It sounds superficially impossible, but my work shows unambiguously that paternal selection impacts mtDNA, for the simple reason that males appear to select females on the basis of maximizing the number of bases they have in common with their female mates. Therefore, if you replace an existing male population with a new male population, the original female population will be selected for on the basis of maximizing the number of bases they have in common with the new male population, which will cause the lower-matching females to die off. See Section 5 of A New Model of Computational Genomics [1]. This will over time cause the two maternal lines to converge (i.e., the maternal line of the new paternal line will converge with the existing maternal line).

Today I developed a new technique that looks at the gaps in matches that occur as a result of insertions and deletions. That is, if you align to genomes, and then shift one of them by a single base at index i, the match count along indexes i + 1 through N (i.e., the genome size) will be reduced to chance. The question is, is there selection in those gaps? The answer is plainly yes, and by testing for it, you can determine paternal ancestry. Specifically, start with a genome, and then compare that genome to every genome in a given population (e.g., a single Ancient Egyptian genome compared to every Norwegian genome in a dataset). If Norwegians played a role in selecting Ancient Egyptian women (probably not true), then in the gaps, we should find evidence of selection, which would manifest as a number of matches that exceed chance. We can then measure the density of these above-chance matches within the gaps, which is consistent with selection by males from that population. Note that the criteria of materially exceeding chance provides an objective test, which is attractive, because you don’t have such a test in the non-gaps.

Doing exactly this for a Pre-Roman Ancient Egyptian genome, produces the distribution above, suggesting that the paternal line of the earliest Egyptians is from Asia, specifically, the ancestors of present day Javanese (JV) and Solomon Islands (SI) people. The full list of acronyms is included in [1]. The Ancient Egyptian maternal line is unquestionably from Asia, specifically the ancestors of modern day Thai people. See [1] generally. This is obvious when you look at the earliest Egyptians, who were visibly Asian, some of whom seem to have had straight hair. The code to produce the distribution above is attached below, and the dataset and any missing code is attached to [1]. Below are Menkaure and Khamerernebty II (circa 2532 BCE), courtesy of Boston MFA, both of whom are visibly Asian people. Overall, this algorithm provides even more support for the hypothesis that many modern Europeans and Africans are actually from Asia. Specifically, the Nigerians have Asian and Classical paternal lines (e.g., Sri Lankan and Phoenician), and the Classical people all also seem to be from Asia, not just the Egyptians. This is consistent with fairly recent academic results showing that there was an even earlier migration back to Africa, from Asia, about 70,000 years ago. My hypothesis is that this happened more than once, and that humanity began in Africa, then migrated to Eurasia and Asia, with many groups coming back to Africa, and some going to Europe, in particular Scandinavia.

Here’s the code:

https://www.dropbox.com/s/6gvcaxxkrskhqy0/Matching_Bases_Loc_Distribution.m?dl=0