How can they deal with the damage to ancient DNA sequences?
One of the things that has become clear about ancient DNA research is that DNA from ancient fossils undergoes various kinds of damage. The most obvious is the fragmentation of the DNA into very small pieces, a problem that both the sequencing approaches have been designed to circumvent. But a more serious problem is that some bases become degraded over time in ways that cause the sequencing methods to misidentify them. For example, cytosine (the “C” base) can be chemically modified over time into a base called uracil, which sequencing methods misidentify as a thymine (the “T” base). There seems to be no way to tell which base pair changes are diagenetic (i.e. DNA damage-induced) and which are genuine Neandertal changes. So, the teams took a radical approach: just ignore all the changes that are possibly damage. Instead of analyzing Neandertal-specific changes, they decided to assess the status of human polymorphisms and human-chimpanzee differences in the Neandertal seqeunce. This meth
