A reticulation + pulse expansion of modern human genetic variation

Posted on by Razib Khan

In response to a little bit of fatigue at the constant stream of ancient DNA, John Hawks digs the knife in a bit deeper. There’s more. Since Hawks is co-author with Lee Berger of Almost Human: The Astonishing Tale of Homo Naledi and the Discovery That Changed Our Human Story, I’m hoping for something related to naledi. But barring that, there is still lots to come down the pipeline (Alexander Kim has a Twitter account worth following to keep up on this line of research).

But I thought I’d enter something else into the record about what we’re starting to understand about the origins of modern human genetic variation.

  1. The “Out of Africa” movement is a real thing. That is, ~50,000 years ago a population seems to have diverged from a broader pan-African group, and replaced archaic hominins across Eurasia (with some admixture at low levels), and then pushed the boundaries of our genus to Oceania and the New World. This does not mean that there were not earlier “Out of Africas.” Just that the dominant signal of variation is due to the pulse that swept out ~50,000 years ago.
  2. Within Africa the story is different and more complicated. The expansion of anatomically modern humans out of Africa occurred relatively rapidly from a small founder population (within an order of magnitude of ~1,000 individuals seems correct). The archaeology and genetics are in pretty good alignment. But within Africa it looks like the lineages which led to modern humans are much deeper, and preserve structure that may be hundreds of thousands of years old. Just as we see admixture events giving rise to new lineages outside of Africa over the last 50,000 years, the same dynamic probably applied to within Africa far earlier.

One way to think about it is that the old “Africa Eve” model is very useful for the 10,000 year period around 50,000 years ago. And, it applies to non-Africans.

The story within Africa though may be more like the old multi-regionalist model, though with stronger biases of gene flow between populations, so that at one time one lineage may be preponderant. Over the last 10,000 years the expansion of certain populations within Africa though (in particular Bantus) has collapsed a lot of the deep structure, and now Africa resembles Eurasia much more (with some Eurasian back-migration too).

Note: I am talking about “modern human genetic variation” because I am starting to think talking about “modern humans” obscures far more than it illuminates.

Origin of modern humanity pushed back 260,000 years BP (?)

Posted on by Razib Khan


The above figure is from a preprint, Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago. The title and abstract are pretty clear:

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region’s human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|’hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) ‘hot spot’ for the evolution of our species.

These results in the outlines were actually presented at a conference. I saw it on Twitter and don’t remember which conference anymore. But this is not entirely surprising.

First, much respect to Mattias Jakobsson’s group for breaking through the Reich-Willerslev duopoly. Hopefully this presages some democratization of the ancient DNA field as expenses are going down.

Second, notice how in most cases ancient DNA shows that modern reference populations turn out to be admixed. This was the problem with much of Eurasia, and why using modern genetic variation to make inferences about the past totally failed.

I am entirely convinced that the genome from Ballito Bay dating to ~2,000 years does not carry the Eurasian inflected East African admixture. The Mota genome implies that Eurasian admixture did not come to eastern Africa much before 4,500 years ago. There needs to be a much deeper big picture analysis of the archaeology of Africa and the genetic information we have to get a sense of what happened back then…but, it seems likely that the Bantu migration has over-written much of the earlier genetic variation.

The fact that ancient genomes always show that our current populations are admixed makes me wonder if the Ballito Bay sample itself is admixed from more ancient populations. That is, if we found a genome from 20,000 years ago, would it be very different from the Ballito Bay samples? The relatively thick time transect from Europe indicates that turnover happens every 10,000 years or so. Australian Aborigines seem to have been resident in their current locations for ~50,000 years, but this seems the exception, not the rule. Do we really think that the ancestors of the Bushmen were living in southern Africa for five times as long as Australian Aborigines?

Another curious aspect of this paper is that it suggests the effective population size of Bushmen is smaller than we might have thought, and they’re somewhat less diverse than we’d thought. That’s because East African (with Eurasian ancestry) gene flow increased heterozygosity, as well as inferred effective population sizes. I’ve mentioned this effect on statistics before. Unless you have a true model of population history (or close to it) your assumptions might distort the numbers you get.

