I’m working on something completely different related to ancient mtDNA, and I happened to find an ancient Khoisan genome in the NIH database. I also noticed earlier today, again working on something different, that both the Nigerians and Kenyans seems to have a relationship to the Denisovans. I already knew that the Kenyans were related to Denisovans, whereas, I never noticed any connection between the Nigerians and Denisovans. This prompted me to ask whether they had at least something more than chance in common with Denisovans, and the answer is yes. Specifically, the Nigerians start to match with Denisovans at about 30% of their genome. This is 5% above chance, and as a consequence, it is not possible that it is the result of chance. See, A New Model of Computational Genomics [1], specifically, footnote 16, which goes through the math.

There are two possibilities: one is that the Nigerians had a fleeting relationship with Denisovans, which caused only subtle changes to their mtDNA (see Section 5 of [1]). The other possibility is that they have an ancient, and possibly archaic connection to Denisovans. There is an ongoing search for so-called “Southern Denisovans”, since Denisovan fossils are typically found in Asia, not Africa. If Denisovans are actually from Asia, then we should not find ancient Denisovans in Africa. As it turns out, this particular genome is closely related to both Denisovans and Neanderthals, and is much closer to Denisovans than Neanderthals. You’ll also note that this genome is related to the Nigerians, again suggesting, an ancient connection between the Denisovans and Nigerians. Though this is not an archaic genome, since it’s only about 3,000 years old, it is ancient, and therefore consistent with the hypothesis that all hominins, i.e., Denisovans, Homo Sapiens, Neanderthals, and Heidelbergensis, all come from Africa. Below is the normalized match count for the Ancient Khoisan genome, at 50% of the genome. All of the code you need to run this analysis is in [1], and the dataset can be found here.