# Black ancestry in white Americans of colonial background

I stumbled upon striking photographs of “white slaves” while reading The United States of the United Races: A Utopian History of Racial Mixing. The backstory here is that in the 19th century abolitionists realized that Northerners might be more horrified as to the nature of slavery if they could find children of mostly white ancestry, who nevertheless were born to slave mothers (and therefore were slaves themselves). So they found some children who had either been freed, or been emancipated, and dressed them up in more formal attire (a few more visibly black children were presented for contrast).

This illustrates that the media and elites have been using this ploy for a long time. I am talking about the Afghan girl photograph, or the foregrounding of blonde and blue-eyed Yezidi children. Recently I expressed some irritation on Twitter when there was a prominent photograph of a hazel-eyed Rohingya child refugee being passed around. Something like 1 in 500 people in that region of the world has hazel eyes! That couldn’t be a coincidence. Race matters when it comes to compassion.

But this post isn’t about that particular issue…rather, the images of enslaved white children brought me back to a tendency I’ve seen and wondered about: the old stock white Americans whose DNA results suggest ~1% or less Sub-Saharan ancestry. These are not uncommon, and I’ve looked at several of them (raw data). I’m pretty sure the vast majority at the 0.5% or more threshold are true positives, and probably many a bit below this (to my experience people from England and Ireland don’t get 0.3% African “noise” estimates with the modern high-density marker sets).

According to 23andMe’s database about 1 out of 10 white Southerners has African ancestry at the 1% threshold. It would be even more if you dropped to closer to 0.5%. And the DNA ancestry here understates the extent of what was going on: at about 10 generations back you are about 50% likely to inherit zero blocks of genomic ancestry from a given ancestor (assuming no inbreeding in the pedigree obviously). And this is exactly when a lot of the ancestry that is being detected seems to have “entered” the white population. In other words, for every person who is 1% African and 99% white American, they have a sibling who is 0% African and 100% white American, even though genealogically they share the same ancestors. Dropping the threshold to closer to 0.3%, and considering that even in the South there was migration from the North, and to a lesser extent Europe, after the Civil War, I wouldn’t be surprised if models of admixture inferred from the distributions we see indicate that over half the lowland Southern white population likely had genealogical descent from a black slave.

This all comes to mind because there aren’t too many records of people “passing” during this period. Those who deal in genealogy and encounter these cases of low fractions, which are nevertheless likely not false positives, almost never find a “paper trail” when they go look. And they look really hard.

The reason is obvious in the context of American history. Thomas Jefferson’s slave Sally Hemings had three white grandparents and one African slave grandparent. Several of her children are recorded to have been totally European in an appearance, and all except one passed into the white population (the two eldest married well into affluent white families in Washington D.C.). Passing as white was a way to escape the debilities of black status in the United States.

That being said, I think our Whig conception of the progressive nature of history sometimes misleads us in forgetting that the dynamics of race relations has had its ups and downs several times in the last few centuries in North America. If you read Daniel Walker Howe’s excellent What Hath God Wrought you observe that racial beliefs about the necessity and institutionalization of white supremacy in the early American republic evolved over time. Though the early republic would never be judged racially enlightened by modern lights, it was certainly far less explicitly racially conscious than what was the norm in the decades before the Civil War.

In particular, the rise of democratic populism during the tenure of Andrew Jackson was connected with much more muscular racial nationalism. To utilize a framework emphasized by David Cannadine in Ornamentalism, colonialism and Western civilization during the 19th and early 20th centuries can be viewed through the lens of race and class. Though the economic inequalities of American society persisted through the 19th century, men such as Andrew Jackson affected a more populist and rough-hewn persona than the aristocratic presidents of the early 19th century.* The white man’s republic had a leveling effect on the nature of elite culture.

But the attitudes toward racial segregation and mixing took decades to harden. Martin van Buren’s vice president, Richard Mentor Johnson, was well known to have had a common-law wife, Julia Chinn, who was a slave. He recognized his two daughters by her. He was vice president from 1837-1841 in the more racist of the two American political parties of the time. It is hard to imagine this being a viable “lifestyle” choice for someone of this prominence in later decades (after Julia Chinn’s death Johnson continued to enter into relationships with slaves).

Which brings us back to what was happening in the decades around 1800. Racism was a fact of life, necessitating the need for passing. But, beliefs about racial purity and the one drop rule had not hardened, so it would not be surprising to me that it was much easier for slaves or ex-slaves with mostly European ancestry to change their identity. Perhaps white Americans of that period were simply less vigilant about someone’s background because they were genuinely less concerned about the possibility that their partner may have had some black ancestry, so long as they looked white.

As the databases grow larger we’ll get a better sense of the demographic and genealogical dynamics. My suspicion is that we’ll see that there wasn’t much diminishment of gene flow into the black-identified community over the past 200 years, as much as the fact that hypo-descent, the one-drop rule, became so powerful in the between 1850 and 1950 we can confirm that passing declined, before rising again in the 1960s as whites became less vigilant due to decreased racism.

* As a middle class New Englander John Adams obviously was no aristocrat, but he was no populist either.