There is another aspect to this preprint mentioned glancingly in the text, and a bit more in the supplements: they seem to only be able to model Yoruba well if you assume that they themselves are a mix of “Basal Humans” (BH) and other African population which gave rise to East Africans and “Out of Africa” populations. Note that the BH seem to diverge from other human populations before the ancestors of Southern Africans like the Ballito Bay sample. That is, BH could push the diversification of the ancestors of modern humans considerably before 260,000 years before the present.

The possibility of deep structure in the Yoruba is pretty notable because they’ve been the gold standard in many human population genetic data sets as a reference population. But this is not result of deep structure is not entirely surprising. For years researchers have been hinting at confusing results in relation to the possibility of Eurasian back-migration. Perhaps the deep structure was confounding inferences?

The authors themselves are quite cautious about their dating of the divergence. It’s sensitive to many assumptions, and in particular the mutation rate being known and constant over time. But I think it’s hard to deny that this is pushing back the emergence of modern humans beyond what we know today. The earliest anatomically modern humans are found in Ethiopia 195,000 years ago from what I know. As I said, I’m convinced that the ancient genome has shown that modern “pristine” populations have some serious admixture. But I’m not as convinced about any specific point estimate, because that’s sensitive to a lot of assumptions which might not hold.

Finally, first a quick shout out to the blogger Dienekes. As early as ten years ago he anticipated the basic outlines of these sorts of results in the generality, if not the details. We really have come a long way from popular science declaring that all humans descend from a small group of East Africans who lived 50,000 to 100,000 years ago. The real picture was much more complex.

Also, I have to admit I considered titling this blogspot “Wolpoff’s revenge.” As in Milford Wolpoff. The reason being that we’re getting quite close to territory familiar to the much maligned multi-regionalist model of modern human origins.

Note: These findings should make us less surprised perhaps by a “modern” human migration before the primary one out of Africa.

St. Augustine knew of the Buddha!

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St. Augustine is a very influential figure in Western Christianity. Partly this is surely due to the fact that the Latin Church favored a doctor who was of their own cultural persuasion, schooled in their mores and folkways, as opposed to the ‘logic-choppers’ of the Greek world. In the intellectual Protestant tradition his influence on Martin Luther and John Calvin is well known.

But it was only recently that I realized St. Augustine may have been moderately familiar with the Dharmic tradition. If you recall, he was a Manichaean for some years in his youth. This religion of Persian provenance is relatively well known has having an expansive geographic reach. The last self-conscious Manichaeans probably lived in China in the years around 1500 AD. But in Late Antiquity Manichaeanism apparently had a presence in the Western Roman Empire.

In any case, though notionally a dualistic religion, Manichaeanism acknowledged a strong influence from the Dharmic tradition, in particular Buddhism. Buddha is explicitly mentioned in Manichaean texts, and noted as a one of the prophets. This is not surprising, as the religion emerged in a diverse and pluralistic Late Antique Persian Empire which ruled over many Buddhist and Hindu peoples on its northern and eastern fringes.

I am not claiming that Buddhism had any direct impact on St. Augustine. But simply putting this into the record to remind ourselves that the extent of what we know about the ancients is pretty limited.

Open Thread, 06/05/2017

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Just a plug for Elements of Evolutionary Genetics by Charlesworth & Charlesworth. These are two great evolutionary geneticists, and we’re lucky to have a “core dump” from them on hand (for those for whom Elements is too spendy, John Maynard Smith’s Evolutionary Genetics is usually available used more cheaply, though it will be a touch out of date).

The curious thing is that there is so much science that is tacit and implicit, that the passing of each generation of scholars means that hidden reaches of knowledge are passing away. This is the flip side of the idea of progress being made through the death of older scholars and the acceptance of novel (and more right) paradigms.

Both Charlesworths are authors on a new paper (along with Nick Barton) in The Proceedings of the Royal Society, The sources of adaptive variation. Here’s the abstract:

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today’s understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.

Another riposte to the EES. Entirely unsurprising that these authors and this venue would offer criticism to a reframing of the field of evolutionary biology. But it gets to the heart of the reality that this is going to be an argument that will be resolved through publication of new papers, not books or long popular science articles. The footprint of the EES in evolutionary biology popular science is heavier than within evolutionary biology itself.

