Here is an interesting Slashdot post. They found that somehow a parasitic bacteria had injected its DNA into the host species. Most DNA injection happens because of sexual/asexual transfer. But if this is borne out, there is a third way that DNA can be passed on. Also interesting is the notion that in the past, scientists that found "foreign" DNA sequences in fruit flys tended to reject that as contamination when, in actuality, they actually may be a part of the fly's genome.
Fascinating. Evolution must be wrong.