Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 04-005

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Graph Grammars as Models for the Evolution of Developmental Pathways

Martin Beck, Gil Benkö, Gunther J. Eble, Christoph Flamm Stefan Müller, Peter F. Stadler

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The large quantity and ready availability of developmental-genetic data, coupled with increased rigor and detail in the characterization of morphological phenotypes, has made the genotype-phenotype map of whole organisms a central challenge in evolutionary developmental biology. This in turn necessitates more general modeling strategies that can efficiently represent different types of biological knowledge and systematically applied across levels of organization, spatiotemporal scales, and taxonomic groups. Graph-based models appear useful in this context but have been remarkably underutilized in biology. Simulation of ontogenetic and evolutionary change by means of graph-rewriting algorithms has been explored as a means of providing a coordinate-free approach to form transformation in time and space. A finite set of rules describing generic graph transformations is used to encode knowledge about morphogenetic steps. Their application to skeletal growth in sea urchins effectively models ontogenesis in terms of topology rather than specific geometry, suggesting a promising approach to general modeling of developmental evolution.

Evolution of Development, Graph Grammars, Computer Simulations

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