The prominent medical genomicist Dan MacArthur stated yesterday:

Not to be churlish, but let me clarify judging by the numbers of people Dan followed there were conservatives and libertarians he followed, he just didn’t, and doesn’t, know who they are. Also, there were several people he followed with center-right or libertarian views as a point of fact. I know because because I’m open about my right-wing views, and these people feel and felt comfortable telling me (privately) that they don’t agree with the vocal Left-liberalism which is pervasive in the political atmosphere on science twitter. Though most science twitter people don’t post much about politics, if they do, a substantial proportion are “social justice” oriented. That’s tolerable for most people because most scientists are on the Left side of the political spectrum.

My tendency to post right-wing political stuff into the feeds of scientists is annoying for many (or as some would say “problematic), but I don’t care. I know I speak for a substantial minority in the aggregate, and in some cases the majority (in terms of the latter, what I mean is that though most scientists are liberal, most are not on that far Left, though they may fear being attacked by the far Left and so are careful not to enter into any public dissent when that contingent starts to get a little out of control).

In a curious inversion with the norm I guess, my Twitter timeline is balanced politically. If anything, it’s more liberal than not. I don’t know what it would be to be in a political silo. I hear it feels good. Then again, I enjoy 300,000 scoville unit hot sauces.

Detecting polygenic adaptation in admixture graphs. Educational attainment and unibrows. Yeah. One thing: “An open question in human evolution is the importance of polygenic adaptation.” This is literally true, but I think it is pretty obvious that the latest work is suggesting there has been a lot of it.

Widespread signatures of negative selection in the genetic architecture of human complex traits.

The Genomic Health Of Ancient Hominins.

The nadir of genetics in the Soviet Union

Posted on by Razib Khan

A fascinating excerpt in Slate from How to Tame a Fox (and Build a Dog), :

This skepticism of genetics all started when, in the mid-1920s, the Communist Party leadership elevated a number of uneducated men from the proletariat into positions of authority in the scientific community, as part of a program to glorify the average citizen after centuries of monarchy had perpetuated wide class divisions between the wealthy and the workers and peasants. Lysenko fit the bill perfectly, having been raised by peasant farmer parents in the Ukraine. He hadn’t learned to read until he was 13, and he had no university degree, having studied at what amounted to a gardening school, which awarded him a correspondence degree. The only training he had in crop-breeding was a brief course in cultivating sugar beets. In 1925, he landed a middle-level job at the Gandzha Plant Breeding Laboratory in Azerbaijan, where he worked on sowing peas. Lysenko convinced a Pravda reporter who was writing a puff piece about the wonders of peasant scientists that the yield from his pea crop was far above average and that his technique could help feed his starving country. In the glowing article the reporter claimed, “the barefoot professor Lysenko has followers … and the luminaries of agronomy visit … and gratefully shake his hand.” The article was pure fiction. But it propelled Lysenko to national attention, including that of Josef Stalin.

Sometimes it is easy to believe that the period in the Soviet Union under Stalin or in China under Mao or in Germany under Hitler, to name a few, were aberrations. But I think that’s the wrong way to look at it. The story of how Lysenko became influential hooks into so many historical tropes and psychological instincts of our species that we should be wary of it.

There have been great scholars without requisite qualifications. Ramanujan and Faraday come to mind. But great scholars are exceptional people. They are not average.

What determines the rate of evolution

Posted on by Razib Khan


The tweet above from Wiley relates to a paper, Polygamy slows down population divergence in shorebirds. It’s a cool paper. I tweeted it. But does it relate to the “rate of evolution”?

There’s no definitive answer to this question. Different people will have different answers, as it was evident on Twitter. For me my surprise was due to my definition for what evolution is: change is allele frequencies over time. This is far more fundamental than speciation. But then I don’t think much about speciation.

Some people brought up divergence. But divergence for me is not necessary, a population could remain unitary but exhibit large allele frequency changes. Then again, if you study phylogenetics on a macroevolutionary scale, as most people who study phylogenetics do, then you would focus on divergence.

