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This approach had been pioneered in the classical work of Dobzhansky and Sturtevant who used inversions in Drosophila chromosomes to construct an evolutionary tree [ 12 ] . Subsequently, mathematical methods have been developed to calculate rearrangement distances between genomes, and, using these, phylogenetic trees have been built for certain small genomes, such as plant mitochondria and herpesviruses [ 13 14 ] . These approaches, however, are applicable only to genomes that show significant conservation of global gene order, which is manifestly not the case among prokaryotes [ 15 16 17 ] . Even relatively close species such as, for example, Escherichia coli and Haemophilus influenzae, two species of the γ-subdivision of Proteobacteria, retain very little conservation of gene order beyond the operon level (typically, two-to-four genes in a row), and essentially none is detectable among evolutionarily distant bacteria and archaea [ 15 16 18 ] . Very few operons, primarily those coding for physically interacting subunits of multiprotein complexes such as certain ribosomal proteins or RNA-polymerase subunits, are conserved across a wide range of prokaryotic lineages [ 15 16 ] . On the other hand, pairwise comparisons of even distantly related prokaryotic genomes reveal considerable number of shared (predicted) operons, which creates an opportunity for a meaningful comparative analysis [ 19 ] [ 20 21 ] .
NSC memo, Sturtevant to Griffin, Levin, Krongard, Watson, and others, July 12, 2001.
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