>Can anyone with domain knowledge chime in on this? Due to the age of the genomes, C's deaminate and are recorded erroneously as T's. The solution is usually t

>Can anyone with domain knowledge chime in on this? Due to the age of the genomes, C's deaminate and are recorded erroneously as T's. The solution is usually to throw out those sites from the sequencing results (which account for a large fraction of the genome in the garbage). By sequencing many different neanderthal individuals you can start to reconstruct some of those lost parts of the genome. https://en.wikipedia.org/wiki/Ancient_DNA#Problems_and_errors https://en.wikipedia.org/wiki/Ancient_DNA#Problems_and_error... >Is the sample set of genomes enough to suggest these mutations were prevalent in the neanderthal population? We aren't really at population scale genomics of neanderthals yet. We are still trying to piece together a truely high-quality reference genome (of one individual). Once that is complete, the next step is a population of about 100. Based on the human genome, the chimpanzee genome, the neanderthal genome and the ancestrally reconstructed most recent common ancestor at each of the nodes in between, we can estimate allele frequencies within the different populations.