Poachers attacking rhinos in the developed world

Posted on by Razib Khan

This is shocking. Poachers Kill Rhino in Brazen Attack at French Zoo:

On Tuesday morning keepers at Thoiry Zoo, in the suburbs west of Paris, found the body of Vince, a four-year-old white rhino, in his enclosure with wounds to his head and one of his horns likely hacked off by a chainsaw, the zoo said in a statement on its Facebook page. His second horn was partially cut off, suggesting that the culprits may have been interrupted or were using defective equipment after they killed the rare animal on Monday night.

The act was carried out “despite the presence of five members of the zoological staff living on site and surveillance cameras,” the zoo said. “The entire staff is extremely shocked.”

…

Tuesday’s gruesome event follows an attack on rhinos at an orphanage in South Africa, home to 70 percent of the remaining 21,000 white rhinos. Armed poachers broke into the Findimvelo Thula Thula Rhino Orphanage on February 22 and removed the horns of two 18-month-old rhinos, Impu and Gugu, after tying up staff members. One rhino was killed, and the other was later euthanized.

Beyond cholula, sriracha, and tabasco

Posted on by Razib Khan

In the United States it seems that the restaurant table top hot sauces are dominated by an oligopoly. Cholula, tabasco, and sriracha are ubiquitous. And there’s a reason for this: they are delicious. All of them have their own unique flavor profiles, as you no doubt know. But there is a whole world of hot sauce and spice beyond these three canonical flavorings.

Recently the Trinidad scorpion pepper Rapture was recommended to me by a friend, and I brought it in the office. Almost immediately it became “the” office hot sauce. It’s complex and delicious flavor, and the high spice content fueled by more than 15 peppers per bottle, have fueled an enthusiasm for hot sauces among my co-workers.

The moral of the story is that readers should explore the a bit more of the world of hot sauce taste than they do right now. Don’t limit yourself to the Pepsi, Coke, and Dr. Pepper of hot sauces.

The material over the ideological

Posted on by Razib Khan

I come not to praise or bury Max Weber. Rather, I come to commend where warranted, and dismiss where necessary.

The problem as I see it is that though a meticulous scholar, Max Weber is the father of erudite sophistry which passes as punditry. Though he was arguably a fox, his genealogy has given rise to many hedgehogs.

Weber is famous for his work on relating the Protestant ethic and capitalism (more precisely, Calvinism). In general I think Weber is less right than he is wrong on this issue. But the bigger problem is that Weber’s style of interpretative historical analysis also has spawned many inferior and positively muddled imitators, whether consciously or not.

To my mind the problems with Weber’s sweeping generalizations, interpretations, and inferences, are clearest on the topic of China. His assertions on the nature of the Chinese mind informed by Confucianism, and how it would relate to (and hinder) modern economic development are very hit or miss.

By the end of the 20th century things had changed in terms of the perception of how Confucianism might relate to capitalism. In the 1990s Paul Krugman famously argued that the East Asian economic miracle did not have to do with a particular model or cultural genius, but simply increases in capital investment and labor force participation (factor inputs). This was too stylized a fact. Though growth has slowed, I think it is undeniable that East Asian economic modernity is here to stay.

And some of that may be attributable to Confucianism in a distant causal sense, because the cultural sensibility does encourage the development of broad-based literacy through self-cultivation. In Strange Parallels Victor Lieberman notes the contrast between Vietnam, with its more Sinic cultural orientation, and the rest of Southeast Asia, with their Indic Theravada Buddhist cultures.

The Vietnamese elites’ orientation toward Confucianism meant that there was stratification in society, as there were constant upward and downward movements across class. The chasm between the Confucian literati and the peasantry was large. In contrast in Cambodia popular religion was relatively unifying due to its accessibility. But it is notable to me that Vietnam in particular is often perceived by those who travel in Southeast Asia to be an industrious and striving nation.

So yes, culture may matter. But simple economic forces, and material conditions, are incredibly important, and our understanding of their origins are more mysterious than we’d like to think.

