As I’ve noted several times, I’ve devised an ancestry test that is impossible to argue with, using whole-genome mtDNA. See Section 6.1 of A New Model of Computational Genomics [1]. Specifically, given whole-genomes A, B, and C, if genome A is the ancestor of both genomes B and C, then it must be the case with near certainty that genomes A and B, and A and C, have more bases in common than genomes B and C. Again, see [1] for an explanation. The test in Section 6.1 of [1] is at the genome level, and as such, using a dataset of genomes, the number of tests required to compare whether an entire population is the ancestor of two other populations grows quickly as a function of population sizes. As a tractable approximation, the attached code uses the average match count between populations A and B, A and C, and B and C, which of course loses information, but should at least help you reduce the number of cases that you investigate exhaustively.
Applying the attached, it turns out, that yet again, the Denisovans test as the common ancestor of humanity (though I now think the Cameroon might be more modern than I first suspected), specifically, the common ancestor of both Heidelbergensis and Neanderthals. Further, the Phoenicians again test as the common ancestor of basically everyone alive today, including the modern Thai, Nigerians, Norwegians, Koreans, the Saqqaq (in B.C. Greenland!), the Swedes, Indians, and Chinese. As a result, I’m fairly convinced early Middle Eastern people settled a significant portion of Europe and Asia, and possibly America (given Greenland), but I can’t put a date on it. Ugarit goes back to 6,000 BC, which should leave enough time, but this is an ordinal test only, and therefore cannot be used to date the relationships. Moreover, I’ve recently cast serious doubt on the idea that mtDNA has a single, stable rate of mutation. The net point is, therefore, the ancestry test is real, and very difficult to argue with, but limited to ordinal testing; further, mtDNA doesn’t seem to have a single, stable rate of mutation; as a result, it looks plausible (1) that the Denisovans are the first humans and (2) that either the Phoenicians or people close to them (on the maternal line) we’re prolific settlers, but we don’t know when either got started.
The code is below, the balance can be found in [1]. One modification I plan to make is to use Monte-Carlo probing on the data that informs the averages. This will allow you to test a fixed portion of the genome-level data that you can scale given the power of your machine. BTW I just bought a Mac Mini running the M2 Pro chip, and I cannot recommend this machine enough, it is more than 10 times faster than my windows laptop. Running the ancestry test described above over 673 full mtDNA genomes takes about 0.5 seconds. I cannot believe this is a retail machine.
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