable Isotopes
  • Population modelling & monitoring
  • Parasitology
  • Conservation & community ecology

Second, the first year of the journal has been enormously succesful – we are getting many very good submissions and as a consequence we will move from 4 issues this year, to 6 in 2011. This is a faster growth than we had anticipated and reflects the superb quality of the papers that we are receiving!

Third, we will be at the British Ecological Society meeting in Leeds next week from the 6-8th Sept. If you have any questions, do drop by the Wiley-Blackwell stand: about 13 members of the editorial team will be at the meeting.

Finally do check out our videos & podcasts – there have been lots of updates.

Methods Digest – December 2009

A round-up of methods papers published in the last month. If there are any papers that you think should be featured, email me or leave a comment and I will add them.

Liam Revell has a paper in Evolution on size correction and principal components analysis of phylogenetic comparative data. Olivier Gimenez and colleagues also have a paper in the same issue on generating fitness landscapes using mark-recapture data.

Systematic Biology has a number of papers with interesting methods: Campbell & Lapointe have a paper on the use and validity of composite taxa in phylogenetic analysis; Fitzjohn et al. have a nice paper on estimating trait-dependent speciation and extinction rates in phylogenies that are not complete; Bui Quang Minh and colleages present an algorithm for efficiently estimating phylogenetic diversity; Michael D. Pirie, Aelys M. Humphreys, Nigel P. Barker, and H. Peter Linder present an approach for dealing with implications of conflicting gene trees on inferences of evolutionary history above the species level.

In Conservation Biology, Angelia Vanderlaan and Christopher Tagaart describe how a voluntary scheme for ships to avoid cetain areas has worked in preventing lethal strikes on right whales.

In Ecological Applications, Cang Hui and colleagues compare approaches for extrapolating population sizes from abundance-occupancy relationships. Matthew Etterson et al. look at the problem of estimating population trends when there is detection heterogeneity and overdipsersion in the data. Paul Beier and co-workers use a case study to examine the use of least-cost modelling to design wildlife corridors.

Oscar Puebla and colleagues describe in Ecology a study that estimates dispersal using genetic distances in a coral reef fish. Sean Connolly et al. have a new bootstrap approach for testing species abudance models in the same issue. Andy Royle et al. present Bayesian method for estimating population sizes using camera trap data. David G. Angeler, Olga Viedma, and JoséM. Moreno present a critique of time lag analysis in time series modelling. David Carslake et al. have a paper presenting useful review of constraints and rules for elasticity analysis in matrix modelling. Finally in that same issue Paul Stapp and Daniel J. Salkeld look at the use of stable isotopes in studying host-parasite interactions.

Finally for this month in Animal Conservation, Heidy Kikillus et al. look at minimising false negatives in predicting distributions of invasive species. (Thanks to Andrew Tyre for pointing this one out).