This is on my mind because of the recent evidence of the power of the slave trade in the Islamic world. Islam gets a bad rap in relation to slavery. This is justified, as Muslim nations have been, and are, the most prominent perpetuators of institutional chattel slavery* in the modern and near-modern world. But it is also correct that in many ways de jure Islamic law gave slaves a degree of dignity and human rights which would not have been called for in Classical antiquity. Though the reality is slaves were often part of the Roman familia in many cases, ultimately they were still human tools, to be abused and disposed as one would domestic animals.

But the genetic data seem clear that African slavery increased greatly during the Islamic period, resulting in a much more human agony, as so many of the slaves died en route (males who were to be eunuchs had a high mortality rate as they had to be castrated before entering Muslim lands). This had nothing to do with the cruelty of Islam per se, but the overall development and advancement of the Eurasian oikoumene, and the role of African slave labor in its post 1000 A.D. economy.

In fact one might argue that the unity of the Islamic world, and its relatively uniform legal and cultural superstructure after the collapse of its political unity, was a factor in fostering the rise of the global slave trade. That is, Islam generated asabiya, social solidarity, within the group, but this ultimately was to the detriment of those who were outside of the group.

A similar story can be told about the New World slave trade. It flourished in the wake of the Reformation and the Renaissance, and just as European society was undergoing a cultural revolution which would usher in modernity. If one looked at the nature of European society in the 17th century, and its increasing moralism, and focus on personal piety, probity, and humanity, would we predict the expansion and scaling up of the European slave trade? No.

That dynamic was driven by economics (in the American case, the triangle trade).

Similarly, the mortality rates of slaves varied greatly by locale and the what they cultivated. The sugar islands were death traps. The rice farmers of coastal South Carolina lived relatively stable lives, even comparable to serfs. Those who grew tobacco were somewhere in the middle. All were under English jurisdiction. The mortality of Brazilian slaves was high, but nominally Roman Catholic jurisdictions were subject to more humanitarian codes. But the primary determinants of mortality, of humanity, were economic. Material, even if ideological variables had an impact on the margin (Rodney Stark has argued that the French legal system was more humanitarian in Louisiana, and one can see this in various vital statistics).

Obviously ideological and material forces interact and influence each other. My point here is to observe that too often public commentary gets caught up on the idea of the great idea driving history. But once we have some distance it is often obvious that on the proximate scale many of the patterns we see are constrained, driven, and conditioned, on material forces and parameters.

And yet ultimately those material forces through gains in productivity relax tight the pressures which constrain ideologically driven change and revolution. Slavery for example was long considered an institution that would always be with us in some form, but over the past few thousand years most societies have frowned upon it. Slave societies, whether ancient Roman or in the antebellum South, develop an unhealthy paranoia. With modern technologically driven economic growth the possibility of a post-slave economy seemed plausible, and opened the window for a practical abolition.

And here we are!

* I said “institutional chattel slavery” specifically to head off annoying nit-picking comments. Please don’t.

Ancient Egyptians: black or white?

Posted on by Razib Khan

One of the most fascinating things about ancient Egypt is its continuity, and our granular and detailed knowledge of that continuity. We can thank in part the dry climate, as well as the Egyptian penchant for putting their hieroglyphs on walls and monuments (as well as graffiti!). And we can also thank the fact that both the ancient Greeks and Hebrews, Athens and Jerusalem so to speak, were deeply connected to and perceived themselves to be indebted to Egyptian civilization. Even before the translation of the Rosetta Stone and the deciphering of ancient Egyptian writing the Hebrews’ interactions with Egyptians, in particular in Exodus, mean that their memory would echo down through the millennia (the newly Christianized Irish interpolated Egyptian ancestry into their own genealogy).

The Greek relationship with Egypt was less fraught and at greater remove than the Hebrews. But the Classical period philosophers correctly perceived that Egyptian civilization was ancient, and preceded their own. Aegean-Egyptian connections were actually more longstanding than the Classical scholars knew, in Brotherhood of Kings: How International Relations Shaped the Ancient Near East, the correspondence in state archives which have been retrieved are rather clear that Minoan civilization was part of the orbit of Egypt early on. Though Egyptians never conquered the Aegean polities, mercantile and diplomatic connections were extremely old and persistent. The late Bronze Age eruption of barbarian Sea Peoples who attacked the whole civilized Near East may have been facilitated in part by the broad familiarity engendered by widespread trade networks.

