Although polymorphic inversions in Drosophila are very common, the origin o
f these chromosomal rearrangements is unclear. The breakpoints of the cosmo
politan inversion 2j of D. buzzatii were cloned and sequenced. Both breakpo
ints contain large insertions corresponding to a transposable element. It a
ppears that the two pairs of target site duplications generated upon insert
ion were exchanged during the inversion event, and that the inversion arose
by ectopic recombination between two copies of the transposon that were in
opposite orientations. This is apparently the mechanism by which transposa
ble elements generate natural inversions in Drosophila.