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NSC memo, Sturtevant to Griffin, Levin, Krongard, Watson, and others, July 12, 2001.
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 ] .
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