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 1

Methods in Ecology and Evolution will be receiving its first Impact Factor in summer 2012 and we are very impressed with how well our articles are being cited. For those of you who have been following Methods from the start, you will notice some papers that we have already mentioned last year in our top cited blog posts. These are still going strong! Over the next few days we’ll be highlighting our most cited papers across a broad range of fields – stay tuned on MethodsBlog.

Statistical methods in ecology & evolution

Modelling species and the environment


Physiological ecology

Tomorrow we will be posting part 2, where we’ll be showcasing our top cited papers in plant monitoring and modelling, stable isotope ecology and community ecology, and come back on Wednesday for part 3, when we’ll be revealing our top papers in population monitoring, climate change, evolutionary ecology and phylogenomics.

Recently accepted articles

We have been very busy this week and we have a whole range of recently accepted articles:

  • Bats as bioindicators – The need of a standardized method for acoustic bat activity surveys
    Peter Stahlschmidt and Carsten Brühl
  • Developing a deeper understanding of animal movements and spatial dynamics through novel application of network analyses
    David Jacoby, Edward Brooks, Darren Croft and David Sims
  • BaSTA: an R package for Bayesian estimation of age-specific survival from incomplete mark-recapture/recovery data with covariates
    Fernando Colchero, Owen Jones and Maren Rebke
  • Designing a benthic monitoring programme with multiple conflicting objectives
    Allert Bijleveld, Jan van Gils, Jaap van der Meer, Anne Dekinga, Casper Kraan, Henk van der Veer and Theunis Piersma
  • Category count models for resource management
    Paul Fackler
  • mvabund – an R package for model-based analysis of multivariate abundance data
    David Warton, Yi Wang, Ulrike Naumann, and Stephen Wright
  • Movement ecology of human resource users: using net squared displacement, biased random bridges and resource utilisation functions to quantify hunter and gatherer behaviour
    Sarah Papworth, Nils Bunnefeld, Katie Slocombe and E.J. Milner-Gulland

Issue 2.5 out today

Issue 2.5 of Methods in Ecology and Evolution is published today, and it’s a special 150 page bumper edition!

The tempo of evolution  heads the bill for this issue, with a strong phylogenetic duo in Measuring the temporal structure in serially sampled phylogenies by Rebecca R. Gray, Oliver G. Pybus and Marco Salemi, and A simple polytomy resolver for dated phylogenies by Tyler S. Kuhn, Arne Ø. Mooers and Gavin H. Thomas. The nature of life-history evolution is also examined, with a re-interpretation of the ubiquity of post-reproductive lifespan in Levitis and Lackey’s A measure for describing and comparing postreproductive life span as a population trait.

Two papers describe improved camera trapping methods, leading towards a practical application of the random encounter model in  Quantifying the sensitivity of camera traps: an adapted distance sampling approach (Rowcliffe et al.), and towards a measure for correcting for observer error in Estimating survival in photographic capture–recapture studies: overcoming misidentification error (Morrison et al.).

An innovative use of stable isotope analysis to the problem of tracking carnivore ranges is explored in Tracking large carnivore dispersal using isotopic clues in claws: an application to cougars across the Great Plains by Hénaux et al., while an inexpensive, convenient and widely applicable assay for comparitive analysis of avian immune function is introduced in A simple assay for measurement of ovotransferrin – a marker of inflammation and infection in birds by Horrocks et al. An improved method for raising honeybees in vitro, with potential to improve urgent research on colony collapse disorder, is proposed by Hendriksma et al. in Honey bee risk assessment: new approaches for in vitro larvae rearing and data analyses.

Three papers deal with predicting and modelling range expansions, invasive migrations, and community upheaval  under climate change. Improving prediction and management of range expansions by combining analytical and individual-based modelling approaches, by Travis et al., and A benefit analysis of screening for invasive species – base-rate uncertainty and the value of information, by Sahlin et al., provide useful tools for improved modelling under these uncertain conditions, while by contrast Heating up the forest: open-top chamber warming manipulation of arthropod communities at Harvard and Duke Forests, by Pelini et al., showcases an ingenious experimental setup for artificially simulating global change on a small scale, and in situ.

