There have been several definitive answers in this thread alone. Nuclear DNA is present in every person. Caylee's known DNA (which includes her mother's contribution and her father's contribution) was compared to the then unknown remains nuclear DNA, which came up as a conclusive match to the known DNA of Caylee.
Where things are getting complicated is that people are assuming that LE knows who Caylee's father is based on his DNA. That might be true; however that information has not been released, and as far as I can see, unless it is pertinent to this case, it will not be. The father, whoever he is, is not owed a notification of the death of a child he never legally took responsibility for, including but not limited to, being listed on her birth certificate.