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.


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!

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!

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).