# Guest Right Is Holocene

With the surfeit of genomic data, whether contemporary or ancient, there is a lot of mileage to be gained by description and inference. That is, looking at the data, generating a result, and drawing some conclusion from that result. But another way to skin the cat is construct an explicit model and then test the data. There are details, and then there are generalities.

I’ll offer up a proposition here then: the transition from hunter-gatherers to agriculture and pastoralism has increased the rate of gene flow between neighbor populations. Several years ago Science published ancient DNA results which showed that there was little gene flow between Mesolithic hunter-gatherers and Neolithic farmers in Germany. Those trained in population genetics will know that only a small rate of gene flow can quickly homogenize difference between neighboring groups. Large genetic distances between neighboring populations requires strong taboos in relation to intermarriage.

It also happens that this summer I saw a poster presented by Anders Bergstrom at SMBE where he reported very high genetic distance values in the highlands of Papua New Guinea. Ethnographically we’re well aware that New Guinea is characterized by high degrees of linguistic diversity as well as xenophobia an war between neighboring groups. But a deeper dive into the genetic patterns suggest common descent in New Guinean from a random mating population on the Pleistocene-Holocene boundary, and more recent barriers to contact. New Guinea’s agriculture, which is gardening horticulture, is somewhat different from cereal cultivation. So there may be some differences there which we need to explore.

But something happened in the Holocene. In Game of Thrones “guest right” is sacred. That may seem like a silly observation, but the same principle is the clear in the Bible. The visitation of the angels to Sodom saw an attempt by the natives of the city attempt to violate the hospitality offered by the family of Lot, to the point where Lot offered his own daughters to the men who aimed to rape the angels.

The most recent genetic work suggest that the past 5,000 years or so have seen massing mixing across the world, and reduction of inter-group genetic distances. This is clearly the consequence of rapid increased rates of gene flow. You can take a cultural evolutionary viewpoint for the reason behind this, as Ara Norenzayan does in Big Gods: How Religion Transformed Cooperation and Conflict. Or you can take a more traditional materialistic route which puts the causal agent in the hands of mechanistic processes having to due with increased density and economic complexity. But whatever the reason, we know a transition occurred.

# Heraclius was a great man, but a dirty old man

The Emperor Heraclius is someone who more people should know. He saved the Byzantine Empire before it truly became the Byzantine Empire in a mature form. When he took power the Persians were on the march, and ruled vast swaths of the Asian and African possessions of the East Roman Empire. Theodore of Tarsus, one of the early Archbishops of Canterbury, grew up under Persian rule. Like Hannibal’s early victories Heraclius’ defeat of the Persians is a tour de force of strategic brilliance. I’ll leave it to the reader to find out why themselves (I recommend A History of the Byzantine State and Society to any reader).

But this post is inspired by pop-culture. People are talking about nephew-aunt relations right now. As it happens Heraclius’ second wife was his niece, Martina. Here is something I found on Wikipedia: “He had two children with Fabia and at least nine with Martina, most of whom were sickly children…Fabius (Flavius) had a paralyzed neck and Theodosios, who was a deaf-mute….” The history of this period can be patchy and unreliable. So I’m not sure there were nine children and most were sickly…but probably inbreeding was causing some serious issues.

# Roman cultural history has almost no demographic imprint

Several friends have asked that I weigh in the recent dust-up between Nassim Nicholas Taleb and Mary Beard. I haven’t for a few reasons. First, I can’t really be bothered to go incognito and see every detail of Taleb’s argument, as he has me blocked on Twitter (he called me a fucking idiot or something at some point). Second, the passion around this topic has little to do with genetics or ancient history from what I can see, two topics which I am actually interested in. Rather, it’s more about contemporary geopolitics. This is interesting too, and I have opinions on that, but I try really hard to keep history and politics in separate silos unless I am explicit about the connections and relevance. That’s because I don’t see classical history as simply something instrumentally important for modern times, but interesting in and of itself (the same goes for population genetics).

And for what it’s worth, Mary Beard says the same in her conclusion to SPQR. The ancients were ancients. Let them be what they were.

That being said, as someone with knowledge sets in ancient history and historical population genetics, I will make a few statements and let others interpret them however they wish (to be frank, I’m not going to cede ground to any of the experts I’ve seen who have spoken on the intersection of these two knowledge sets, so I figured it was time to put something somewhere beside Twitter).

* The prior probability that a Roman officer of the period in Britain would have visible black African ancestry (as seems clear by the cartoon, though no one has asked the cartoonists what their intent was) probability seems rather low. But it is non-zero, because a small minority of Roman subjects and citizens would have been defined as black by their physical appearance if they were alive today (they are mentioned passingly in the literature and texts from the period). Including in Britain.

* The probability conditional that he was based on an officer in Britain who was a native of Tidis is low, but higher. Several historians have pointed out in defense of the cartoon’s plausibility that there were many North Africans in Roman service, as well as prominent North Africans in Roman history (to name three of note, Septimius Severus, Tertullian, and St. Augustine). Whole tribes of what we’d today term Berbers enrolled in the Roman military a federates.

