Closing the Complexity Gap of the Double Distance Problem

Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application of rearrangement distance methods and more advanced phylogenetic tasks is becoming common practice, given the availability of many completely sequenced genomes. Several genome rearrangement models have been developed over time, sometimes with surprising computational properties. A prominent example is the fact that computing the reversal distance of two signed permutations is possible in linear time, while for two unsigned permutations it is NP-hard. Therefore one has to always be careful about the precise problem formulation and complexity analysis of rearrangement problems in order not to be fooled. The double distance is the minimum number of genomic rearrangements between a singular and a duplicated genome that – in addition to rearrangements – are separated by a whole genome duplication. At the same time it allows to assign the genes of the duplicated genome to the two paralogous chromosome copies that existed right after the duplication event. Computing the double distance is another example of a tricky hardness landscape: If the distance measure underlying the double distance is the simple breakpoint distance, the problem can be solved in linear time, while with the more elaborate DCJ distance it is NP-hard. Indeed, there is a whole family of distance measures, parameterized by an even number k, between the breakpoint distance (k = 2) at the one end and the DCJ distance (k = ∞) at the other end. Only little was known about the hardness border that lies somewhere on the way between these two extremes. Precisely, beneath the two border cases the (linear) problem complexity was known only for k = 4 and k = 6. In this paper we close the gap, giving a full picture of the hardness landscape when computing the double distance.