The Roman, the Hun and the sun


I chose a fortuitous time to read Kyle Harper’s The Fate of Rome: Climate, Disease, and the End of an Empire. This is a great book, and a nice compliment to Bryan Ward-Perkins The Fall of Rome: And the End of Civilization. Where Ward-Perkins attempts to convince you that Rome did indeed fall, and that that fall mattered, Harper takes it as a given that you accept this position. Rather, he tries to show you in The Fate of Rome that a series of contingent and necessary causal factors set the Roman system up for its fall. The fall of Rome is not just an idea, but a material event that was given a strong push by material factors.

As the The Fate of Rome was published in the fall of 2017, so it was written well before recent work which highlights both the nature and role of steppe barbarians in triggering the changes which we dramatically term the “fall of Rome” and the “barbarian migrations.” A few months ago I wrote about a paper which reported that post-Hunnic people of the Balkans were genetically different from typical Europeans in that they exhibited some East Asian admixture. Harper does assume that the Huns were barbarians whose ultimate provenance was somewhere in the region of modern Mongolia, but emphasizes that their peregrinations transformed them.

As so it did. A new paper in Nature, 137 ancient human genomes from across the Eurasian steppes, nails the overall dynamics. As illustrated in the figure above the early steppe was dominated by peoples of a West Eurasian provenance, while the latter steppe shifted toward a more East Asian shifted population.

These early groups go by various names. But the Cimmerians, Scythians, and Sarmatians have origins on the Pontic steppe. Flourishing in the first millennium before Christ, I should precisely label them “Iranian,” but that might mislead readers a bit since some of these groups were never resident within Iran. The Scythians were a presence across a huge zone of Inner Asia and were a force in Eastern Europe, West Asia, South Asia, and in Eastern Asia. Likely emerging out of the Andronovo culture, genetically the results from the paper confirm early work that Scythians mixed with the local substrate where they went. In this way, they prefigure later steppe populations. Being a nomad was a lifestyle, the genetic correlates to some extent an accident.

In The Fate of Rome  the Huns have a role to play as a push for the migration of Goths into the Roman Empire, which eventually leads to their rebellion and a collapse in both the prestige and military manpower of the Roman state. The genetic evidence above and elsewhere is strongly indicative of the likelihood that the Huns were originally part of the Xiongnu confederacy. As they moved west they mixed with post-Scythian and other Iranian and Siberian elements, and presumably by the time they arrived on European frontier of Rome they had picked up some Germanic and proto-Slavic ancestry. In 137 ancient human genomes from across the Eurasian steppes the authors also report that the East Asian gene flow was somewhat “male-mediated” in the later steppe. Similarly, earlier work on proto-Iranian peoples in the Altai region is strongly suggestive of male-mediation in West Eurasian gene flow.

The obligate and exclusive Eurasian nomad lifestyle was one dominated by men, though as one can see the importance of Genghis Khan’s wives and daughters women maintained independence as well.

For whatever reason, full-blown nomadism only became a feature of the landscape north of what became China in the last few centuries before Christ. The mobile and militarized nomadic lifestyle that emerged in western Eurasia in the years around 1000 BC seem to have taken five centuries to penetrate the far eastern fringes. Until the crushing of the Dzhungar’s by the Manchus in the 18th century, 2,000 years later, the dynamic between nomad and settled was a defining feature of Chinese statecraft and political culture. And, it was also a major feature of nomad culture, because the wealthy Chinese state was an almost irresistible attraction to steppe elites as a source of plunder and tribute.

But human action is not the only relevant parameter in human history.  The Fate of Rome  is fundamentally a work of history, but it also takes ecology and evolution seriously. In fact, it foregrounds them. Kyle Harper makes the argument that the expansionary phase of the Roman Empire was not necessarily coincidental, or at least it was lucky indeed because there was a climatic optimum, similar to the one which preceded the demographic expansion of medieval Europe. In contrast, in the 6th century, the world went through some of the coldest years in the Holocene because of a combination of fluctuations in solar radiation and volcanic explosions. I assume that the likelihood of the latter is Poisson distributed, so the combination of decreased radiation and several successive volcanic events can be chalked up to randomness. But its consequences were not random at all.

