Comparisons of Neandertal mtDNA with modern humans and modern chimpanzees

Very nice plot. The chimp-chimp comparison is a little misleading, however. Since they lumped two species into a single value (an odd thing to have done), the chimp-chimp comparisons won't produce anything like a single normal curve; the distrbution should have two peaks, one around 75 (for chimp-bonobo comparisons) and the other a broad peak centered around 20 or so (for within-species comparisons).(Note that the human-Neandertal difference is smaller than the differences between chimp subspecies, so it's not obvious just from the genetic distances that humans and Neandertals were different species.)Steve

They do give the difference between bonobos and all chimps (75.7). Probably so -- human mtDNA diversity has been measured to be quite low compared to chimp. For nuclear diversity, humans are lower than central chimps (~factor of 2), higher than western chimps. Not necessarily. A handful of key mutations may make hybridization difficult or impossible. Raw genetic distance can't tell you whether they've occurred or not. (Of course, small distance does make it less likely, but not certain.)

Sorry, I wasn't paying attention. (Maybe I shouldn't have had a Buffy episode on in another window.) Yu N, Jensen-Seaman MI, Chemnick L, Kidd JR, Deinard AS, Ryder O, Kidd KK, Li WH. Low nucleotide diversity in chimpanzees and bonobos.
Genetics. 2003 Aug;164(4):1511-8.There's also data from the chimp genome effort on western and central chimps -- it's the actual source I was using, but it hasn't been published yet. It will be available Real Soon Now.

I would find this very surprising. Mitochondria have much higher mutation rates than nuclei do -- their DNA polymerase lacks proofreading capability that the nuclear polymerases have.