There are several separate issues to note. First, of the many North African genotypes I’ve seen detectable Sub-Saharan ancestry is found in almost all of them. But, many (most?) North Africans do not look visibly of Sub-Saharan African ancestry (see list of heads of states of Algeria). Second, both historical and genetic evidence indicates that this admixture from Sub-Saharan Africa is overwhelmingly (though not exclusively) from the period after Islam and the rise of a much bigger trans-Saharan trade (see Genomic Ancestry of North Africans Supports Back-to-Africa Migrations). Modern North Africa does have a large population today of people who are black or of obvious part-black ancestry, but this is due to the slave trade under Islam, and not antiquity.

* As evidence of the lack of non-European ancestry the paper The fine-scale genetic structure of the British population has been submitted. This is a great paper with best-of-breed methods and a massive data set of native English, with regional data. How do we resolve textual and archaeological evidence of people born outside of Britain during the Roman period in Britain with their lack of long-term genetic footprint among native modern Britains?

These sorts of questions need to be integrated in a broader context of the demography and genetics of antiquity that we have. On the whole looking at papers on modern and ancient DNA I am surprised by the lack of perturbation on the genetic structure attributable to the Roman period across Western Eurasia. I will offer two likely reasons that are related.

First, Classical civilization was an urban one, and the textual evidence we have is going to be highly skewed culturally in terms of our perception. The Roman world was predominantly written in cultured Latin and Greek (from what I have read the early translations of the Bible are indicative of a more pedestrian background of Christians due to the class markers of their lexical choices and idioms). But it was not necessarily spoken in cultured Latin and Greek across vast swaths of its territory. Even in St. Augustine’s time Punic was still spoken in the North African countryside, while the persistence and resurgence of Basque and Berber, and perhaps Brythonic Celtic in Britain, attest to vast reservoirs of people who were under the Roman peace, but not of it (also, the persistence of Albanian from a native Illyrian substrate). Because of the resources historians have on hand, text, there is going to be a major lacunae in our understanding and perception of the past. We hear the urban elites speaking to us. Not the rural majority.

Second, Classical civilization was an urban one, and this might have a major impact on the demographic consequences of migration. At any given size the effective breeding population is smaller than the census population, and the breeding population may not be representative of the overall population in terms of their genetic character. More specifically, it seems highly possible that the cosmopolitan urban Roman cities were massive demographic sinks. Rome before the Gothic Wars was a very populous city, not too far on the path of decline from its early imperial peak. But by the year 600 it had decreased its population to the point that vast swaths of the city were abandoned. Where did these people go? No doubt some of the elites scattered. Cassiodorus simply moved when barbarism came to his front step. But this was less possible for the urban proletariat. There is strong evidence that slaves in the ancient world were not replacing themselves reproductively due to brutality under which they lived. Some of the same was likely true of the urban proletariat.

* There is a difference between the inheritance pattern of culture and genes. In The Geography of Recent Genetic Ancestry across Europe this passage has always stuck out for me: “There is relatively little common ancestry shared between the Italian peninsula and other locations, and what there is seems to derive mostly from longer ago than 2,500 ya…The rate of genetic common ancestry between pairs of Italian individuals seems to have been fairly constant for the past 2,500 years, which combined with significant structure within Italy suggests a constant exchange of migrants between coherent subpopulations.”

The straightforward conclusion from this is that the Latinization of the Italian tribes and Magna Graecia occurred with no great demographic transformation. Modern Italy has within it the ghost of tribes long gone. This is notable because if you read the historical records of the Roman period you see evidence of trade, transport, and migration. But the genetic data would not lead you to this conclusion outside of Sicily and a few parts of Southern Italy.*

Above I have presented my reasoning for why this might be. But I think what it tells us that genetic data can informs us when there is a demographic turnover, and therefore a cultural turnover, but it will miss cultural turnovers which don’t have demographic impacts. These are many. To give a few examples, the rise of Islam in South Asia and Southeast Asia, the Latinization of the Western Mediterranean, the de-Latinization of Britain after the withdrawal of Roman legion and before the mass arrival of Saxons, and arrival of Buddhism in East Asia. All these are massive historical and cultural events, but they would not be visible in the genetic record.

If you want to learn about Roman history there are many books you could read. But I do recommend you try Bryan Ward-Perkins’ The Fall of Rome: And the End of Civilization. It’s a nice materialist take, and I think it gets to the underlying dynamics of institutional fragility of ancient civilization which was so easily wiped away by barbarism.

Addendum: The migration of the Slavs, Anglo-Saxons, and the Islamic Empires, all seem to differ from antiquity in having a major demographic impact. Why? In the case of massive institutional collapse, as in the first two cases, very old dynamics of inter-group competition arise, and famine probably does the rest of the trick. For Islam, it was a genuinely cosmopolitan civilization, with a more complex gradation between free and slave than in antiquity. Though it was quite brutal, African and Turkish slaves became free, and their genetic impact can be seen throughout the Islamic world.

* Like Spain, a substantial proportion of the Sicilian gene flow exchange is almost certainly due to the Islamic period. There are segments of North African and Sub-Saharan ancestry in Sicilians, albeit to a smaller extent than in Spain (in keeping with the shorter time period as part of the Islamic world).

