The divergence date of Neandertal and human sequences is estimated at around 520,000 years ago. What does that mean?
First, what it doesn’t mean. It doesn’t mean that the human and Neandertal populations diverged 520,000 years ago. I noted above that the estimate of the genetic divergence time comes from the proportion of chimpanzee-human differences for which the Neandertal shares the human allele. But of course, some living humans have the ancestral, chimpanzee-like allele for many polymorphisms, so this comparison of polymorphisms is not saying that Neandertals were like chimps. Instead, we are just disregarding the Neandertal-specific evolutionary events. I’m sticking with the 520,000 year genetic divergence estimate from Green et al. (2006), instead of the older estimate from Noonan et al. (2006), because of the vastly larger sample in the Green paper. Still, most of the discussion does not hang too critically on the precise date; although the date changes the interpretation by degrees. The real interesting observation is the Neanderal-human genome draft difference compared to the human-human di
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