I’ve noted many times that some Finns and Ashkenazi Jews are very closely related to Denisovans, with about 70% of their mtDNA genomes matching to Denisovans. See A New Model of Computational Genomics , generally. I’ve also noted that the Iberian Roma and Papuans are even closer to Heidelbergensis, with about 95% of their mtDNA genomes matching Heidelbergensis. I occasionally chip away at this work in my free time, and so I tested Sephardic mtDNA tonight, honestly expecting to find something different from Ashkenazi Jews, given that they really are different people, with different histories. It turns out, instead, that the three Sephardic genomes I found on the NIH website were also related to Denisovans, though they are however closer to the Munda people of India than Ashkenazis. This is surprising but not impossible, it just means that Jews really are a genetically distinct group of people, despite being a diaspora.
However, this got me thinking, that perhaps many people descend from Denisovans, since I was totally unable to find an archaic species that had an analogous relationship to the bulk of the dataset. That is, the Roma and Papuans (and many others scattered about the world) are extremely close to Heidelbergensis, suggesting they descend from Heidelbergensis. Similarly, some Finns and Ashkenazi and Sephardic Jews (and some others, again scattered about the world) are closely related to Denisovans, suggesting they descend from Denisovans. Many people are also a 95% match to Neanderthals, and they seem to be roughly the same group of ethnicities that are close to Heidelbergensis. The obvious question is, where do the rest of us come from?
To test this, I lowered the minimum match count to 30% of the genome, and compared the full dataset of genomes to Denisovans, Heidelbergensis, and Neanderthals. The results are plotted below, where the x-axis shows the acronym of the population in question, and the y-axis shows a normalized count of matching genomes, where a given genome constitutes a match if it has at least 30% in common with the applicable archaic genomes. The table of acronyms can be found at the end of , and there are links to the dataset I used in  as well. All genomes are complete mtDNA genomes taken from the NIH website.
There is at least one Neanderthal genome that has no connection to Heidelbergensis at all. In contrast, the Denisovans are related to both the Neanderthals and Heidelbergensis. This implies that the Denisovans are the common ancestor of both Heidelbergensis and at least that particular Neanderthal. See Section 6.1 of . As a consequence, it seems we all descend from Denisovans. Also, out of curiosity, I lowered the match threshold for the Ancient Romans as well, since I’ve been otherwise unable to find a match, and it seems they have basically the same distribution as the Basque, Igbo, Munda, and Northern Europeans, all of whom are closely related, despite being totally different people.
The Ancient Egyptians were plainly wiped out, given that their appearance changed drastically over a very short period of time, and this is actually reflected in their genetics as well, with Pre-Roman Egyptians a distinct genetic group from Egypt during the time of Rome. These things of course do happen in history, but the shift is drastic, from what are plainly Asian people (genetically and morphologically) to European people. That’s just not normal, and there’s no history to my knowledge that explains it. On the left is Menkaure and Queen Khamerernebty II (c. 2,530 BCE), courtesy of MFA Boston, in the center is Nefertiti (c. 1,370 BCE), courtesy of Wikipedia, and on the right is Cleopatra (c. 50 BC), courtesy of Wikipedia, who plainly looks nothing like the rest of them.
Moreover, there are literally no living people that are a 90% match to the Ancient Romans. This is simply impossible, without deliberate genocide, as plenty of people are a 99% match to a far older Ancient Egyptian genome, and plenty of other ancient peoples. Keep in mind, Rome was an enormous empire at its heights, far larger than Ancient Egypt. The logical conclusion, is that the Ancient Egyptians and Ancient Romans were related people, and both were subjected to comprehensive genocide.