Just a heads up to readers, Amazon Empires of the Word: A Language History of the World is 1.99 right now. I’d highly recommend you get this book if you are interested in this general topic. Here is my review from about seven years ago. # On the precipice of the Kali Yuga The idea of decline is an old one. See The Idea of Decline in Western History for a culturally delimited view. But whether it is Pandora opening her box or Eve biting the apple, the concept of an idyllic past and the ripeness of imminent decline seems baked into the cake of human cultural cognition. It was always better in the good old days. Of course there is the flip side of those who presume that the Eternal City will continue as it always was unto the end of time. Meanwhile, cornucopian optimists of our modern era, such as Steve Pinker, are the historical aberration. But they are influential in our age. Tanner Greer has a profoundly pessimistic post up, Everything is Worse in China, which is getting some attention (as I’ve stated before Tanner’s blog in general is worth a read). Rod Dreher has two follow up posts in response. First, A: Confucius, Basically, which is somewhat an answer to Tanner. And then an email from Tanner himself. It is here that he suggests to Rod’s readers Xunzi: The Complete Text. That is all for the good (for a broader view, A Short History of Chinese Philosophy). Readers can probably read between the lines that I have been gripped somewhat by Sinophilia of late. I am rather pessimistic about the state of American culture and the prospects for the American republic as we have known it. I don’t see any of the major political factions offering up a solution for the impending immiseration of the middle class. So I look to the east. Much of the history of the world has been a history of Asia, and it seems we are going to go back in that direction. If we are pessimistic about China, to a great extent we are pessimistic about the world. Perhaps then we need to abandon the idol of the nation-state, or in China’s case the nation-civilization. Rod Dreher has the Benedict Option for orthodox Christians* But we need to think bigger. Men and women of civilized inclinations may need to band together, and form secret societies shielded from the avarice of the institutional engines which channel human passions toward inexorable ends. We need a strategy for living as civilized people in an anarchic world, an archipelago of oligarchy in the sea of barbarism. Sooner, rather than later. History comes at you fast. * I mean here Trinitarian Christians of a traditionalist bent, not Eastern or Oriental Orthodox Christians. # The sons of Ham and Shem Recently I had the pleasure of having lunch with David Reich and he asked me about my opinions in relation to the Afro-Asiatic languages. I thought it was a strange question in that I get asked about that in the comments of this weblog too. Why would I have any particular insight? I gave him what I thought was the likely answer: Afro-Asiatic languages probably emerged from the western Levant. The ancient textual evidence indicates that to the north and east of Mesopotamia the languages were not Semitic. Though Akkadian, a Semitic language, was present at the dawn of civilization, Sumerian was the dominant language culturally in the land between two rivers, and it was not Semitic. As Lazaridis et al. did not detect noticeable Sub-Saharan African ancestry in Natufians, or later Near Easterners, I have become skeptical of any Sub-Saharan African origin for Afro-Asiatic. But after the earlier post I made a few mental connections, and so I’ll put something up which pushes forward my confidence on a few issues. They lean predominantly on Y chromosomes. I understand that this sort of phylogeography has been shown to be not too powerful in the past, but in the scaffold of the ancient DNA framework it can resolve some issues. About a decade ago study of Adolf Hitler’s paternal lineage (through male relatives) indicated that his haplogroup was E1b1b. Though reports that Hitler was non-European, because this is a very common lineage in non-Europeans, as well as Jews, were incorrect, it does turn out that Hitler’s paternal lineage is not associated with the Indo-European migrations. That is, unlike me, Adolf Hitler does not descend from the All-father, but rather one of the men who were conquered and assimilated by the steppe pastoralists. But E1b1b is an interesting lineage. First, it is very common in much of Africa, especially the north. Second, it is common among the Natufian people according to Lazaridis et al. In contrast the Neolithic Iranian farmers seem to have harbored haplogroups J. Today the Near East is a mix of the two, which makes sense in light of the fact that reciprocal gene flow has occurred in the last 6,000 years. Looking at E1b1b frequencies you notice a few things. The highest frequencies with large N’s are in the Cushitic and Berber languages. Haplogroup J has a different distribution, being skewed more to West Asia. In Ethiopia E1b1b is more common, but J is far more prevalent among the Semitic Amhara than the Cushitic Oromo. Though it is subtle autosomal DNA makes it clear that the Semitic speaking populations in Ethiopia-Somalia have more Eurasian ancestry than the Cushitic ones. I believe this is evidence of the multiple migration pattern discerned earlier. If you go further south in East Africa and compare E1b1b and J you see a skew in the ratio. E1b1b declines in frequency, but J basically disappears. Among the Masai, who have a clear minor West Eurasian ancestral component, albeit far less than Ethiopians, 50% carry E1b1b. Among the Sandawe, who are a language isolate with clicks, but exhibit Cushitic genetic affinities, 34% carry E1b1b. Among their Hadza hunter-gatherer neighbors, 15% do so. Among many Khoisan groups the frequency of E1b1b is 10%. Most of these groups exhibit no J haplogroup. This aligns easily with what Skoglund was reporting earlier: the first pastoralists had no “eastern farmer,” but did have “western farmer.” The Natufians were E1b1b. The wider reach of E1b1b in Africa in comparison to J is likely due to the fact that the admixed pastoralists were pushing into relatively virgin territories. Later Eurasian backflow events, which brought Semitic languages, encountered a much more densely populated Africa. The hypothesis I present is that after the descendants of the Natufians made the transition to farming, some immediately pushed into areas of Africa suitable for farming and/or pastoralism. They quick diversified into the various Berber and Cushitic languages. The adoption of Nilo-Saharan languages, and later Khoisan ones, was simply the process of successive and serial admixture into local populations as these paternal lineages introduced their lifestyle. In the Near East many distinct Semitic languages persisted across the Fertile Crescent, and for whatever reason the various non-Semitic languages faded and Semitic ones flourished. # The great Bantu expansion was massive Lots of stuff at SMBE of interest to me. I went to the Evolution meeting last year, and it was a little thin on genetics for me. And I go to ASHG pretty much every year, but there’s a lot of medical stuff that is not to my taste. SMBE was really pretty much my style. In any case one of the more interesting talks was given by Pontus Skoglund (soon of the Crick Institute). He had several novel African genomes to talk about, in particular from Malawi hunter-gatherers (I believe dated to 3,000 years before the present), and one from a pre-Bantu pastoralist. At one point Skoglund presented a plot showing what looked like an isolation by distance dynamic between the ancient Ethiopian Mota genome and a modern day Khoisan sample, with the Malawi population about\frac{2}{3}\$ of the way toward the Khoisan from the Ethiopian sample. Some of my friends from a non-human genetics background were at the talk and were getting quite excited at this point, because there is a general feeling that the Reich lab emphasizes the stylized pulse admixture model a bit too much. Rather than expansion of proto-Ethiopian-like populations and proto-Khoisan-like populations they interpreted this as evidence of a continuum or cline across East Africa. I’m not sure if this is the right interpretation of the plot presented, but it’s a reasonable one.

