Molecular systematics: assembling and using the Tree of Life

The Tree of Life represents the fundamental framework for ordering biological information. In this paper, we argue for concerted efforts to reconstruct the green plant clade of the Tree of Life, as well as the rest of the Tree, and suggest ways in which the Tree can be used further for inferring and testing hypotheses of evolution. We suggest characters, from DNA sequences to genomic characters, for use in reconstructing the phylogeny of plants. Challenges in data analysis must also be met, if we are to reconstruct the phylogeny of nearly half a billion species of green plants. Phyloinformatics, the storage, retrieval, and use of phylogenetic data and phylogenetic trees, must play an increasingly important role in plant systematics and the systematics community as a whole. Both functional and comparative genomics will benefit from integration with phylogenetic information, and these fields may provide new characters for phylogeny reconstruction. A synthetic view of plant phylogeny requires the incorporation of fossils; a major challenge facing paleo-botanists and plant systematists is the integration of these disciplines. In sum, molecular systematics, through interfaces with many other fields, from genomics to computer science to paleobotany, will long remain an unending synthesis.