Multiple introductions and deletions of mobile elements.

Each introduction or deletion in a node of the genealogy is counted only once, even if that introduced mobile element is present in multiple descendent genomes. The number of distinct sequence variants within each category is indicated by (Number) after Type. Where mobile elements integrated into multiple locations within the genome, each such integration was associated with a distinct sequence variant (Dataset S1), and they represent independent insertions. Additional, unrelated non-IS mobile elements were each introduced on a single occasion (Dataset S1), consisting of 2 ICE/IMEs, 3 bacteriophages, 3 plasmids and 4 other genomic islands, for a total of 95 introductions of non-IS mobile elements. Five other genomic islands were each deleted once, for a total of 22 deletions of non-IS mobile elements. Similarly, five IS elements were introduced on one occasion each (Table S8, S9), for a total of 54 introductions.