TETAME - Estimating the parameters of the neutral model with dispersal limitation

Jérôme Chave and Franck Jabot

Laboratoire EDB UMR5174, Université Paul Sabatier Toulouse

The neutral theory of biodiversity (Hubbell 2001) has received a considerable amount of interest among community ecologists, and beyond. One of the difficulties in testing this theories is related to the nature of the diversity data themselves. The neutral theory predicts species abundance distributions as a function of two parameters, theta (the diversity in the species pool), and m (the immigration rate into the sampled community).

May 4th, 2006 - The Tetame software jointly estimates these parameters based on species abundance data collected from a single site. It implements an optimal maximum-likelihood estimation technique (Etienne 2005). The downloadable version of Tetame runs on Windows and Linux plateforms. If you are a mac user, you may want to contact us for the source code and compile it e.g. in the Darwin environment. This code has been used to calculate the values reported in Chave, Alonso & Etienne (2006). The software has been cited by Pennington et al. (2006), and by Walker & Cyr (2007). Thanks to Rampal Etienne and to David Alonso for their comments!

May, 20th 2008 - Release of Tetame 2.0. A new version of the Tetame software is available. This release provides the same features as Tetame-1.0 if a single species abundance dataset is provided, but it also a couple of new features. First, if the likelihood profile has two maxima, both are reported (Etienne et al. 2006). Second, a multi-site version is implemented. If several species abundance distributions are provided, the software computes m for each sample, assuming that the species abundances pooled over the samples reflect the regional species abundances. The theory for this new implementation is provided in Jabot et al. (2008). Thanks to Andrea Manica for troubleshooting the software!

March 11th 2010 - Tetame 2.1. A bug was fixed in Tetame 2.0

References:
Hubbell S.P. The Unified Neutral Theory of Biodiversity and Biogeography. (Princeton University Press, Princeton NJ 2001).
Etienne, R.S. A new sampling formula for neutral biodiversity. Ecol. Lett. 8, 253-260 (2005).
Chave J, Alonso D, Etienne, R.S. Comparing models of species abundance. Nature 441 E1 (2006).
Etienne, R.S., Latimer AM, Silander Jr, JA, Cowling RM. Comment on Neutral Ecological Theory Reveals Isolation and Rapid Speciation in a Biodiversity Hot Spot. Science 311 610b (2006).
Pennington, RT, Richardson, JE, Lavin M. Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure. New Phytologist 172: 605–616 (2006).
Walker SC, Cyr H. Testing the standard neutral model of biodiversity in lake communities. Oikos 116:143-155 (2007).
Jabot F, Etienne, R.S, Chave J. Reconciling neutral community models and environmental filtering: theory and an empirical test. Oikos (2008)

Last update June 15th, 2011