When Surya left Olga of the Birch Forest


In the recent film The Northman the protagonist, Amleth, has a romantic relationship with a woman, “Olga of the Birch Forest.” Amleth was a Viking who raided Kievan Rus, and Olga was a Slavic woman who was captured in a raid.

Birch trees flourish across the temperate zone, but they’re particularly dominant in the north, due to being hardier. When I wrote about Finnish genetics, history and culture last year I stumbled upon the fact that early Finns who arrived in America (usually they were identified as “Swedes” because they were ruled by the Swedish Crown) often found an immediate affinity with northern Native American tribes. One explanation is that Finns and northern Native Americans are both “birch forest people.” Many aspects of their culture were similar, down to their moccasins.

As it happens, a long long time ago, and far far away, my forefathers were also birch forest people. Long before Olga’s kith and kin occupied the birch forests of northwestern Russia, they were occupied by the Fantyanovo-Balanovo culture. Until recently this cattle-raising society on the northern edge of the Indo-European world was assumed to perhaps be Baltic-speaking due to local hydronyms, but ancient DNA retrieved from Fatyanovo-Balanovo suggests a different answer. The vast majority of the men in their burial grounds carry Y chromosomal haplogroup R1a-Z93. This lineage is now found overwhelmingly in Indo-Iranian people, as well as in the Altai region.

The ancient DNA transect and succession is clear
– Fatnyanovo-Balanovo expanded eastward
– Turned into the Abashevo copper miners west of the Urals
– Gave rise to the Sintashta on the southern slope of the Urals into northwest Kazakhstan

At this point the Sintashta around 2000 BC exploded and turned into the Andronovo Horizon that covered much of Central Eurasia between 2000 and 1500 BC:

At some point Olga of the Birch Forest was left behind. A recent paper estimates that about 8% of the mtDNA lineages among populations like the Kalash and Pashtun in northern Pakistan is of steppe provenance. This is in contrast to about 2% to the south and east in “mainland” South Asia. This is contrast to the frequency of R1a in this region of Pakistan, about 50%, and 25% in mainland South Asia. In terms of total genome ancestry, about 25-30% of the ancestry in northern Pakistan among these groups is steppe, with an average across the subcontinent a bit below 15% (I did a weighted calculation a while ago).

What you see here is a massive drop off in maternal lineages of steppe Indo-Iranians, and a strong persistence of Y chromosomes, with total genome content being about in the middle. Figure 4c of Narasimhan et al. shows the same thing, with R1a fractions way higher than total genome content of steppe heritage.

This sex-specific admixture is not limited to South Asia. It can be found in the European context as well, though rarely as extreme.

So what’s going on here? One thing to note about Indo-European people is that on the whole they are patrilineal and patrilocal and exogamous. That is, one’s identity was determined by one’s father. Women moved into the household’s of their husband, and tended to be unrelated to them. This seems to be a perfect recipe for the assimilation of women into a society. But that’s not the reason all of these culturally and genetically different women are being brought into Indo-European societies. It is because the men are moving, and migrating very long distances.

In a podcast last year with myself and Patrick Wyman David Anthony claimed that they have detected Yamnaya individuals buried in western Mongolia and in Europe who are clearly related to each other. This means that Yamnaya cultural and social networks spanned Eurasia due to their mobility. In The Northman Olga was shipped from Russia all the way to Iceland. But this was the exception, not the rule. As Indo-European men expanded out of the core Eurasia zone, they moved as bachelor groups, and assimilated local women.

And not just Indo-Europeans. Among Uralic people, as well as some Siberians, a particular Y chromosome is very dominant from the Baltic all the way to eastern Siberia.

It’s a branch of N, and it is clearly East Asian in origin. It seems to have shown up in the Baltic region about 2,500 years ago, and it’s now the dominant haplogroup in Finland, and the Baltic countries. And yet the total genome content of modern day Finns that is East Asian is about 5% or so, even if N3a (TAT-C) is about 70%. There are almost no Siberian mtDNA lineages among Finns (OK ~1%). Among the Saami, about 25% of the genome is Siberian, but less than 10% of the mtDNA. Just like the Indo-Europeans, there seems to have been a male-mediated migration west. Why didn’t they bring women?

