Modern genetic variation is poor representation of past genetic variation

Seven-DaughtersThere’s a new open access paper in AJHG, Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians, which is nice in that it uses state-of-the-art methods to analyze the genetics of a part of the world that warrants greater investigation. As the title of the paper implies the authors are focusing on a region which is likely the site of the exit of an ancient African population ~50-100,000 years ago which is responsible for over 90 percent of the ancestry of non-Africans. In short, they’re looking at the variation of modern populations across the region, and relating it to populations outside of the region, to infer historical relationships. This method has a long pedigree, at least by the standards of historical population genetics. About 15 years ago the Oxford geneticist Bryan Sykes wrote Seven Daughters of Eve, where he traced ancient European migrations to the most common mtDNA haplogroups in the continent. Using these results Sykes asserted that most of the ancestry of modern Europeans derives from Paleolithic hunter-gatherers; not Middle Eastern farmers. More precisely, modern Europeans exhibit overwhelming continuity with the Pleistocene populations. It turns out that this is wrong.

We know this because of ancient DNA, which is coming to various novel conclusions and overturning older understandings. One of them is that the genetic variation you see in a locale today has limited time depth into the past. That is why I state that it is likely that Cro-Magnons may contribute to less than 1 percent of the ancestry of modern Europeans. There are regions, such as the New World, where over the past 10,000 years genetic turnover on the whole has been modest, to negligible (most of the Holocene turnover in the New World before the arrival of Europeans is in northern North America). But this seems the exception rather than the rule. In South Asia, Africa, Europe, Siberia, East Asia and Southeast Asia, there is no dispute that the Holocene witnessed enormous changes in the genetic and demographic makeup of the dominant population. The flip side is that very ancient “archaic” lineages in some regions of the Eurasia have modern descendants. That is why I say we need to update our priors; the ancient branches of our family were mostly, but not entirely pruned, while many of the recent branches were mostly or even entirely pruned.

This brings me to the main question: how plausible it is that the genetic patterns on evidence in the paper in AJHG tell us about human evolutionary history with time depths of ~50,000 years. Color me skeptical. There are some specific issues that I’m confused by, in addition to the bigger framework. Greg Cochran has already put them into focus rather trenchantly. First, this section of the paper:

Using ADMIXTURE and principal-component analysis (PCA)18 (Figure 1A), we estimated the average proportion of non-African ancestry in the Egyptians to be 80% and dated the midpoint of the admixture event by using ALDER to around 750 years ago (Table S2), consistent with the Islamic expansion and dates reported previously.

300px-Fayum-34A plain reading implies that 750 years ago non-African ancestry admixed into the population of Egypt so that it’s now 80% of the ancestry. Obviously this is insane. Egypt has a long history, and all the evidence that is not genetic indicates that ancient Egyptians were predominantly a population with Near Eastern and North African, not Sub-Saharan, affinities. The Roman era Fayum portraits suggest a people who resemble by and large modern Egyptians. Some do seem to have aspects of appearance which strike one as Sub-Saharan, but the presence of Nubians, as well as likely an ancient admixture event that occurred when Middle Eastern farmers arrived in the Nile Valley, can explain that. But when ascertaining the “Out of Africa” event you need to focus on the oldest element of ancestry. So you would have to look the people who contributed indigenous African ancestry well before the emergence of Egypt as a distinct civilization.

Here is the confusing part which inverts expectations. This last component is most likely to be within the “Non-African” segments of the Egyptian genome. I say this because the latest period of a mass population movement into Egypt from the Near East is ~8,000 year ago. 8,000 years is a long time, so recombination every generation would break apart the association between tracts of ancestry traceable to the newcomers, and that traceable to indigenous hunter-gatherers. Over time a new synthetic populatoin with its own distinctive population profile emerges. This is the case with South Asians, who are genetic compound of two very distinctive groups with extremely diverged histories. The latest evidence suggests that the admixture occurred on the order of ~4,000 years ago. That’s half the time depth of what likely occurred in ancient Egypt.

61kCcH+1C9L._SY344_BO1,204,203,200_And about the African ancestry they did focus on, the 750 year time depth gives you a clue about where it came from: the rise of the Islamic empires and trans-Saharan trade enabled by camel triggered a massive influx of slaves from Africa into North Africa and the Near East (there was also an influx of slaves from the Caucasus and Central Asia, and for a time Europe, in large part because Islamic law banned the enslavement of believers). In the Maghreb these slaves were from West Africa. In the Persian Gulf the sources were diverse, but many were from East Africa. The natural source of Egyptian slaves is likely to be from the Sudan, what was ancient Nubia. Also, the Gumuz, who are used as a relatively unadmixed Ethiopian population (i.e., low Eurasian admixture fraction), are themselves of possible Sudanic origin and background!

I can agree that the Nubian/Sudanic ancestry exhibits a closer relationship to the population basal to non-Africans than West Africans. But, to me this paper does not make a strong case for a “northern” route through Egypt compared to the “southern” route, via the Bab-el-Mandeb. First, 50,000 years is a long time. My null assumption is that there has been enough population movement in Northeast Africa even before the Holocene to obscure the signal. Second, even without this consideration in mind, it strikes me that the African ancestry in Egyptians that they are focusing on is not a good geographic proxy in the first place, since it derives from Sudanic groups from further south. Finally, I do observe that this region of the world is relatively dry, making ancient DNA a possibility. So I have optimism that greater clarity will be achieved in the near future.

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