Implicit Transpositions in DCJ Scenarios.

Genome rearrangements are large-scale evolutionary events that shuffle genomic architectures. The minimal number of such events between two genomes is often used in phylogenomic studies to measure the evolutionary distance between the genomes. Double-Cut-and-Join (DCJ) operations represent a convenient model of most common genome rearrangements (reversals, translocations, fissions, and fusions), while other genome rearrangements, such as transpositions, can be modeled by pairs of DCJs. Since the DCJ model does not directly account for transpositions, their impact on DCJ scenarios is unclear. In the present work, we study implicit appearance of transpositions (as pairs of DCJs) in DCJ scenarios. We consider shortest DCJ scenarios satisfying the maximum parsimony assumption, as well as more general DCJ scenarios based on some realistic but less restrictive assumptions. In both cases, we derive a uniform lower bound for the rate of implicit transpositions, which depends only on the genomes but not a particular DCJ scenario between them. Our results imply that implicit appearance of transpositions in DCJ scenarios may be unavoidable or even abundant for some pairs of genomes. We estimate that for mammalian genomes implicit transpositions constitute at least 6% of genome rearrangements.