Virtual Issue: Evolution 2013

Evolution 2013 coverTimed for Evolution 2013, we have just put up a Virtual Issue highlighting some of the papers with an evolutionary theme published in the last year.

The link between ecology and evolution is important to MEE: the research papers we have highlighted include excellent examples of these such as modelling dispersal and testing for niche conservatism. Barcoding methods are included, which increasingly are used in an ecological context; the Applications and research papers include a high proportion of papers that describe methods for comparative analyses, which underpin both ecological and evolutionary studies. This selection therefore showcases the excellent range of research that we have published spanning both ecology and evolution.

Enjoy & enjoy Snowbird!

Watch the CEE meeting, Integrating ecology into macroevolutionary research

By way of an introduction to this blog post, watch this!

Back in March the Centre for Ecology and Evolution in London organised a meeting that brought together top researchers in macroevolution. The idea of the meeting was to highlight how advances in the study of macroevolution could be made by a closer integration with ecology, and the incoroporation of ecological ideas and ecological models.

The meeting had a terrific line-up of speakers, and a synthesis of the science is now available in Biology Letters.

As with any meeting of course, a limitation was that you had to be in London and free on the days of the symposium: I couldn’t make it as I was in the other side of the country and committed for the whole two days. However, in what is an innovation for evolutionary and ecological research, the organisers of the symposium recorded the talks and have now made them available to watch online. MEE, via our publishers Wiley-Blackwell, we were glad to sponsor the costs of making the talks available online. Not least as it meant that I could watch them!

Having now watched all of the talks, some highlights for me are:

However, all the talks are excellent and really worth watching.

I think this is an excellent resource for the evolutionary community: the videos have been professionally recorded and edited, and are easy and effective to watch. Given the modest costs of doing this, I hope that more meeting organisers will follow this lead.

MEE now to be found on ISI Web of Knowledge

Just a quick post to highlight that Methods in Ecology and Evolution is starting to be indexed on the Web of Knowledge, with 3 of our issues included  for the first time this week in the online database. This is great news: it will make our papers visible to a wide audience and eventually we will get an impact factor. We are already getting lots of downloads, and citation figures from Google Scholar indicate that our papers are being read and used. So hopefully inclusion on WoK will add further to our progress.

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!

A year of podcasts and videos

We have been uploading videos and podcasts for a year now – these have proved really popular, both with authors and readers of the journal. I thought I would just take this opportunity to highlight some of the online content that is supporting articles from the first 3 issues:

Our podcasts include:-

We also have video interviews with our authors, including:

What we are hoping to do is to maximise the utility of our published papers for readers, as well as ensure that the methods we publish reach as wide an audience as possible. Please do give feedback on any of our content, and we are always open for suggestions for new ways to promote new methods!

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 – June 2010

Here is the methods digest update for June 2010 – do let me know if there is anything that you think I should feature.

In Oikos Novak & Wooton have a paper on using indices to quantify the effects of comeptition and Landau & Ryan present new ‘null model tests for presence-absence data’ (NMTPAs).

A paper in Conservation Letters by Michael Kearney et al. evaluates species distribution models by comparing the output of correlative and mechanistic models.

In the Journal of Ecology the debate about how to measure the intensity and importance of competition continues to rage. Walker et al. also review the use of chronosequences in studies of succession. Hautier et al. look at how to model the growth of parasitic plants (see also the editorial commentary by Mark Rees).

In the current issue of Systematic Biology, Susana Magallón applies a method using fossils to break long branches to molecular dating of the angiosperm phylogeny. Carstens & Dewey have a new method for species delimitation. Haartman et al. have a paper on sampling trees from evolutionary models.Towsend & Lopez-Giraldez look at the optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships.

Salvador Pueyo et al. in Ecology Letters look at the problem of testing for criticality in ecosystem dynamics. Kuhnert et al. review the use of expert knowledge in Bayesian modelling.

In the latest issue of Ecology Bailey et al. look at estimation in multistate models with unobservable states. Mérigot et al. look at goodness of fit measures for dendrogram analyses.

Hines et al in Ecological Applications present a new approach for occupancy modelling for cluster sampling. In the same issue Waddle et al. present a new approach for estimating co-occurrence of interacting species.

Finally, in the American Naturalist Hamilton et al. look at the problem of estimating the uncertainty in estimates of species richness, and Solow & Smith look at how to estimate abundance from occupancy.

Detecting effects of predators on prey: the method matters

In a paper published online today in Methods in Ecology and Evolution, Malcolm Nicoll and Ken Norris look at a controversial issue, that of detecting effects of predators on bird populations. This is controversial because some predators, especially raptors, were formerly rather scarce, but have become more abundant in recent years – in the case of raptors because organochloride chemicals are not used any more. At the same time mammal predators have also increased in numbers. This has led to suggestions that increases in predators may be a contributory factor to declines in some groups of birds, such as farmland birds, and there has been a great deal of discussion and debate over the issue.

Unfortunately this is a hypothesis that is not very easily addressed, unsurprising given the spatial and temporal scales that may be involved. Experimental approachs would be the ‘gold standard’, but these are difficult. Gradients of predator abundance have to be created by means of barriers or removal, which is expensive, logistically challenging and potentially expensive.

More usually opportunistic, observational evidence has to be relied upon. For example, this might take the form of statistically comparing populations in birds in areas with high numbers of predators with those with low numbers of predators. Whilst more practicable, such studies can suffer from the possibility of confounding: if a third ‘hidden’ variable also varies between sites, then this could generate problems for the interpretation.

The previous literature has presented mixed results: some studies have demonstrated effects of predators on prey populations, others have not. Whether this variation has an ecological basis is not clear.

In this new study, Nicoll & Norris re-evaluate previous observational studies by means of meta-analysis. They look at the effects of the quality of data and the number of predator species studied on the outcome of analyses. Importantly they find that the probability of detecting an effect depends on both the quality of data and the number of predators studied.

There are several implications of this work. Studies with poor quality data and that include small numbers of predators cannot reliably tell whether there are effects of predators or not, they are simply inconclusive. Nicoll & Norris go as far as to say that one should be skeptical about any short-term observational study that reports no effects of predators. They also suggest that the combined effects of predators are likely to be more important than that of any single predator, and that future studies should account for this.

Finally this study highlights the importance of methods in ecology: one cannot interpret evidence unless the method used is shown to be reliable and fit for purpose. Nicoll & Norris’ study is a good example of how re-evaluation of methods can help improve ecological understanding.