The most recent book devoted to ancient Egypt I have read was Toby Wilkinson’s The Rise and Fall of Ancient Egypt. Synthesizing extensive written material with archaeology, perhaps the most impactful argument in Wikinson’s narrative was the persistence of the temple based institutions from the Old Kingdom down to the Ptolemaic era. Religious institutions carried on even with the shocks of Nubian and Libyan conquest in the post-New Kingdom period, down to Late Antiquity. The temple at Philae in southern Egypt was an active center of the traditional religion, and therefore the culture which dates to the Old Kingdom in continuous form, down to the 6th century A.D. (when it was closed by Justinian in his kulturkampf against ancient heterodoxies).

For various ideological reasons though many people are very curious about the racial characteristics of the ancient Egyptians. There are two basic extreme positions, Afrocentrists and Eurocentrists. Though I have not done a deep dive of the literature of either group, I’ve read a few books from either camp over my lifetime. In fact I believe the last time I read the “primary literature” of Afrocentrist and Eurocentrism was when I was an early teen, and it was rather strange because both groups seem to be recapitulating racial disagreements and viewpoints relevant to the American context, and projecting them back to the ancient world.

In college I stumbled upon Mary Lefkowitz’s Not Out Of Africa, a book length argument against the more sophisticated Afrocentrist views articulated in the wake of Martin Bernal’s Black Athena: The Afroasiatic Roots of Classical Civilization. Lefkowitz was a classicist, so many of her objections were exceedingly scholarly. The reality is that the best refutation of an Afrocentrist view of of ancient Egypt, which reduces to the idea that ancient Egyptians would be recognizably black African today, are the Fayum portraits. It is notable to me how similar these portraits are to modern Copts. In fact the actor Rami Malek, of Coptic background, looks strikingly like someone who stepped out of the Fayum portraits.

I have read no book length refutation of the Eurocentrist, usually Nordicist, perspective. Mostly because this is a view associated with white supremacism, and that ideology is generally attacked on normative, not positive, grounds. But the visible evidence of the Fayum portraits is a strong refutation of the Nordic model. Of course, there is the reality that we now know that the Nordic phenotype, and the genetic components which congealed into that typical of Northern Europe today, was only coming into existence when the Old Kingdom of Egypt was already a mature civilization.

Both Afrocentrists and Eurocentrists will reject the evidence of the Fayum portraits became they came from the Roman era, and they would argue that the demographic nature of Egyptians changed quite a bit between that period and the end of the New Kingdom. And they are not incorrect that the period between the arrival of the Romans and the fall of the New Kingdom was characterized by a great deal of change. There were Libyan dynasties, Nubian dynasties, and periods of rule by Assyrians, Persians, and Macedonians. Large colonies of Greeks, Macedonians, and Hebrews-becoming-Jews were also resident in Egypt. Especially, but not limited to, the urban areas.

But now we have ancient DNA! Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods:

Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.

Because modern people care about the Afrocentrist question, the extent of Sub-Saharan African ancestry is highlighted in this paper. I do not think this is actually the most interesting aspect. But I’ll get to that. Since this post will be read by a fair number of people I’ll talk about the relationship of ancient and modern Egyptians to (Northern) Europeans and Sub-Saharan Africans.

The figure to the left is looking at 90 ancient Egyptian mitochondrial genomes (and some modern ones in the two rightmost columns). Since mtDNA is copious it was relatively easy to extract and analyze.  Haplogroup L, the red to orange shades in the bar plots, are associated without dispute with Sub-Saharan Africa. Haplogroup U6, M1 and a few others may be “back to Africa” variants of different periods (they are generally found in Afro-Asiatic groups).

What you can see is that somewhat more than half of Ethiopia’s mtDNA lineages are L, in keeping with the whole genome estimate of Sub-Saharan African ancestry in most Cushitic populations. In Egypt there is a difference over time; haplogroup L goes from low frequencies to much higher frequencies in modern periods. The ~20% fraction in the modern samples is in line with the population wide admixture one sees in modern Egyptians of Sub-Saharan admixture.