Can you imagine women and children moving fast across the zone of Eurasia north of the birch forest???

I think the common thing that connects the Indo-European groups here and the Uralic people is that there was a period when they were highly mobile over very long distances. This does not mean that women and children could never be involved. Some women were moving with their men judging by the mtDNA here and there. But, on the whole these were strongly male biased migrations. These were young and robust groups of men with few ties that moved rapidly across territory. There wasn’t time or inclination to have a baggage train.

Another way to look at it is from the gene’s-eye first view. Let’s look for explosive punctuated clusters within haplogroups.

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Avars were Rourans

genomes reveal origin and rapid trans-Eurasian migration of 7th century Avar elites:

The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar’s empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population.

No big surprises, but I think it is important to note that it looks like the East Eurasian Avar elites brought a lot of Iranian-steppe people as cadet elites. So a lot of the elite non-East Eurasian ancestry turns out to be non-European, and more Central Eurasian (probably Alanic and the like).

The Afanesievo live!

Bronze and Iron Age population movements underlie Xinjiang population history:

The Xinjiang region in northwest China is a historically important geographical passage between East and West Eurasia. By sequencing 201 ancient genomes from 39 archaeological sites, we clarify the complex demographic history of this region. Bronze Age Xinjiang populations are characterized by four major ancestries related to Early Bronze Age cultures from the central and eastern Steppe, Central Asian, and Tarim Basin regions. Admixtures between Middle and Late Bronze Age Steppe cultures continued during the Late Bronze and Iron Ages, along with an inflow of East and Central Asian ancestry. Historical era populations show similar admixed and diverse ancestries as those of present-day Xinjiang populations. These results document the influence that East and West Eurasian populations have had over time in the different regions of Xinjiang.

This is a hard paper to read. The terminology could be clearer, and the narrative crisper. Perhaps this is just due to the need to compress into the length science wanted, I don’t know. But I find it hard to read, I doubt others will find it easier.

Here’s the main figure:

Click to enlarge

Here are my general summaries

1 – ~5,000 years ago the indigenous people of “Xinjiang” (northern half = Dzungaria, southern half = Uighurstan) were mostly distantly related to “Ancient North Eurasians” (the Tarim Basin mummies)

2 – Around this time early Indo-Europeans, the Afanasievo culture, begin to migrate south of the Altai pasturelands to the north. The Afanasievo are basically genetically 100% Yamnaya initially; their culture was really just an eastward migration of Yamnaya. They immediately start mixing with the indigenous ANE-related population, and also to some extent with small numbers of people from Northeast Asia.

3 – After 2000 BC two new entrants arrive on the scene. First, Indo-Iranians, second-wave Indo-Europeans who are different from the Afanesievo in having “Anatolian farmer” ancestry due to their provenance in the borderlands of Poland, Belarus and Ukraine. The Indo-Iranians, part of the Andronovo horizon, assimilate with the local populations, and almost certainly are responsible for some of the Iranian languages prominent in early historical records in the southwestern part of the Tarim Basin (e.g., Khotanese). Ad this time there is also a clear influx of Central Asian/Turanian ancestry related to the BMAC culture. These are basically pre-Indo-European Iranians, and you can think of them as strongly skewed to Zagrosian ancestry, along with some ANE/WSHG admixture, and minimal but nontrivial Anatolian farmer (the ancestors of the Indus Periphery population are zeroed out for Anatolian farmer).

If you look at admixture analyses of modern Uyghurs you see some Persian-related ancestry. This may in fact be Iranians from the medieval period, but perhaps more likely they’re due to the mixture between Andronovo and BMAC ancestry, which would perfectly mimic Persian ancestry.

At least period you also start seeing more East Asian ancestry with a southern affinity.

4 – By the historical period, you have the migration of populations from Central Asia, Siberia, and East Asia. Some of these you recognize. The Sakas and the Old Uyghurs for example. Others, you may not.

Looking at the admixture, one of the historical era samples is clearly Northwest Indian in ancestry. There is some evidence of Indian ancestry as early as the Bronze Age as well. This is a small component, but it is clearly not trivial. This particular result puts Kumarajiva in perspective.

