Modelling static and dynamic variables

Jessica Stanton discusses the problem of accounting for both static and dynamic variables in designing species distribution models under climate change in our newest author video.

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Biodiversity estimates from DNA sequences

The complexity of new methodologies can present a challenging barrier towards their uptake. Recognising this, Jeff Powell,  author of Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data, has put together an excellent tutorial to guide people through the implementation of his objective, theory-based method for predicting species boundaries, which explicitly incorporates uncertainty in the classification system into biodiversity estimation.

The tutorial is available to view and download from Slideshare, and the relevant R code can be found as supplementary material on Wiley Online Library.

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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.

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.

Virtual Issues on Forests and Global Change

In celebration of the UN’s International Year of Forests, and the British Ecological Society’s Symposium on Forests and Global Change, the Journal of Applied Ecology and Methods in Ecology and Evolution have worked together to bring you two complementary virtual issues in these areas: one dealing with environmental management, and the other the most relevent new methodological developments in forest and global change research.

Sample papers from the Methods virtual issue include:

We hope that you will find these virtual issues both useful and engaging, and that they will help to contribute to future research in this highly relevant field!

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 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.

New papers – problems with matrix models & measuring species richness

We have two new papers online this week:

In the first, David Watson looks at the problem of measuring diversity in highly diverse vertebrate communities. He shows that methods usually used for arthropod communities can be applied to monitoring bird populations. The analyses he performed answered important questions, such as: what effort is required to completely inventory a site? And, what is the least effort required to yield robust estimates of species richness?

In the second paper, Ian Stott & colleagues highlight some problems with population projection matrices, one of the most commonly used tools in population modelling. They find that ~25% of published models have a structural problem (they are reducible, i.e. do not contain pathways diretly or indirectly linking each stage to each other), and that ~16% are non-ergodic, i.e. there is more than one growth rate / stable state. This is clearly a previously unappreciated issue in modelling, and Stott et al. present simple approaches for diagnostic analysis.

Other papers currently online and available pre-publication include:

A list of currently accepted papers is here, and do check out our podcast and videocast interviews with authors.

Methods Digest – May 2010

Here is the latest methods digest:-

In Evolution Marta Szulkin, Nicolas Bierne and Patrice David have  perspective piece on measuring correlations between fitness and heterozygosity. Günter Wagner introduces a new approach to measuring fitness. Max Shpak and colleagues introduce an approach to coalescent modelling in populations that are structured and fluctuate seasonally. Richard Reynolds and colleagues look at the problem of measuring selection gradients.

Valério Pillar and Leandro Duarte present in Ecology Letters a new approach to analysing phylogenetic structure in metacommunities. Andy Fenton and colleagues look at the the problem of detecting interspecific interactions between macroparasites from ecological data. Johan Dahlgren has a contribution to the debate on regression methods.

In Proceedings B Peter Henderson and Anne Magurran present a new method for plotting species abundance distributions and linking to biomass. Tatsuya Amano et al. present a new approach for developing phenological indices.

William Morris and colleagues have in Ecology a paper looking at cost-benefit curves for pollination mutualisms. Michael Greenacre considers the problem of correspondance analysis of unstandardised data. Stephanie Carlson, Athanasios Kottas and Marc Mangel describe how Bayesian methods can be used to analyse size-dependent over-winter survival.

In Ecological Monographs Dennis Heisey et al. look at the problem of estimating spatio-temporal dynamics from cross-sectional data. Kyle Dexter and colleagues ask how accurate are identifications of tropical trees, using DNA data to test accuracy.

In Systematic Biology Christian Klingenberg and Nelly Gidaszewski describe new methods for measuring phylogenetic signal and homoplasy in morphometric data.  Thomas White et al. describe a network approach to studying karyotypic evolution. Liat Grievink et al. consider phylogenetic reconstruction when the proportional of variable sites varies across a tree. Stéphane Guindon and colleagues assess the performance of PhyML.

Finally for this month, in Journal of Applied Ecology, Jim Hone et al. look at estimates of maximal rates of population growth of mammals and applications in management, and Thomas Ezard and colleagues deal with the issue of transient dynamics in population management.

If there are any papers that you think should be featured, please do contact me.

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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