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Utilizing Phylogenetic Information

A reconstructed phylogenetic tree guides our interpretation of the evolution of organismal characteristics, indicating in what lineages traits arose and under what circumstances, thus playing a vital role in studies of adaptation and evolutionary constraints. Patterns of divergence of species lineages indicated by the phylogeny inform us of the dynamics of speciation and extinction, the forces that generate and reduce biodiversity, including the assembly and maintenance of species in ecological communities.

Phylogeny informs far more than evolutionary biology, however. The evolutionary histories of genes bear the marks of the functional demands to which they have been subjected, thus allowing phylogenetic analysis to elucidate functional relationships within living cells. For instance, pharmaceutical companies are increasingly using phylogenetic analyses to make functional predictions from sequence data banks of gene families, and applying this information in the development of vaccines and antimicrobials. Molecular biologists use phylogenies to determine the relevance of model organisms for research in such diverse fields as agriculture and human health.

Finally, phylogenetic reconstruction is used well beyond the boundaries of biology and biomedicine: it is a crucial tool in forensic studies (for instance in the HIV murder trial and recent work on the anthrax terrorist attacks), in security applications for networks and computers (such as artificial immune systems for computers), and in a variety of disciplines such as historical linguistics.