Population structure and community connectivity are addressed in Powney et al.’s Measuring functional connectivity using long-term monitoring data, and Joppa & Williams’ The influence of single elements on nested community structure.

Two papers on population modelling round off the issue, with Transient sensitivity analysis for nonlinear population models by Taverner et al., and Estimating abundance from presence/absence maps by Wen-Han Hwang and Fangliang He.

Don’t forget that your library can get free access in perpetuity to the first two years of Methods in Ecology and Evolution (including this issue!) by just completing this request form.

Top cited papers – part 1

ISI has only been indexing Methods in Ecology and Evolution for a short time, but some of our papers are already accumulating an impressive number of citations. Over the next few days we’ll be highlighting our most cited papers across a broad range of fields – just in case they’ve slipped you by.

Statistical methods in ecology & evolution

Modelling species and the environment

Physiological ecology

Check back tomorrow here for part 2, where we’ll be showcasing our top cited papers in plant monitoring and modelling, stable isotope ecology and community ecology, and come back on Monday for part 3, when we’ll be revealing our top papers in  population monitoring, climate change, evolutionary ecology and phylogenetics.

Estimating seed predation rates

Seed predation plays an important role in global plant demography. In this video, Adam Davis, of the University of Illinois, demonstrates how field experiments and statistical models can can enable the extrapolation of long-term seed predation rates from short-term data.

A full treatment of this can be found in the paper Temporal scaling of episodic point estimates of seed predation to long-term predation rates, recently published in Methods in Ecology and Evolution.


Methods digest – update

A round up of recent methods-relevant research published recently: it is ages since we did this, largely because the journal has been so busy with papers coming in and being published. Do send through links to any new methods papers to me or to the journal, or post a comment below.

In Evolution, Werthelm & Sanderson look at how estimates of diversification rates are influenced by improved estimates of divergence times; Robert Lanfear introduces a new method for comparing rates of molecular evolution on trees.

In Systematic Biology Eric Stone has an extremely interesting article on why common comparative methods are robust to tree misspecification. Martin Linder et al. evaluate Bayesian models of substitution rate evoluton, whist Chung & Ané compare Bayesian methods for gene and species tree reconstructions. Simon Ho et al. have a short paper on Bayesian estimation of substitution rates from ancient DNA sequences.  Leaché & Rannala compare the accuracy of species tree estimation under different methods. Anne Kupczok explores the consequences of different null models for shape bias of supertree methods. John Huelsenbeck et al. compare phylogenetic models with the ‘No Common Mechanisms Model’.

In the Journal of Animal Ecology Andrew Jackson & co. have a paper on a new R package (SIBER) for comparing isotopic niche widths.

Sophie Smout et al. look at how heterogeneity of detection and mark loss affect estimates of survival in grey seals in Journal of Applied Ecology. Issue 1 of 2011 has a special profile introduced by Julia Jones on monitoring species abundance.

Eve McDonald-Madden et al. have a paper in Ecological Applications on how to allocate conservation resources when the persistence of a species in not certain. Mary Beth Rew and colleagues look at the problem of how many genetic markers should be used to tag an individual in the presence of close relatives.

A paper by Adam Algar et al. in Ecology looks at how it is possible to quantify the roles of trait-based filters in determining local and regional species composition. Florent Bled, Andy Royle & Emmanuelle Cam have a paper on testing hypotheses about nesting site dynamics by combining population and fitness data.

In Oikos, Sofia Berg et al. have a paper on the use of sensitivity analysis to identify keystones in foodwebs.

Finally for this update, in Ecography Simon Linke and co look at how multivariate analysis can produce conservation planning that addresses the needs of practitioners. Steinar Engen et al. describe a new approach to measuring the similarity of communities and Canrain Liu et al. have a paper on measuring the accuracy of species distribution models using presence absence data.

I’ll try to do another update in the next couple of weeks to cover some of the journals I have missed in this one.