The major finding of this paper seems to be that Xinjiang has not seen population replacement, but assimilation. The indigenous Tarim Basin ANE-derived population still make a substantial contribution to modern Uyghurs, as do the Afanasievo early Indo-Europeans, later Indo-Iranians, Xiongnu, Han Chinese and Central Asians.

Finally, it does look like the admixture between Afanasievo and ANE-derived indigenous populations dates to between 2500 and 3000 BC. Judging from the distinctiveness of Tocharian languages the authors claim that this means that it seems likely Tocharian is an Afanesievo language (and if that is true, then the original Yamnaya spoke something similar to Tocharian).

The face of Agamemnon


The genomic history of the Aegean palatial civilizations:

The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.

Nothing that surprising, but adds a lot of clarity. Here’s my summation:

1) the main pulse of Indo-Europeans, the proto-Greeks, arrived ~2300 BCE to “mainland Greece” (i.e., the north). This notwithstanding other earlier contacts noted in the text between the Pontic steppe and the Balkans

2) The Minoans and other peoples of the Aegean did not have this ancestry. This is not surprising. But, this works seems to confirm a likely pulse of ancestry into the Aegean ~4000 BCE with roots in eastern Anatolia and/or the Caucasus. This is a minority component, but seems correlated with the arrival of Y chromosomal group haplogroup J2, and has been detected as far west as Sicily.

3) The above component is related to the contributor to about half the ancestry among the Yamnaya samples. But, the Yamnaya samples themselves are about half “Eastern Hunter-Gatherer” (EHG), which itself can be decomposed as 25% “Western Hunter-Gatherer” (WHG) and 75% “Ancient North Eurasian” (ANE). This EHG component was lacking entirely in the Minoans of the Bronze Age and is lacking in modern Cypriots (who are mostly ethnically Greek). In contrast, the EHG component begins to increase in the Balkans during the late Neolithic.

4) There seems to have been a further dilution of the steppe component among the Bronze Age Greeks as they moved from the north to the south. The largest component of Greek ancestry then, and now, remains “Early European Farmer” (EFF), related to and descended from “Anatolian Farmer” (AF).

5) Modern Greek samples have more steppe than late Bronze Age samples (Mycenaeans). I am confident this is due to early medieval Slav tribes, who moved as far south as the Peloponnese in large numbers. I’ve looked at a fair number of Greek samples, and some of them have way less steppe ancestry than others, with the latter matching those labeled “northern Greek” by the Estonian Biocentre dataset. I think many of these former are likely island Greeks from the Aegean or Greeks who descend from early 20th century migrants from Anatolia.

All this has to be placed in the context of the broader Indo-European migrations. David Anthony in The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World mentions that there is a lot of circumstantial cultural evidence of contacts between the proto-Greeks and Indo-Iranians in the Proto-Indo-European urheimat. This would make sense if the proto-Greeks migrated from Russia and the Pontic steppe relatively late, rather than being secondary migrants from the post-Corded Ware zone of northeastern Europe. Look up the R1b and R1a ratios of the Greeks. The former outnumber the latter in the south, and the latter the former in the north. I think this is the impact of later Slavic migrants on top of an earlier R1b bearing centum Indo-European population.

Thor Herydhal was right!

Native American gene flow into Polynesia predating Easter Island settlement:

The possibility of voyaging contact between prehistoric Polynesian and Native American populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas…while critics have argued that these botanical dispersals need not have been human mediated…The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South American populations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui)2. Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested…Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing…individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesian individuals with Native American individuals (around AD 1200) contemporaneous with the settlement of remote Oceania…Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesian individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia.

I already recorded a podcast on The Insight with the first author that should post tonight. So I’m not going to put a long post, just subscribe to The Insight and listen to what the first author has to say.

The major finding using high density SNP chips and local ancestry deconvolution seems to be that a group of people from mainland South America, probably coastal Columbia, was admixed into the population of the Marquesas. It is from the Marquesas that this genetic ancestry propagated across the eastern fringe of Oceania, including Easter Island.

Update: The podcast has been pushed live. It should propagate in the next hour or so.

