Three hypotheses for the evolutionary dynamics of the roo and rooA element in the 12 Drosophila genomes. Red and blue branches indicate species harboring roo and rooA, respectively. Black branches indicate the loss of both elements. a) Roo/rooA may have originated in the common ancestor of all 12 Drosophila genomes with the split between the two elements shortly thereafter. Both elements were then vertically transmitted, as shown by the red and blue branches. Roo was lost in 3 species and rooA in six or seven (depending on the correctness of the rooA element in D. mojavensis (see text for details)). b) Roo/rooA may have arisen in the common ancestor of the Sophophora group and split shortly thereafter into separate lineages. Both elements were vertically transmitted to all descendant genomes, with a loss of roo in one genome and of rooA in four genomes. In this scenario, a horizontal transfer of roo to the genome of D. mojavensis took place after the split from D. willistoni (red arrow), but the exact time point of transmission cannot be determined. c) Roo/rooA might have originated in the common ancestor of all 12 genomes. With the split of the Sophophora group the element evolved into the roo element in the Sophophora group, and into the rooA element in the other three genomes. While roo was vertically transferred to all genomes, rooA is today only present in the D. mojavensis member of this clade. A horizontal transfer of roo to the genome of D. mojavensis took place after the split from D. willistoni. Later, another horizontal transfer, this time of rooA, took place from D. mojavensis to the common ancestor of the melanogaster subgroup where it then spread in all five genomes.