A paper published in the non-peer reviewed BioRxiv last March (see my post on it) has been now published in Science, on July 30, 2026 (Yulin Zhang et al., Recovering signatures of archaic hominin introgression using ancestral recombination graphs. Science 0,eaef8874 DOI:10.1126/science.aef8874). It discusses ghost introgressions in modern human populations. My original post highlighted its main points. Today, re-reading the article, I found some interesting points, which I discuss below.
Heterozygosity and archaic introgression
All research about Amerindians and all other non-Africans, stresses that they have higher homozygosity than Africans, a signal of a lower diversity in their genes. They are less heterozygous. I have argued in several posts that the higher heterozygosity observed in Africans could come from their recent admixture with archaics that survived until recently, within Africa.
This paper reported that (highlighting is mine) "Several additional lines of evidence support our results of ghost ancestry in modern humans. First, we find that genomic regions harboring ghost ancestry exhibit elevated heterozygosity levels, a pattern also observed for Neanderthal and Denisovan segments (fig. S25). The elevation in heterozygosity is consistent with a model of introgression from a deeply divergent lineage..."
The authors note that sub-Saharan Africans have the highest levels of super-archaic ghost admixture, and non-Africans have much lower values, but they attribute it to a bottleneck effect following the Out Of Africa (OOA) migration, ignoring the possibility of recent admixture within Africa: "We find that ghost ancestry peaks are over-represented in sub-Saharan African populations relative to non-African populations, which is consistent with the lower genetic diversity in non-Africans."
Africans and admixture there, in Africa
Regarding "deserts" where ghost presence is lacking, they attribute it to the same cause, the OOA migration: !We also identify 97 deserts of ghost ancestry (i.e., regions that are at least 10 Mbp long and have less than 0.1% frequency of ghost ancestry). These deserts are only found in non-African populations, with nearly half (43.3%) shared between different non-African groups, likely formed during the OOA bottleneck (supplementary section S6.3 and figs. S37 and S38). We do not identify any ghost ancestry deserts in sub-Saharan Africans." A plausible explanation for this is that ghosts introgressed within Africa, leading to a total lack of deserts there, while in the rest of the world, deserts point at a lack of superarchaic admixing.
In my original post I highlighted their comment about the source of the ghost population, I will once again quote the authors comments: "The ghost lineage, with a divergence time similar to Neanderthals, could plausibly correspond to Middle Pleistocene Homo groups or African Homo heidelbergensis populations that directly admixed with modern human ancestors before the OOA dispersal. For the super-archaic lineage, one potential candidate—compatible with the split time of approximately 1.8 Mya—is Homo erectus, as suggested by earlier studies."
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