The climatic changes can have demographic and social consequences obviously. Desperate armed pastoralists can overwhelm states, and change the course of history, just as peasants can rebel from taxes and subordination. And, pastoralists can also bring Yerisina pestis, the plague. Climate is an abiotic pressure which is to some extent an exogeneous shock which occurs randomly, and does not react to human feedbac k.* Disease though is a biotic pressure, and though it may relate to abiotic forces, human interaction and agency matter quite a bit.

The Fate of Rome clearly hinges on abiotic factors as initial drivers: a good harvest is good for the state. But the biotic factors, disease, are partly under the control of the state. The Romans did not have germ theory, and were under constant stress due to the high pathogen load, especially of the cities. Harper presents the evidence of high mortality within Roman society well. Because of the endemic ubiquity of disease even elites were impacted by it. But Rome was not just affected by endemic ailments, it was subject to pandemics and plagues. Three loom large in  The Fate of Rome:

  • The Antonine Plague, which ended the expansionary phase of the High Empire in the middle to late 2nd century.
  • The Plague of Cyprian of the middle 3rd century which ushered in a period of state collapse.
  • And finally, the Justinian Plague which marked the end of Late Antiquity and the beginning of the “Dark Ages.”

One of the major insights that Kyle Harper reiterates is that these plagues, these pandemics, are a feature/bug of the Roman imperial system. They are not just the consequence of simply settled agricultural society. As described in books such as Pandora’s Seed, agriculture and settled society transformed the lifestyles of human groups, and many diseases which were rare in hunter-gatherer populations probably became common among farmers. But The Fate of Rome the author argues that pandemics were a novel outcome of complex imperial state-systems with long-distance trade-networks. Small-scale pre-state Neolithic chiefdoms did not have the scale and interconnections to foster plague.

Mass pandemics of smallpox, plague, and influenza are then aspects of civilized life, not, settled agricultural life. This puts the argument of Charles C. Mann in 1493 into greater focus. It wasn’t just more extensive and intensive agriculture in the Old World which left Amerindians vulnerable, it was also that the Old World had thrown up several massive imperial systems which had incubated pandemic producing pathogens (smallpox and influenza epidemics were a major issue in New World societies). These were unleashed at once upon New World societies.

It also suggests to us why adaptation seems to be occurring in the last few thousand years. Bouts of plague which persisted for generations may have driven immunological responses.

Kyle Harper also seems to agree with the general thesis in The Fall of Rome that this period in European civilization was in some ways proto-modern, with economic specialization resulting in a modicum of affluence in ways unimaginable in times before, or after. Trade and some level of mass production allowed British peasants to eat off tableware that was standardized, and not homemade. In contrast after Britain’s post-Roman regression a more local economy had to step in. The most curious fact from The Fall of Rome is that pollution in British ponds did not attain Roman levels until the early modern period, with the rise of industrialization. Again and again  The Fate of Rome emphasizes that social and economic complexity achieved in the Roman Empire was not attained in Europe again to the same scale as the early modern period.

Roman wealth was fundamentally due to the returns on scale and specialization that are the hallmark of Smithian growth. Though the Romans did invent a few things, Roman prosperity was not fundamentally driven by innovation. Rather, the Roman peace was a framework for trade and exchange that took advantage of abiotic clement conditions (the Roman climatic optimum highlighted in The Fate of Rome).

But this political system had biotic costs, as well as being subject to biotic shocks. Though Romans may have been wealthier than their Iron Age predecessors in things, and also wealthier than their early medieval successors, they were also a smaller people. Using isotope data Harper suggests that this is not due to Malthusian immiseration as the imperial population pushed up against food supply. Apparently Romans did not subsist on gruel alone, but ate a fair amount of meat, especially pork. Rather it was the high pathogen load enabled by the advancement of Roman urban life and its scale. Rome was a world of intense morbidity.

Unlike physical/abiotic forces biological/biotic pressures on human existence are adaptive. Moderns know this with the rise of antibiotic resistance, it’s the eternal race. The Romans were not aware of the consequences of their means of prosperity, and were not ready for the exogenous shocks of climate and disease which were to perturb their state system.

