Figure 1.

(A) A schematic diagram of syntenic regions in three species, with a repeat insertion in A, B, and C. The lightly shaded areas correspond to regions that align well, indicating that the repeat is present in A, B, C and absent in D, E, F. Neither presence nor absence can be verified for G. (B) A likely phylogeny consistent with a parsimonious explanation of the data. Species A, B, and C belong in a clade that can be separated from D, E, and F, and the repeat was inserted in a common ancestor of the three species. There is no constraint on where G might occur. Also note that there are no constraints on where D, E, and F occur, other than they do not fall in a clade defined by the earliest ancestor of A, B, C.