I actually recomputed the haplogroups to a finer granularity from the supplements. A quick inspection of mtDNA haplogroup frequencies shows that ancient Egyptians are not typical of modern Europeans. Not that much H, and lots of T, J and K. What that does remind me of are Early European Farmers. These people, who brought agriculture to Europe from Anatolia contributed a large fraction of the ancestry of modern Southern Europeans, and a lesser component to Northern Europeans.

But ultimately what’s great about this paper is that they have ancient autosomal DNA. That is, genome-wide results.

They got three samples of reasonably high quality. More precisely: “Two samples from the Pre-Ptolemaic Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs.”

You can see the three samples on this bar plot. What is interesting is that they’re all pretty similar.

What you can see here is that to a great extent ancient Egyptians were descended from a population closely related to Natufians, or Natufians themselves. This easily explains the mtDNA affinity to Neolithic farmers: Natufians and Anatolian Neolithic populations were sister populations. The f3 statistic which looks at shared drift shows an affinity of ancient Egyptians with ancient farmer populations with Near Eastern provenance, but also with modern Sardinians. This is a common pattern, as ancient groups do not have later migration waves, with the Sardinians the modern population closest to this.

You see in the bar plot that northern Levantine populations are placed between Anatolian Neolithics and Natufians, as one might expect based on their geographical position and gene flow between these two regions. Additionally, the cyan color is associated with eastern farmers from the Zagros. I’ve already talked about gene flow from this area to the Levant recently. If you compare the Bronze Age Sidon samples I think you’ll see broad affinities with these Late Period Egyptians.

The PCA gives us results consonant with the model-based clustering. If you plot the genetic variation of ancient Egyptians they’re closest to Neolithic eastern Mediterranean populations. No great surprise.

Not the modern Egyptians. Why? It’s pretty clearly because modern Egyptians are shifted toward Sub-Saharan Africans. But there is also another component: modern Egyptians have more of the cyan eastern farmer component. What could this be?

An immediate thought comes to mind. We focus a great deal on Sub-Saharan African slavery. One reason is that it is visible. Black Africans are physically distinct from most Middle Eastern populations. But Egypt was long the center of another slave trade: “white slaves” from the Caucasus. Circassians. For hundreds of years Mamluks were recruited from the Caucasus as military slaves. They eventually became the ruling class of Egypt, until their decimation in the 19th century under Muhammad Ali (who himself was an Albanian Ottoman who never learned to speak Arabic well).

As noted in the paper earlier work looking at patterns in ancestry tracts and LD decay had made it obvious that much of the admixture of Sub-Saharan ancestry in Egypt, as in much of the Middle East, is relatively recent. In particular, it dates to the Islamic period, when trade and conquest took on new dimensions in Africa and north into Central Asia. One way ethnic minorities like Assyrians and Lebanese Christians differ from their Muslim neighbors is that they have much lower fractions of Sub-Saharan African ancestry, and no East Asian component. The latter might surprise, but remember that Central Asian Turkic slaves have been prominent in Muslim armies since at least the 9th century.

But some of the Sub-Saharan ancestry in Egyptians is old. The ancient Egyptian samples have it. To have none of it would seem strange, considering the history of contact between Nubia and Egypt, dating back to the Old Kingdom. Second, there is evidence of low levels of Sub-Saharan African gene flow into Southern Europeans. How did that happen? The highest fractions are in Spain, and can there be attributed to the Moorish period. But that explanation does not hold in much of Italy, where there are a few percent of haplogroup L. This probably is due to south-to-north gene flow across the Mediterranean during the Classical period. Some of the peoples on the south shore of the Mediterranean almost certainly already had some Sub-Saharan African admixture.

Not getting into the details of it, there are ways to explicitly model gene flow into a target population from donors defined by a phylogeny. In this case the authors tested various models of gene flow from Sub-Saharan Africans and Eurasians (non-Africans) to generate allele frequency patterns we see in modern Egyptians and ancient Egyptians.

What they consistently found is that modern Egyptians are about twice as much Sub-Saharan African as ancient Egyptians. The proportions for modern Egyptians ranged from ~10 to ~20 percent Sub-Saharan African against a Eurasian background, with a bias toward the higher values (depending on which populations you put into the phylogeny for non-Africans), and ~0 to ~10 percent for the ancient Egyptians, again with a bias toward the higher values. The pattern is consistent in these tests.

