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In the NYTimes news article No Bones About It: Scientists Recover Ancient DNA From Cave Dirt I've read:
Although DNA sticks to minerals and decayed plants in soil, scientists did not know whether it would ever be possible to fish out gene fragments that were tens of thousands of years old and buried deep among other genetic debris.
I haven't read the original article yet, but I'd like to double check, this is bare DNA molecules, stuck to minerals or other detritus in 14,000 to 550,000 year old compacted dirt? Roughly speaking at least? In layman's terms, just laying around in some caves?
Has something protected the DNA from degradation, or is DNA just more environmentally stable and robust than I thought?
There is also discussion in the Science commentary No bones? No problem: DNA left in cave soils can reveal ancient human occupants.
The NYTimes article goes on to say:
The new study involved searching for ancient DNA in four caves in Eurasia where humans were known to have lived between 14,000 and 550,000 years ago.
Dr. Meyer and his colleagues figured out which DNA in the cave sediment was prehistoric by looking for telltale signs of degradation at the ends of the molecules.
What are the "telltale signs of degradation at the ends" of DNA molecules described in the paper?
To be clear they are not finding long DNA strands but short fragments. DNA becomes more robust the shorter it gets. Fragments can last millions of years. The local chemical conditions have a huge influence on how long DNA lasts the oldest being hundreds of millions of years old under ideal conditions.
The ones the archeologists are finding are not even close to enough to rebuild an intact strand but it can be used for matching. Of course contamination is a big problem, anything that dies leaves DNA in the soil. With humans it becomes especially problematic becasue the archaeologists themselves are a major source of contamination.
For an indepth look at contamination protocols, some of which as still questionable, can be found here. Sorry its behind a pay wall.
Likely they are referring to deamination cytosine substitution, which creates mismatched pairs of DNA and occurs more and more as DNA ages.