DNA in bones, in ideal conditions, will completely disappear after ~6.7 million years. Researchers have successfully recovered dna fragments from a 2 million year old mastodon, for instance.

There are numerous ways to identify the origin of ancient remains. FTA about the non-Denisovan remains:

>Unfortunately, the bones were in such small fragments that they were nearly impossible to identify by sight. Instead, the researchers analyzed the bone collagen using mass spectrometry to figure out what species they belonged to.

DNA