Measuring the importance of species to ecosystems

In this video to accompany their paper Randomization tests for quantifying species importance to ecosystem function, authors Nicholas Gotelli and Fernando Maestre discuss the introduction of simple tests for measuring the effect of species on ecosystem variables, and give us an insight into the logistics required for their paper’s “natural experiements” – involving the collection and preparation of over 25,000 lichen samples!

The methodology presented in this paper provides a simple way of determining and testing species importance, and could form the basis for future theoretical and experimental studies investigating species occurrence and ecosystem function.


Heating up the forest

In our latest video Shannon Pellini demonstrates experimental equipment designed to simulate the effects of warmer air temperatures on forest ecosystems – and, particuarly, on arthropod communities.

You can read a full account of their experimental methods, and results from two contemporaneous trials at Harvard Forest and Duke Forest, in their recently published paper, Heating up the forest: open-top chamber warming manipulation of arthropod communities at Harvard and Duke Forests.


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 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.

Methods Digest – March 2010

The first thing to point out this month is that issue 1 of the journal is now online here. To accompany the issue we have a podcast and a videocast. There is also now a  journal correspondence site to host feedback and discussion of published papers, more on this soon.

The one day journal launch symposium is accepting bookings, with a good response so far. However places are still available, and the booking form is here.

We hope that Methods in Ecology and Evolution will be listed on ISI as soon as possible – if you have 2 minutes to spare we would be really grateful if you would fill out the nomination form. This will help us get noticed by them.

To begin this month’s round up of recent methods papers, Ecological Monographs has a paper  by James Grace and colleagues on structural equation modelling. In this paper they outline how meta-models can be used to aid the translation of theory into SEMs.

In Ecological Applications, Lester Yuan describes how observational data and propensity scores can be used to estimate the effects of excessive nutrients on stream invertebrates.

In Ecology Fitsum Abadi and colleagues perform an analysis of the performance of integrated population models, particularly focussing on the issue of independence of data. Pierre Legendre et al. look at how ‘space-for-time’ experiments can be analysed in the absence of replication. Toby Patterson et al. look at how state space methods can be used to correct telemetry data and the limits to this approach. Etienne Laliberté & Pierre Legendre present a new approach for measuring functional diversity, along with R code.

Richard P. Brown and Ziheng Yang in Systematic Biology look at the problem of dating shallow phylogenies with relaxed clocks using Bayesian methods. Jeremy Brown et al. discuss the problem of very long branch length estimates in trees generated using Bayesian methods, compared with ML alternatives. R. Alexander Pyron presents a Likelihood method for assessing molecular divergence time estimates with the placement of fossils.

In Ecology Letters Colleen Webb et al. present a new approach to develop trait based theory for predicting community composition and ecosystem function.

The latest issue of the Journal of Applied Ecology has a section on ‘Modelling Distributions’. This includes methods papers on the use of proxy-based methods for mapping ecosystem services,  estimating individual survival using occupancy data, estimation of immigration rates using integrated population models, and the ability of habitat suitability models to predict the recovery of threatened species.

In the American Naturalist Bart Haegeman and Rampal Etienne look at the relationship between entropy maxization and species distributions.

Thanks to Rua Mordecai for pointing out an interesting paper in the Auk by Jason Riddle and colleagues on incorporating estimates of prior detections in estimating occupancy, abundance and probability of detection.

Please let me know if there are any papers that could be featured in the next month’s digest update.

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Four new papers published in January

Four new papers have been published online this month. These cover a range of topics including ecological modelling, measuring diversity, detecting range shifts and physiological ecology.

In the first paper, Gideon Gal and William Anderson outline a new method for detecting regime shift in ecosystems.  Regime shifts occur when the state of an ecosystem changes markedly and rapidly, usually with a dramatic shift in species composition. Such shifts can be difficult to identify, particularly if the system in question is very noisy. The new method borrows techniques from statistics and econometrics and has the advantage that it does not rely on any pre-determined threshold value. The technique is used to show a regime shift in the zooplankton assemblage of a lake ecosystem.

Jan Beck and Wolfgang Schwanghart look at the problem of estimating species diversity from inventories.  They specifically deal with the issue of undersampling, that is when inventories are incomplete owing to lack of coverage. In their study they simulate data with known levels of undersampling, and ask which estimates of diversity give the least biased estimates of true diversity.

A modelling paper by Clive McMahon, Barry Brook, Neil Collier and Corey Bradshaw describes a spreadsheet-based tool for exploring the strategic management of invasive species. Designed for predicting how different culling strategies affect the densities of invasive ungulates, the tool is aimed at managers and those with little familiarity with theory and modelling. The approach is applied to the control of feral pigs, buffalo and horses in Kakadu National Park Australia – the general framework could easily be applied to any similar system.

Finally for this update, Elizabeth Freeman and colleagues describe a new enzyme immunoassay for monitoring progestagens in elephants. This assay is a step forward as it is relatively easy and cheap, does not require expensive equipment and can be performed in the field. Hormone monitoring is an important conservation tool, allowing for example the reproductive states of animals to be monitored.

This is an exciting, diverse and high quality set of papers – more are on there way, the list of the latest papers to be accepted can be found here.

p.s. The first paper published in the journal by Alain Zuur and colleagues was downloaded over 1100 times in the first month after publication!