Malawi is considerably to the north of modern Khoisan populations. This is not surprising. From what I have read Khoisan archaeological remains seem to be found as far north as Zimbabwe, while others have long suggested a presence as far afield as Kenya. Perhaps more curiously: the Malawi hunter-gatherers exhibit not evidence of having contributed genes to modern Bantu residents of Malawi.

Surprising, but not really. If you look at a PCA plot of Bantu genetic variation it really starts showing evidence of local substrate (Khoisan) in South Africa. From Cameroon to Mozambique it looks like the Bantu simply overwhelmed local populations, they are clustered so tight. Though it is true that African populations harbor a lot of diversity, that diversity is not necessarily partition between the populations. The Bantu expansion is why.

Of more interest from the perspective of non-African history is the Tanzanian pastoralist. This individual is about 38% West Eurasian, and that ancestry has the strongest affinities with Levantine Neolithic farmers. Specifically, the PPN, which dates to between 8500-5500 BCE. More precisely, this individual was exclusively “western farmer” in the Lazaridis et al. formulation. Additionally, Skoglund also told me that the Cushitic (and presumably Semitic) peoples to the north and east had some “eastern farmer.” I immediately thought back to Hogdson et al. Early Back-to-Africa Migration into the Horn of Africa, which suggested multiple layers. Finally, 2012 Pagani et al. suggested that admixture in the Ethiopian plateau occurred on the order of ~3,000 years ago.

Bringing all of this together it suggests to me two things

1. The migration back from Eurasia occurred multiple times, with an early wave arriving well before the Copper/Bronze Age east-west and west-east gene flow in the Near East (also, there was backflow to West Africa, but that’s a different post….).
2. The migration was patchy; the Mota sample dates to 4,500 years ago, and lacks any Eurasian ancestry, despite the likelihood that the first Eurasian backflow was already occurring.

Skoglund will soon have the preprint out.

# Rome fell fast, and so did we

The fall of Rome has obviously been a topic of much interest and discussion. It is, after all, a conversation about the fall of civilization as we knew it.

If you read my blog you are probably aware that I lean toward a thesis of genuine and rapid fall. One of the most revelatory books I’ve read in the past 20 years is Bryan Ward-Perkins’ The Fall of Rome: And the End of Civilization. Ward-Perkins’ tale is an apocalyptic one. The material basis of Roman civilization the West collapsed. Perhaps the most relevant and evocative fact for me is that pollution due to manufacturing production in England did not match that of the Roman period until the industrial revolution. Though the Roman economy never achieved the industrial revolution’s gains in productivity, it did attain a level of Smithian efficiency and interdependence on the margins of the factors of production.

From a totally different perspective Peter Heather in The Fall of the Roman Empire broadly agrees with Ward-Perkins’ contention. The Roman Empire fell, and it fell fast, and the imperial elites didn’t see it coming. Remember, the Roman Empire was dismembered and disordered during the “crisis of the third century”. Under Diocletian and his successors in the 4th century it came back to health and strength before the distress of the 5th century in the West. But at the time contemporaries did not view the shocks and exigencies of these decades as any more distressing then the events of the 3rd century, and the Eastern Empire around Constantinople was reasonably robust.

Ultimately though 476 was a coup de grace to the Western Empire. The Gothic wars tore apart the fabric of the Italian peninsula in the 6th century, and the substantive reality of the old empire faded away. There was no going back. Of course I’m well aware of the argument that the Roman world evolved, that it did not collapse. And Late Antiquity and its continuities with the Classical world, and how it bridged itself to the Medieval world, are fascinating. But I do not accept that the preservation of Roman motifs and ideals in the courts of barbarian German warlords is evidence that substantively nothing changed.