Version alpha of trying to understand East Asian population history is now out!

We’ve been waiting for ancient DNA to answer some questions about eastern Eurasia for a while. I always thought Qiaomei Fu would spearhead it, but it doesn’t seem like it worked out that way. That’s because she’s not on a new preprint, The Genomic Formation of Human Populations in East Asia, which fills in a lot of gaps and confusing aspects of what has been reported from fragments of publications that came before (e.g., this clarifies a lot of things with Japan, see below). Since there has already been ancient DNA work on eastern Siberia and Southeast Asia, this is really focusing on the area in and around what is today the Peoples’ Republic of China. The first author has an affiliation with a university in Fujian, a province in southeast China.

Much of the analysis can be understood as organized around language families, and the demographics associated with them. In this way, it goes back to L. L. Cavalli-Sforza’s correlations between gene trees and language trees, as well as his later work on the agricultural Diasporas.

First, there isn’t something radically surprising here in their results. As I suggest above, the mass of ancient DNA in the preprint and model-building just snap together a lot of what you can see in other work, some going back decades.

Let’s start with the “Onge-like/related ancestry. ”

Below you see the strange pattern of Y chromosomal haplogroup D. It’s common in Tibet, Japan, and among the Andamanese.

In the preprint, the authors argue that there is a deep division among East Eurasian populations, going back further than 40,000 years, between a set of populations descended from groups related to Tianyuan man, and populations with affinities to the indigenous peoples of southeast Eurasia and Australia (“Ancestral Ancestral South Indians”, AASI, the Onge, the Negritos of Malaysia and the Phillippines, and Oceanians). Modern populations in East Asia can be thought of as a mix between these two groups, in various pulses and waves. The finding that some peoples in the Amazon had “Australo-Melanesian” affinity is very strange, but note that there’s no guarantee that the geographic distribution of the two clades was so skewed in the past in a north-south manner.

The Onge-related ancestry is apparently found as the deepest layer in the Tibetan plateau and contributes 45% of the ancestry to the Jomon of Japan. Among ancient proto-Austronesian peoples of Taiwan, it contributed 14% of the ancestry. Earlier work on Southeast Asia indicated that even before the expansion of Austro-Asiatic farmers out of southern China they mixed with a basal East Eurasian lineage related to the Onge.

Chinese annals record the presence of dark-skinned peoples in Yunnan nearly into historical periods. These could very well be legends or rumors, or, they could be the last relic populations that had not been fully absorbed into the Tianyuan-descended farmer expansion.

Moving more recently into the past, the preprint findings that of the Tianyuan descended populations in East Asia there is a northern and southern grouping. The northern grouping has been discussed before, it is the classic Amur-river valley population. It turns out that a sample from 5,000 years ago in northern Shaanxi, just to the north of the hearth of classical Chinese civilization in Henan, resembles these Amur-river valley populations. Though the authors don’t have samples from southern China, or even the Yangzi, they use modern samples from southern Chinese peoples, as well as ancient samples from Taiwan, to infer that it is likely that the Yangzi river valley was inhabited by a somewhat different group during prehistory than the modern Han Chinese.

In the preprint, the argument is made that Austronesian, Tai-Kadai, and Austro-Asiatic all emerged out of the Yangzi valley and its rice cultures. As noted above, other papers have already outlined the peopling of Southeast Asia using ancient DNA, so I will ignore that. But, note that for Austro-Asiatic populations, ~1/3 of the ancestry is Onge-related. Some of this was mixed in while in southern China, but some of it probably accrued later on in Southeast Asia.

Modern Austro-Asiatic populations can then be thought of as a compound of Tianyuan, and various  Onge-related groups.

China:  

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Why Bronze Age steppe people replaced the farmers they conquered

One of the major revisions in my own mind about the demographic and historical processes of the Holocene in relation to humans has been the reality that large and dense agglomerations of agriculturalists could be marginalized by later peoples, to the point of having a smaller genetic footprint in the future than anyone might have imagined. If you had asked me ten years ago I just wouldn’t have believed that the first farmers of Europe or South Asia wouldn’t account for the vast majority of the ancestry of the contemporary populations of the region. By “first farmers” I don’t even mean migrants. At that point, I had assumed a primarily Pleistocene indigenous hypothesis for the origin of Europeans and South Asians, with farming diffusing through a mixture of a few migrants along a demographic wave of advance.

