Why does this bone have such a low level of contamination compared to other Neandertals?
I should start by pointing out that “contamination” here means “modern human sequence”. All fossil bones are loaded with exogenous DNA, like bacterial and fungal genomes that invaded after the animal died. From a certain point of view, those exogenous genes are contaminants — we are generally not interested in their sequences, and sorting them out from the endogenous Neandertal DNA is a real nuisance. But because we have a reference genome from humans to compare with the sequences from the ancient bone, we can sort out these bacterial and other exogenous sequences. So although they do “contaminate” the bone, they don’t distort our picture of the sequence. The real problem is that there are contaminating sequences from recent humans in the ancient bones. These sequences come from excavators, anthropologists who studied the bones, museum personnel, graduate students who cleaned and prepared the bones for sequencing, other samples from the labs doing the work, and who knows where else. I