Much of it depends on how you weight material vs. ideological parameters. The idea of Rome cast a shadow centuries beyond its substantive material integrity. After, the Byzantines called themselves Romans until the conquest of their city-stateless in 1453. But no matter the name, they were not Romans as the Romans were in 400 A.D.

The theoretical context of all this is that it strikes me cultures can go through rapid nonlinear shocks which induce very quick and unexpected changes. In the human past this would often entail collapses and regressions. The “Dark Age” after the chaos of the late Bronze Age is a case in point. In one generation the citadel society of Mycenanean Greece disappeared across much its extant range. The gap between 1966 and 1969 in much of the West was arguably greater than between 1956 and 1966.

The United States today is the most powerful nation in the world. And our cultural centrality and ascendency is such that we don’t challenge our implicit position as the premier power in the world. But I believe that we’ve become a inward looking involuted culture. There’s no point in litigating this, and obviously I may be wrong. But too often we confuse our own petty internecine squabbles with the concerns of the world. The world is passing us by….

# Indian genetic history: before the storm

Over at Brown Pundits I’ve mentioned the continuing simmer of controversy over a recent piece, How genetics is settling the Aryan migration debate. This has prompted responses in the Indian media from a Hindu nationalist perspective. One of these notes that the author of the piece above cites me, and then goes on to observe I was fired from The New York Times a few years ago due to accusations of racism (also, there is the implication that I’m just a blogger and we should trust researchers with credibility like Gyaneshwer Chaubey; well, perhaps he should know that Gyaneshwer Chaubey considers me “unbiased” according to an email exchange which I had with him last week [we all have biases, so I think he’s wrong in a literal sense]).

I was a little surprised that a right-wing magazine would lend legitimacy to the slanders of social justice warriors, but this is the world we live in. Those who believe that everything written about me in the media, I invite you to submit your name and background to me. I have contacts in the media and can get things written if I so choose. Watch me write something which is mostly fact, but can easily be misinterpreted by those who Google you, and watch how much you value the objective “truth-telling” power of the press all of a sudden.

There’s a reason so many of us detest vast swaths of the media, though to be fair we the public give people who don’t make much money a great deal of power to engage in propaganda. Should we be surprised they sensationalize and misrepresent with no guilt or shame? I have seen most of those who snipe at me in the comments disappear once I tell them that I know what their real identity is. Most humans are cowards. I have put some evidence into the public record to suggest that I’m not.

Perhaps more strange for me is that the above piece was passed around favorably by Sanjeev Sanyal, who I was on friendly terms with (we had dinner & drinks in Brooklyn a few years back). I asked him about the slander in the piece and he unfollowed me on Twitter (a friend of Hindu nationalist bent asked Sanjeev on Facebook about the articles’ attack on me, but the comment was deleted). It shows how strongly people feel about these issues.

I’m in a weird position because I’m brown and have a deep interest in Indian history. But that interest in Indian history isn’t because I’m brown, I’m pretty interested in all the major zones of the Old World Oikoumene. Aside from some jocular R1a1a chauvinism I don’t have much investment personally (I just told said Hindu nationalist friend who turns out to be R2 to clean my latrine; joking of course, though I’m sure he resents that I’m descended on the direct paternal line from the All-Father & Lord of the Steppes and he is not!).

In the aughts I accepted the model outlined in 2006’s The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations. But to be frank it always struck me as a little confusing because the tentative autosomal data we had suggested that many South Asians were closer to West Eurasians than deep divergences dating to the Last Glacial Maximum would suggest. Since I’ve written something like 5 million words in 15 years, I actually can check if I’m remembering correctly. So here’s a post from 2008 where I express reservations of the idea of long term deep heritage of Indians separate from other West Eurasians. The reason I was so impressed by 2009’s Reconstructing Indian Population History is that it resolved the paradox of South Asian genetic relatedness.

To recap, Reich et al. proposed that modern Indians (South Asians) could be modeled as a two way mixture between two distinct populations with separate evolutionary genetic histories, Ancestral North Indians and Ancestral South Indians (ANI and ASI). How distinct? ANI were basically another West Eurasian population, while ASI was likely nested in the clade with Eastern Non-Africans. Additionally, there was a NW-to-SE and caste admixture cline. In other words, the higher you were on the caste ladder the more ANI you had, and the closer your ancestors were from the north and west, and more ANI you had. The difference between Y and mtDNA, male and female, could be explained by sex-biased migration.

But there were still aspects of the paper which I had reservations about. After all, it was a model.

• Models are imperfect fits onto reality. The idea of mass migration seemed ridiculous to me at the time, because even by the time of the Classical Greeks it was noted that India was reputedly the most populous land in the world (to their knowledge). But ancient DNA has convinced me of the reality of mass migrations.
• I wasn’t sure about the nature of the closest modern populations to the ANI. The researchers themselves (in particular, Nick Patterson) told me that the relatedness of ANI to Europeans was very close (on the order of intra-European differences). But modern Indians do not look to be descended from a population that is half Northern European physically. Again, ancient DNA has shown that there was lots of population turnover, and it turns out that Europeans and ANI were likely both compounds and mixed daughter populations of common ancestors (also, typical European physical appearance seems to have emerged in situ over the past 5,000 years).
• The two way admixture modeled seemed too simple. I had run some data and it struck me that North Indian populations like Jats had something different than South Indian groups like Pulayars. In 2013 Priya Moorjani’s paper pretty much confirmed that it was more than a two way admixture along the ANI-ASI cline.

