Archaic admixture in Africans

Question

I've been investigating the ideas circulating in some of the more classy white supremacist circles. Some of them have referenced studies like this one:

We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans.

Of course they interpret this to mean that there are literally west Africans alive today who are 19% African neanderthal or some other nonhuman species. Here is a typical example from Stormfront,

But he unknowingly was raising a good question, one that has been raised before, and by smart people, too: are Black people 100% human? One guy just recently said that Blacks are roughly 8% (eight percent) non-human, historically speaking. Is this true? I don't know. He pointed to this 2017 study as proof of that: (First, I'll quote the commenter on the study, and then, I'll give the URL to the study): Quoting the commenter: "Blacks are proto-humans; modern man evolved from Blacks by hybridizing with the large-brain Neanderthals: Blacks = 2% Archaic hominid admixture and 7.9% non-human ghost DNA. Whites = 3% Neanderthal. Asians = 3% Neanderthal + Denisovan. Modern man evolved from Blacks when they cross-bred with the large-brain Neanderthals (literally a different species). Blacks are the only race with no Neanderthal DNA. Civilizations didn’t begin until the Neanderthal hybridization created the larger brains in modern man." 1. Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation | Molecular Biology and Evolution | Oxford Academic (Note: the Neanderthals could be called "early or archaic humans"). If that is true (if Blacks are not 100% human), it would certainly explain a lot

What is the missing context here? Right off the bat, the idea that one person could be 19% and another 2% when they've been "mixing it in" for 50,000 years is completely impossible, so there must be something deficient with the way most people would interpret this. In other words, why is it not accurate to compare this 19% or 8% figure to the 3% Neanderthal figure for Eurasians?

Answer 1

Why is it not accurate to compare this 19% or 8% figure to the 3% Neanderthal figure for Eurasians?

In short, because:

• 19% is an upper bound (the 2% lower bound sounds less dramatic)
• That 19% is mostly on top of the 3% Neanderthal influence
• All "modern humans" are probably descended from the population where this mixing occurred

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The paper referenced measures something called the "conditional site frequency spectrum" of one genome with respect to another. The key basis is this:

Theory predicts that ... CSFS is expected to be uniformly distributed when alleles are neutrally evolving under a demographic model in which the ancestor of modern and archaic humans ... split with no subsequent gene flow between the two groups.

The observed data didn't match this prediction:

In contrast to the uniform spectrum expected from theory, we observe that the CSFS_YRI,N has a U-shape with an elevated proportion of SNPs with low- and high-frequency–derived alleles relative to those at intermediate frequencies.

They then attempted to predict the CSFS under various simplified models of gene flow between different ancestral populations. 19% is the upper bound of an estimate for the contribution from "an archaic ghost population" in the model which fits most closely - but several other models also have quite a good fit.

Wait, are they saying Africans are 19% ghosts? Of course not, "ghost" here just means that we haven't sequenced DNA from any fossils that can be identified as the population in the model, so we don't have a specific population or "species" name for it. All the model can show is that it is distinct from Neanderthal and Denisovan branches, and that it probably split from the direct ancestors of modern humans before either of those.

However, the most important finding for refuting the racist interpretation is this (emphasis mine):

Given the uncertainty in our estimates of the time of introgression, we wondered whether jointly analyzing the CSFS from both the CEU (Utah residents with Northern and Western European ancestry) and YRI (Yoruba from Ibadan) genomes could provide additional resolution. Under model C, we simulated introgression before and after the split between African and non-African populations and observed qualitative differences between the two models in the high-frequency–derived allele bins of the CSFS in African and non-African populations (fig. S40). Using ABC to jointly fit the high-frequency–derived allele bins of the CSFS in CEU and YRI (defined as greater than 50% frequency), we find that the lower limit on the 95% credible interval of the introgression time is older than the simulated split between CEU and YRI (2800 versus 2155 generations B.P.), indicating that at least part of the archaic lineages seen in the YRI are also shared with the CEU (section S9.2).

To paraphrase: the best fitting models assume that both African and Eurasian populations have ancestors from this unknown branch of the hominin family tree.