Zen

Eco-evolutionary Software

Figure 1

Ecology

Ecological models with an evolutionary component allow to study several biological phenomena: host-pathogens interactions, coevolution of plants and pollinisators, mimicry, development of the immune system, evolution of cooperation, evolution of life history traits, and more generally biodiversity and speciation.

What is simulated by ZEN ? The evolution of populations under the mutation-selection process 

ZEN uses an individual-based (in fact ‘phenotype-based’) approach with 3 components:

• Stochastic equations in discrete time describing the dynamics of finite populations
• Adaptive traits and their mutations (mutation rates and distributions)
•  Ecological interactions between phenotypes

During the ZEN simulation, mutant phenotypes created by the triggering of mutations interact with resident phenotypes. They persist or go extinct, possibly leading to evolutionary branching and polymorphism (Figs. 1, 2).

 

How does ZEN work ?

Models are described in a text file using a reduced declaration language, and studied by means of a simple interface with convenient graphics. The ZEN kernel is a symbolic evaluator handling ‘polymorphic’ variables.

 

 

Figure 2

 

Theoretical Context

The first evolutionary models in biology are verbal arguments, like Fisher’s proof that the primary sex ratio is 1/2. Theoretical evolutionary models started to develop in the 80’s with quantitative genetics and game theory. In this context originated the important notion of Evolutionary Stable Strategy (ESS), which had premises in the work of Hamilton on kin selection.

The recent theory of adaptive dynamics (Metz et al. 1996, Dieckmann & Law 1996) is based on population dynamics, and incorporates implicitly an hereditary mechanism operating on continuous adaptive traits. The evolutionary outcome is determined from the persistence of rare mutants in a resident population by computing their fitness gradient in the ecological setup.

A great achievement of the theory is the classification of the possible evolutionary outcomes, making a synthesis of previous results. A fascinating eventuality is that of evolutionary branching, which stems from the biological nature of the models, and does not appear in physical systems. In this situation, ecological constraints lead to disruptive selection, and possibly to sympatric speciation.

 

ZEN DOWNLOAD

ZEN is distributed free of charge. Users are under their own responsibility.

Computer / System	DOWNLOAD	Comments
PC Windows	Self-extracting file autozen.exe	Double-click on autozen.exe.  It will expand in directory c:/zen
PC Linux	Compressed file zen.tar.gz	Linux version is identical to Windows version Expand distribution file zen.tar.gz using command tar -xzf zen.tar.gz For installation, consult file ZenLinuxInstall.txt
MAC OS X	Compressed file zenc_mac.zip	Console version, no graphics Program file: zenc

The ZEN package is provided with example model files and a complete user’s manual.
 

After installation, the ZEN directory should contain:

• ZEN program zen.exe
• example model files *.zen
• reference manual zenref.pdf

 

Run 

Drag and drop any model file *.zen on the ZEN program icon. The program is run with the file as input. Click to process the file, and  to run the model. Consult the reference manual zenref.pdf for more information.

 

References

• Dieckmann U & R Law. 1996. The dynamical theory of coevolution: a derivation from stochastic ecological processes. Journal of Mathematical Biology 34:579-612.
• Ferrière R, JL Bronstein, S Rinaldi, R Law & M Gauduchon. 2002. Cheating and the evolutionary stability of mutualisms. Proceedings of the Royal Society of London B: 269, 773-780.
• Kisdi E & SAH Geritz. 2001. Evolutionary disarmament in interspecific competition. Proceedings of the Royal Society 268 B: 2589-2594.
• Metz JAJ, RM Nisbet & SAH Geritz. 1992. How should we define fitness for general ecological scenarios? Trends in Ecology and Evolution 7:198-202.
• Metz JAJ, SAH Geritz, G Meszéna, FJA Jacobs & JS van Heerwaarden. 1996. Adaptive dynamics, a geometrical study of the consequences of nearly faithful reproduction. In Stochastic and spatial structures of dynamical systems, J van Strien & SM Verduyn Lunel, eds. KNAW Verhandelingen, North Holland, Amsterdam, pp 183-231.
• Ravigné V. 2000. Spéciation et sélection de l’habitat. Rapport de DEA, Institut des Sciences de l’Evolution, Université de Montpellier II.

Author 

Stéphane Legendre

Web site of Stéphane Legendre

Mail to Stéphane Legendre

Ackowledgements

The ZEN computer project was funded by an Action Incitative Bioinformatique from the CNRS.

 

Collaboration

Laboratoire d’écologie Ecole Normale Supérieure Paris   Jean Clobert Régis Ferrière Minus van Baalen

Institut des sciences de l’évolution Université Montpellier 2 Montpellier   Isabelle Olivieri Ophélie Ronce Virginie Ravigné