But The Fate of Rome is not just a story of exogenous factors, climate and disease. Rather, Harper puts into stark relief the variables which might push an empire over the edge, or eat into its seed corn of human capital. That does not negate the fact that endogenous variables matter. The Roman elite of the early centuries exhibited some level of asabiyyah, social cohesion. The Empire was fundamentally not a strong state in comparison to modern ones. It was a thin skein of cities and fortifications binding together an overwhelmingly rural population of villages. Its achievement of peace and prosperity was bound up in an ideology and identity focused project which bound together an elite (or bound together elites).

The origins of this elite were not always arbitrary. Though the Empire was famously cosmopolitan, The Fate of Rome crystallizes something that anyone who had sat back and thought about could see: certain groups bound the imperial state together as a ruling caste. Harper observes that between the reign of Claudius and Phocas, from 268 to 602, 75% of the Emperors were of Illyrian/Balkan stock. That is, 75% of the Emperors were drawn from 2% of the Roman Empire’s territory. The exception being the Theodosian dynasty, which was of Iberian origin and jumped into the breach after the defeat of Valens at Battle of Adrianople.

This is a fascinating fact in and of itself. Harper points out that these Emperors from the Danube frontier did not enrich their own region to the detriment of others. They were ideological heirs of the earlier Roman project, and their identity was as Romans first, Illyrians and Thracians of Latin stock second (or third, after Christianization). But they brought particular skills of administration and an overall martial attitude which served to lead the Empire through a period of greater stress than it had been subject to during the earlier climatic optimum.

The Fate of Rome does not plumb the depths of ideological and social change but emphasizes their interaction with biotic and abiotic factors. Harper observes that public temple building decreases sharply after the Cyprian plague. Why? Perhaps there was a loss of faith in the old religious institutions. Though popular paganism remained dominant, new elite religious ideologies such as the cult of the Invincible Sun and later Christianity came out of the shadows during this period.

These cultural and political aspects remain bit players and mostly offstage in The Fate of Rome. If you are interested in political narrative, then something like Peter Heather’s The Fall of the Roman Empire may be more to your taste. If culture, then Mary Beard’s SPQRBut ultimately social, political, economic, biological, and climatological factors are critical and interconnected. The rise of plague is hard to understand outside of the context of trade, which was enabled by political power and unity. Ecological factors may have driven Yerisina pestis out of its Central Eurasian reservoir, and those ecological factors may have been triggered by climatic variables.

The fall of Rome is a huge topic. I’m just glad that we’re beyond the revision of the previous generation which denied that it happened in the first place. The reason that it occurred is probably contingent in the details, though inevitable over the long-term. All things must end, even the Roman peace.

* This is not totally true, but over the time-scales we’re talking about probably mostly true.

The bourgeoisie baby blues


There are those instances when you see a plot that resonates with your experience so much that you don’t need to say anything. You just share it. Those who know, know. Those who don’t know, won’t know until they are in a position to know.

Median household income in the United States today is $59,000. “Household” is a broad category. All families are households, but not all households are families. The median family income is $72,000. If the plot above is correct households in the bottom 25% and somewhere in the top 1% are above demographic replacement. The 1% cut-off is $430,000, and from what I can tell poking around the households making $1,000,000 per year are probably the 0.1%. In other words, between the 75th percentile and 0.10% percentile Americans are below replacement in total fertility.

There is a particular trough between $50,000 and $250,000. From the core of the middle class into the heart of the upper middle class.

From $50,000 a year household income of $250,000 a year may look comfortable, but these are the children of Epictetus. The modern world is filled with those who lack freedom but live with some modicum of comfort, as well as avenues for leisure and self-cultivation. But freedom is reserved for capital, in particular, those with a lot of liquid capital.

It is a truth universally acknowledged that a slave with a substantial income remains but a slave at the end of their days. Their comforts persist only at the sufferance of those who have inherited or grasped their freedom.

 

The peoples of the Maghreb have some Pleistocene roots

Moroccan Berber man

The Maghreb is an important and interesting place. In the history of Western civilization, the tension between Carthage, the ancient port city based out of modern-day Tunisia, and Rome, is one of the more dramatic and tragic rivalries that has resonances down through the ages. Read Adrian Goldsworthy’s chapter on the Battle of Cannae in The Punic Wars for what I’m alluding to (and of course there was Cato the Younger’s dramatic remonstrations).

