Two different most parsimonious scenarios that transform the order of the 11 synteny blocks on the mouse X chromosome into the order on the human X chromosome. The arrangement of synteny blocks in the ancestor is unspecified (and is assumed to coincide with one of intermediate arrangements) because it cannot be inferred without availability of a third genome (33, 41). Breakpoint uses are shown as short vertical yellow lines, and breakpoint region reuses are shown as double yellow lines. In the first scenario (Left) the breakpoint reuses are located in human in breakpoint regions (3,4), (4,5), and (5,6), whereas in the second one (Right) they are located in (5,6), (6,7), and after block 11. In the second scenario, a potential hidden block is shown as a black dot; it restricts the set of possible most parsimonious scenarios, and it separates two breakpoint uses that would have been a breakpoint region reuse. Our theory implies that any rearrangement scenario based on these 11 blocks has at least three reuses of breakpoint regions (possibly including chromosome ends).