An issue here is that we’re going off three samples. That being said, the authors observe that despite differences in contamination/quality and time period they’re very concordant with each other. If I had to bet I think Old Kingdom samples would have somewhat less Sub-Saharan and eastern farmer ancestry. But the basic pattern persisted down to the Roman period, and was only shifted by admixture due to slavery.

And not to belabor the point, but a paper from a few years ago which had some Copt samples looks familiar in its broad outlines. You see that the Copts have very little Sub-Saharan African ancestry, though it does seem to be evident (the marker set is in the hundreds of thousands of SNPs). Additionally, they are quite distinct from the Qatari Arab sample.

Unfortunately the data for this paper just published is not on the European Nucleotide Archive. I really want to dig a little deeper into it.

What are the takeaways here? Egypt has been the sink for a lot of migration and gene flow over the past several thousand years, and probably earlier. Not surprising considering that it was relatively wealthy in the aggregate. The Natufian population that the Late Period Egyptians resemble the most did not have Sub-Saharan African ancestry according to earlier research. These Late Period Egyptians do have some. This is reasonable in light of the long interaction with Nubia which is historically attested. Similarly, there was clearly gene flow from Southwest Asia. This is again historically attested, especially in the Nile Delta (though foreign garrisons of mercenaries are recorded in Upper Egypt as well).

The Roman period probably did introduce some gene flow from Southeast Europe and Southwest Asia. But these populations are not that distinct from Egyptians.

Similarly, the Islamic period also brought in different peoples from Arabia and the Caucasus. But the most salient dynamic during the Islamic period was a massive trans-Saharan slave trade (though the Caucasus impact may have been comparable, and I think these results support the proposition that it was).

It seems entirely likely that the Copts are descended from a mix of Roman era Egyptians. Not only do they resemble the people in the Fayum portraits, but the circumstantial genetic data is that they have fewer “exotic” components which increased in frequency during the Islamic era. This would be exactly parallel to ethno-religious minorities in the Levant and Iraq.

One curious element to me is the suggestion gene flow before ~5,000 BCE between Sub-Saharan Africa and the lower Nile valley was low. If it hadn’t been low, it seems unlikely that the fraction of Sub-Saharan ancestry (or shift in that direction in relation to other Eurasians) in Copts would be so small.

So what explains the lack of earlier gene flow? I think the answer is going to be the fact that the human demographic landscape is characterized by lots of local population extinctions. As ancient DNA sampling coverage gets better and better meta-population dynamics are coming into focus, and we see gene flow, and die offs, in several areas. It is fashionable to say that human population variation is characterized by clines. But much of this clinal aspect is an outcome of the period after massive admixture over the last ~10,000 years.

And yet it may not be that the period before the Holocene was not clinal. Rather, it may be that large depopulations of areas of human occupation fragmented clinal ranges, and resulted in new range expansions from “core” zones.

About ~8,000 years ago there was a major desertification period in the Sahara desert. Many trans-Saharan populations may have gone extinct during this time due to rapid climate change. Eventually repopulation may have occurred from outside of the Sahara, so that post-Natufian Levantines and Sub-Saharan Africans from what today call the Sahel pushed up and down the Nile drainage basic respectively, meeting in the zone of Nubia on the boundary of history and prehistory.

Unlike many other areas of the world we have a long attested record of Egyptian history. As we get more mummy samples it seems likely that we’re get a crisper, clearer, picture. And the time transects will not be narrative blind; we already know the general arc of Egyptian history. If, for example, we see a new ancestral component around ~1500 B.C., in Egypt it’s not mysterious what this might be: the Hyksos.

This is just the prologue to a fascinating book that will be written over the next decade.

Related: Blog post analyzing one Copt’s results suggests that Sub-Saharan admixture is more like Dinka than Yoruba (in contrast, Muslim Egyptians have a mix of both, the latter probably coming during the Islamic slave trade, while the former is probably ancient admixture).

Citation: Schuenemann, V. J. et al. Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nat. Commun. 8, 15694 doi: 10.1038/ncomms15694 (2017).