That’s not what it looks like according to ancient DNA. In Northern Europe, it seems that around half or more of the ancestry is due to the incursions of a pastoralist steppe population during the Bronze Age. In Southern Europe and South Asia, the fraction is closer to 10-25%. But even in the latter case, the fraction of steppe ancestry is far higher than I had expected.

I had assumed that the steppe migrants would contribute 1-5% of the ancestry of Europeans and South Asians and that the spread of Indo-European languages was a matter of elite transmission and emulation. Think the Hungarians, for example, as an example of what had assumed.

So what explains what really happened?

During the Mongol conquest of Northern China Genghis Khan reputedly wanted to turn the land that had been the heart of the Middle Kingdom into pasture, first by exterminating the whole population. Part of the motive was to punish the Chinese for resisting his armies, and part of it was to increase his wealth. One of his advisors, Yelu Chucai, a functionary from the Khitai people, dissuaded him from this path through appealing to his selfishness. Chinese peasants taxed on their surplus would enrich Genghis Khan far more than enlarging his herds. Rather than focus on primary production, Genghis Khan could sit atop a more complex economic system and extract rents.

Most of you at this point can see the general framework then. For thousands of years, pastoralist people of the Inner Asian steppe and forest would extract rents out of the oikoumene by threatening them with force. The reason the East Roman Empire did not face the Hunnic onslaught during the lifetime of Attila is that they paid the horde tribute. Imperial China did the same during some periods. In other instances, civilized states found in the barbarians of the steppe useful confederates. The Tang dynasty did not collapse during the 750s because of the intervention of the Uyghurs, who suppressed the rebellion of An Lushan. In 9th century Baghdad the rise of the Turks was enabled by their usefulness in court politics and distance from any given faction.

The rise of the “gunpowder empires” during the 16th century and the eventual closing of the Inner Asian frontier with the crushing of the last embers of the Oirat confederacy between the Russian and Chinese Empires in the 18th century marked the end of thousands of years of interaction between the farmland and pasture.

But this makes us ask: when did this dynamic begin? I don’t think it was primordial. It was invented and developed over time through trial and error. I believe that the initial instinct of pastoralists was to turn farmland into pasture for his herds. This was Genghis Khan’s instinct. The rude barbarian that he was he had not grown up in the extortive system which more civilized barbarians, such as the Khitai, had been habituated to.

In these situations where pastoralists expropriated the land, there wouldn’t have been an opportunity for the farmer to raise a family. Barbarian warlords throughout history have aspired to be rich by plundering from the civilized the peoples…but would the earliest generations have understood the complexity of the institutions that they would have to extract rents out of if there wasn’t a precedent?

Instead of conventional historical dynamics of predatory elites and static peasantry, a better way to understand what occurred with the incursion of steppe pastoralists during the Bronze Age might be a simple ecological model of intra-specific competition. In a pre-state society defined by clan and tribal ties, steppe elites may have seen the farmers who were earlier residents in the territories which they were expanding into as competitors rather than resources from which a life of leisure might be obtained. In other words, instead of conquest, the dynamic was of animal competition.

Of course, pre-modern societies did not have totalitarian states and deadly technology. Rapid organized genocide in a way that we would understand was unlikely to have happened. Rather, in a world on the Malthusian margin, a few generations of deprivation may have resulted in the rapid demographic extinction of whole cultures. You don’t need to kill them if they starve because they were driven off their land.

In fact, we have some precedent of this historically. The Spaniards were intent on extracting rents out of the native peoples of the New World and living a life of leisure, but in many areas disease and exploitation resulted in demographic collapse. Imagine a conquest elite as vicious as the Spaniards, but without thousands of years of precedent that conquered peoples were more useful alive rather than dead. 

Addendum: The fraction of haplogroup M, which is probably derived from Pleistocene South Asians, is greater than 50% in places like Sindh. This indicates that the steppe migrations were strongly male biased in the initial generations.

Ancient Egyptians: black or white?

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).