Common intervals and symmetric difference in a model-free phylogenomics, with an application to streptophyte evolution

The common intervals of two permutations on n elements are the subsets of terms contiguous in both permutations. They constitute the most basic representation of conserved local order. We use d, the size of the symmetric difference ( the complement of the common intervals) of the two subsets of 2({1,...,n}) thus determined by two permutations, as an evolutionary distance between the gene orders represented by the permutations. We consider the Steiner Tree problem in the space (2{1,...,n}, d) as the basis for constructing phphylogenetic trees, including ancestral gene orders. We extend this to genomes with unequal gene content and to genomes containing gene families. Applied to streptophyte phylogeny, our method does not support the positioning of the complex algae Charales as a sister group to the land plants. Simulations show that the method, though unmotivated by any specific model of genome rearrangement, accurately reconstructs a tree from artificial genome data generated by random inversions deriving each genome from its ancestor on this tree.