In my previous post I mentioned the TCC→TTC mutation anomaly, which is higher among Europeans than Africans or East Asians.
Gao, Zhang, Przeworski, and Moorjani, 2022 reported that there were several other mutation discrepancies between these three popilations.
They also looked into mutation raties that differ in "old polymorphisms that predate the out-of-Africa migration" and suggest that this case is due to the different proportion that the ancient archaic ancestors contributed to modern African and non-African people. They also point out that age of reproduction (generation time) can't explain their observations and suggest that "other factors —genetic modifiers or environmental exposures— must have had a non-negligible impact on the human mutation landscape".
Aging fathers tend to pass on to their children more T→C mutations, and mothers contribute more C→G mutations.
They noticed different T→C/T→G mutations among archaic populations (over 28,800 generations ago) compared to more recent ones in all three populations. They were surprised by this difference: (YRI is Yoruba African, CEU is Caucasian and CHB is Chinese from Beijing):
"Unexpectedly, we detected significant differences between YRI and the other two populations, CEU and CHB, in the mutation spectra of polymorphisms that are estimated to long predate the OOA migration. Specifically, the T>C/T>G mutation ratio is elevated in the very old allele age bins compared to more recent bins for all populations, with a significantly higher ratio seen in YRI than in CEU and CHB. We showed that the inter-population differences cannot be explained by differential gene flow from sequenced archaic hominins —Neanderthals or Denisovans— into the ancestors of non-Africans and such introgression alone cannot explain the shift in the older bins in all modern human populations.
Instead, we found evidence that the signals come from extremely old variants that emerged prior to the split of modern humans and archaic hominins at least ∼550,000 years ago (Prüfer et al. 2014). This suggests that the observed differences between contemporary populations could have arisen from the complex demographic history of ancestral populations. Based on observed polymorphism patterns in contemporary African populations and using simulations, several recent studies have suggested that one or more ghost archaic populations may have introgressed into the ancestors of Africans and possibly into the common ancestors of all modern humans (Hammer et al. 2011; Ragsdale and Gravel 2019; Speidel et al. 2019; Durvasula and Sankararaman 2020). After the ancestors of non-Africans migrated out of Africa, the ghost archaic group(s) may have continued interbreeding with remaining populations in Africa, leading to higher ancestry in YRI. An alternative model is deep population structure in modern humans. Under this model, two or more long-lasting, weakly differentiated ancestral populations contributed differentially to contemporary human populations through continuous gene flow or multiple merger events (Ragsdale et al. 2022). In both models, a greater contribution from a group with a higher T>C/T>G ratio to the ancestors of African individuals would explain differences between YRI and non-African population samples as well as the elevated ratio in old variants for all three contemporary human populations. Our analysis further showed that the T>C/T>G signal comes from T>C mutations rather than T>G mutations, suggesting that one or more of the remote ancestral populations had a higher T>C mutation rate relative to their contemporaries as well as to modern humans."
Time and time again we have evidence of archaic introgression into Africans that has not been passed on to Eurasians. These contriuted to their heterozygosity, diversity, and different mutation rates. This renders many conclusions based on molecular clocks and differences in alleles obsolete. It makes the Africans look more divergent but in fact this may be the outcome of swapping bodily fluids after the OOA event.
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