This March BMC Evolution Biology published Silva et al’s A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. It has made a huge splash in India, arguably triggering the write up in The Hindu. But for me it was a bit ho-hum. If you read my 2008 post it is pretty clear that I suspected the most general of the findings in this paper at least 10 years back. It is nice to get confirmation of what you suspect, but I’m more interested to be surprised by something novel.

Nevertheless A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals has come in for lots of repeated attack in the right-wing Indian press. This is unfair, because it is a rather good paper. I suspect that it wasn’t published in a higher ranked journal because most scientists don’t consider the history of India to be that important, and they didn’t really apply new methods, as opposed to bringing a bunch of data and methods together (in contrast, the 2009 Reich et al. paper was one of the first publications which showed how to utilize “ghost populations” in explicit phylogenetic models with relevance to human demographic history).

As it happens I will be writing up my thoughts in detail in an article for a major Indian publication (similar circulation numbers as The Hindu). This has been in talks for over six months, but I’ve been busy. But a month or so ago I thought it was time that I put something into print for the Indian audience, because I felt there was some misrepresentation going on (i.e., the Aryan invasion theory has not been been refuted by genetics, but this is what many Indians assert).

For any years people have told me there are certain topics that shouldn’t be talked about. I have offended people greatly. There are many things people do not want to know. I have come to the conclusion this is not an entirely indefensible viewpoint (though if you accept this viewpoint, I think acceptance of authoritarianism is inevitable, so I hope people will toe the line when the new order arrives; knowing their personalities I think they will conform fine). But my nature is such that I continue to have nothing but contempt for the duplicitous and craven manner in which people go about these sorts of private conversations. I assume that as someone with the name “Razib Khan” I will be attacked vociferously by Hindu nationalists, who will no doubt make recourse to the Left-wing hit pieces against me to undermine my credibility. The fact that these groups are fellow travelers should tell us something, though I will leave that as an exercise for the reader.

I will write my piece that reflects the science as I believe it is, without much consideration of the attacks. That is rather easy for me to do in part because I live in the United States, where denigrating the deeply held views and self-esteem of Hindu nationalists is not sensitive or politically protected (unlike say, Muslims). And Hindu nationalists are less likely to kill me by orders of magnitude than Muslim radicals, and they have far less purchase in this nation then the latter (though you may be interested to know that very conservative Muslims follow me on Twitter; they’re actually more open-minded than many SJWs to be entirely honest).

Let me go over some general points that I see coming up over and over on the relationship between Indian (pre)history and genetics in the critiques .

One of the major critiques has to do with the nature of R1a-Z93 and its subclades. Basically this Y chromosomal haplogroup, the greatest that has ever been known, exhibits a strong signature of very rapid expansion over the past 4,000 years or so. It is divided from Z282. While Z93 is found in South Asia, Central Asia, and Siberia, Z282 is European, with its dominant subclade the one associated with Eastern Europeans. Both of these clades of R1a have gone through massive expansion. In the Altai region R1a is 40% of the heritage of peoples who are now predominantly East Eurasian today. But they are Z93. Additionally, ancient DNA from the Pontic Steppe dated ~4,000 years ago from Srubna remains is Z93, as are Scythian remains from the Iron Age.

Much of the argument comes down to dating, and citing papers that give deep coalescence numbers between difference branches of R1a1a. Hindu nationalists and their fellow travelers point to recent papers which give dates >10,000 years ago, and so place the origin of Z93 plausibly in the Pleistocene. The problem is that Y chromosomal coalescence dating is something of a mug’s game. Often they use microsatellite data whose mutational rates are highly uncertain. In contrast, using SNP data, which has a slower mutation rate but requires a lot more data, you get TRMCA (common ancestry) between Z93 and Z282 around ~5,800 years ago. But coalescence estimates often have wide confidence intervals of thousands of years. And even with these intervals, the assumptions you make (e.g., mutation rate) strongly influence your midpoint estimate.

The Y chromosomal data is powerful, but its interpretation is still buttressed upon other assumptions. The really big picture framework is the nature of ancient genome-wide variation across Eurasia. Lazaridis et al. 2016 condition us to a prior where much of Eurasia was subject to massive population-wide genetic changes since the Holocene. Therefore, I am much less surprised if there was massive genetic change in India relatively recently. The methods in Priya Moorjani’s paper and in other publications make it obvious that mixture was extensive in South Asia between very distinct groups until about ~2,000 years ago. In fact, Moorjani et al. using patterns of variation across the genome to come at a number of two to four thousand years ago as the period of massive admixture.

Though we don’t have relevant ancient DNA from India proper to answer any questions yet, we do have ancient DNA from across much of Europe, Central Asia, and the Near East. What they show is that Indian populations share ancestry from both Neolithic Iranians and peoples of the Pontic steppe, who flourished ~5 to ~10,000 years ago. To some extent the latter population is a daughter population of the former…which makes things complicated. Conversely, no West Eurasian population seems to harbor ancient signals of ASI ancestry.