Volume 2 Issue 1: Now online

We launched Methods in Ecology in Evolution because we thought that there was a huge demand for methods papers: 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. Our first volume has exceeded all expectations and we are really pleased to announce that the first issue of volume 2 is online on time and is full of a diverse range top quality papers.

The range of papers in this new issue is extra-ordinary – the scope includes everything from statistics, to energetic modelling and stable isotope methods. The applications of the methods are as varied as measuring food web dynamics, uncovering the drivers of farmland bird declines and the use of phylogenetic methods for reconstructing the history of the molluscs.

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 :

In fact almost all of the papers in this issue are supported by either a podcast, a videocast or online supplements. These latter include the user manual explaining how to used the WaderMorph modelling software, amongst others.

This issue contains an important “application” paper: Thomas Etherington gives an outline of the tools he has developed for visualising genetic relatedness in landscape genetics. Look out for more of these, describing the latest software tools, on our Early View page.

We are pleased to see that our papers are beginning to be used: the 10 papers published just a year ago in issue 1 have been cited (according to Google Scholar) a total of 34 times in the first twelve months since publication, i.e. an average of 3.4 times per paper. This is fantastic – for comparison, a journal wilth a Thomson ISI© Impact Factor of 3.4 receives an average of 3.4 citations per paper in the two years following the year of publication.  This is hopefully an indication of good things to come!

Methods in Biogeography

The International Biogeography Society has just held their 5th meeting in Crete and I thought I would pick some highlights that are methods relevant.  This meeting brings together a range of researchers from the intersection of ecology, evolutionary biology, geography, geology and systematics: a truly diverse grouping.

Biogeography is, in essence concerned with the distributions of species and how these change with time. It is no surprise then that phylogenetic analysis was the focus of many talks. Indeed, if there is one thing that sets the talks I saw at this meeting apart from those at more ‘ecological’ meetings, it is the heavy reliance on phylogenetic methods. Relatively recently developed methods for looking at phylogenetic structure in ecological communities were particularly in evidence.

Three talks were particularly methods focussed and described really interesting new approaches and perspectives.

Andy Purvis of Imperial College, UK, looked at how macroevolutionary questions could be tested using different methods and data. His talk emphasised that evolutionary models can be varied and that broad-scale analyses that assume single models could be misleading. For example, using data on all mammal species he showed that the evolution of body mass could be described using an ‘early burst’ model; however when broken up into individual orders, the picture was a highly variable one with different models fitting best to some orders rather than others, and very different rates across groups.

Andy also dealt with niche conservatism, another big theme at this meeting. Niche conservatism is the idea that closely related species share their niches because they inherit them from ancestors. If niches are generally conserved then this is important because, for example, changes to climate or habitat may affect taxonomic groups of species that share similar requirements, or that are historically slow to adapt. Andy made the good point that current definitions are sometimes at odds with each other, and that notions of niche conservatism need to be clearly spelled out.

Also from Imperial, Ally Phillimore took a different perspective. The aim in his research is to link small-scale ecological processes with macroevolution. He described an elegant method for linking within and between population spatial and temporal variation to explore the degree to which adaptation and plasticity drive phenological responses to climate change. Using data on data gathered by the public on egg laying dates in frogs in the UK, Ally showed how his approach could be used to predict how fast populations need to evolve in order to keep up with climate change.

A major issue in the analyis of biogeographical and macroecological data is how to deal with spatialautocorrelation. Pedro Peres Neto from the University of Quebec and Montréal described simulation results that showed how autocorrelation affects the outcomes of statistical tests, and provided some guidelines on the expected outcome of methods. He pointed out that the strength of a relationship between two variables and the source of dependency (whether in the residuals or the predictors) could be factors. One point well made was that spatial and phylogenetic methods for trait data analysis share a lot of similarity and there is a lot of potential for interchange.

These are just three talks I have highlighted as I found them particularly stimulating (and methods relevant), overall the meeting was really enjoyable interesting. And, following the coldest UK December in 100 years, I really do have to congratulate the organisers on their choice of Crete a venue!