One scientist who holds to the position that most South Asian ancestry dates to the Pleistocene argued to me that we don’t know if ancient Indian samples from the northwest won’t share even more ancestry than the Iranian Neolithic and Pontic steppe samples. In other words, ANI was part of some genetic continuum that extended to the west and north. This is possible, but I do not find it plausible.

The reasons are threefold. First, it doesn’t seem that continuous isolation-by-distance works across huge and rugged regions of Central Eurasia. Rather, there are demographic revolutions, and then relative stasis as the new social-cultural environment crystallizes. This inference I’m making from ancient DNA and extrapolating. This may be wrong, but I would bet I’m not off base here.

Second, it strikes me as implausible that there was literally apartheid between ASI and ANI populations for the whole Holocene right up until ~4,000 years before the present. That is, if Northwest India was involved in reciprocal gene flow with the rest of Eurasia over thousands of years I expect there should have been some distinctive South Asian ASI-like ancestry in the ancient DNA we have. We do not see it.

Third, one of the populations with strong affinities to some Indian populations are those of the Pontic steppe. But we know that this group itself is a compound of admixture that arose 5,000-6,000 years ago. Because of the complexity of the likely population model of ANI this is not definitive, but it seems strange to imagine that ANI could have predated one of the populations with which it was in genetic continuum as part of a quasi-panmictic deme.

Finally, many of the critiques involve evaluation of the scientific literature in this field. Unfortunately this is hard to do from the outside. Citing papers from the aughts, for example, is not wrong, but evolutionary human population genomics is such a fast moving field that even papers published a few years ago are often out of date.

Many are citing a 2012 paper by a respected group which argues for the dominant model of the aughts (marginal population movement into South Asia). One of their arguments, that Central Asian migrant should have East Asian ancestry, is a red herring since it is well known that this dates to the last ~2,000 years or so (we know more now with ancient DNA). But the second point that is more persuasive in the paper is that when they look at local ancestry of ANI vs. ASI in modern Indians, the ANI haplotypes are more diverse than West Eurasians, indicating that they are  not descendants but rather antecedents (usually the direction of ancestry is from more diverse to less due to subsampling).

There are two points that I have make here. First, local ancestry analysis is difficult, so I would not be surprised if they integrated ASI regions into ANI and so elevated the diversity in that way (though they think they’ve taken care of it in the paper). Second, if the ANI are a compound of several West Eurasian groups then we expect them to be more diverse than their parents. In other words, the paper is refuting a model which is almost certainly incorrect, but the alternative hypothesis is not necessarily the true hypothesis (which is a more complex demographic model than many were testing in 2012).

But there are many things we do not know still. Many free variables which we haven’t nailed down. Here are some major points:

• Y chromosomal lineages have a correlation with ethno-linguistic groups, but the correlation is imperfect. R1b and R1a seems correlated with Indo-European groups, but both these are found in high proportions in groups which are putatively mostly “pre-Indo-European” in origin (e.g., Basques, Sardinians, and South Indian tribals and non-Brahmin Dravidian speaking groups). Also, haplogroups like I1 in Europe expand with Indo-Europeans locally, suggesting there was lots of heterogeneity in Indo-Europeans as they expanded. In other words, Indo-European expansion in relation to powerful paternal lineages did not always correlate with ethno-linguistic change.
• There are probably at minimum two Holocene intrusions from the northwest into South Asia, but this is a floor. The models that are constructed always lack power to detect more complexity. E.g., it is not impossible that there were several migrations of Indo-Europeans into South Asia which we can not distinguish genetically over a period of a few thousand years.
• If one looks over all of South Asia it may be that ASI ancestry in totality is >50% of the total genome ancestry. I don’t have a good guess of the numbers. If this is correct, perhaps most South Asian ancestors 10,000 years ago were living in South Asia (though the fertility rate are such in Pakistan that ANI ancestry is increasing right now in relative rates).
• But, this presupposes that ASI were present in South Asia in totality 10,000 years ago, rather than being migrants themselves. If ancient DNA confirms that ANI were long present in Northwest India, I hold then it is entirely likely that ASI was intrusive to South Asia! The BMC Evolutionary Biology Paper does a lot of interpretation of deep structure in haplogroup M in South Asia. I’m moderately skeptical of this. Europe may not be a good model for South Asia, but there we see lots of Pleistocene turnover.

So where does this leave us? Ancient DNA will answer a lot of questions. Pretty much all scientists I’ve talked to agree on this. My predictions, some of which I’ve made before:

1. The first period of admixture is old, and dates to the founding of Mehrgarh as an agricultural settlement. The dominant ANI component dates to this period and mixture event, all across South Asia. The presence in South India is due to expansion of these farming populations.
2. A second admixture event occurred with the arrival of steppe people. Those who argue for the Aryan invasion model posit 1500 BCE as the date. But these people probably were expanding in some form before this date.
3. We still don’t know who the antecedents for the Indo-Aryans were. Probably they were a compound of different steppe groups, and also other populations which were mixed in (by analogy, in Europe it is obvious now that there was some mixture with the local European farmers and hunter-gatherers as Europeans expanded their frontier westward; the same probably applies for Indo-Aryans are the BMAC).