Later Roman Africa, which really encompassed northern Morocco, coastal Algeria, and Tunisia and Tripolitania, became a major social and economic pillar of the Imperium. Not only did men such as the emperor Septimius Severus and St. Augustine have roots in the region, but these provinces were a major economic bulwark for the Western Empire in its last century. The wealthy Senators of the 4th and 5th century were often absentee landlords of vast estates in North Africa. The fall of these provinces to the Vandals and Alans in the 430s began the transformation of the Western Empire based in Rome into a more regional player, rather than a true hegemon (perhaps an analogy here can be made to the loss of Anatolia by the Byzantines in the 11th century).

Another important aspect of North Africa is that it is the westernmost extension of the region possibly settled by Near Eastern farmers in Africa. The native Afro-Asiatic Berber languages seem to have been dominant in the region despite the influence and prestige of Punic and Latin in the cities when Muslim Arabs conquered the region in the late 7th century. The genetic-demographic characteristics of the region are relevant to attempts to understand the origins of the Afro-Asiatic languages more generally since Berber is part of the clade with the Semitic languages.

A preprint and a paper utilizing ancient DNA have shed a great deal of light on these questions recently. The paper is in Science, Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. The preprint is Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. They are in broad agreement, though they cover somewhat different periods.

The figure below is the big finding of the Science paper:

They retrieved some genotypes from a site in northern Morocco, Taforalt, which dates to ~15,000 years before the present. This is a Pleistocene site, before the rise of agriculture. The Taforalt individuals are about 65% Eurasian in affinity, and 35% Sub-Saharan African. This confirms that the Eurasian back-migration to northern Africa predates the Holocene, just as many archaeologists and geneticists have reported earlier.

The samples from the preprint date to a later time. IAM in the samples dates to 7,200 years before the present, and KEB to ~5,000 years before the present. It seems pretty clear that the IAM samples in the preprint exhibit continuity with the Taforalt samples. Though it is not too emphasized in the preprint the lower K’s seem to strongly suggest that the IAM samples have Sub-Saharan African ancestry, just like the Taforalt samples which are nearly 8,000 years older. In the KEB samples, the fraction drops, probably diluted in part by ancestry related to what we elsewhere term “Early European Farmer” (EEF), related to the Anatolian farming expansion.

Both the Taforalt and IAM samples, in particular, seem to exhibit strong affinities to Natufian/Levantine peoples. Additionally, many of these samples carry Y chromosome haplogroup E1b, just like some of the Natufians. These results indicate that the Natufian-North African populations were exchanging genes or one cline rather deep in the Pleistocene.

Though various methods have suggested that there is a lot of recent Sub-Saharan African admixture, dating to the Arab period, in North Africa, these results suggest that much of it is far older. The Mozabites, as an isolated Berber group, reflect this tendency. Though some individuals have inflated African ancestry due to recent admixture, much of it is older and evener. And yet the Mozabites seem to have less Sub-Saharan African ancestry on average than the IAM sample.

There aren’t enough data points to make a strong inference about the temporal transect, but these few results imply a decline in Sub-Saharan ancestral component after the Pleistocene with further farming migration, and then a rise again with the trans-Saharan slave trade during the Muslim period. Another issue, highlighted in the preprint, is likely heterogeneity within the Maghreb in ancestry (lowland populations in modern North Africa tend to have more Sub-Saharan ancestry due to where slaves were settled).

In the Science paper the authors make an attempt to adduce the origin of the Sub-Saharan contribution to the Taforalt individuals. The result is that there is no modern or ancient proxy that totally fits the bill. These individuals have affinities to many Sub-Saharan African populations.  The Sub-Saharan component is likely heterogeneous, but attempts to model European genetic variation during the Ice Age ran into trouble that divergence from modern populations was quite great. Until we get more ancient DNA there probably won’t be too much more clarity.

On the issue of the Eurasian ancestry, it’s clearly quite like the Natufians. But curiously the authors find that the Neanderthal ancestry in these samples is greater than that found in early Holocene Iran samples. From this, the authors conclude that they may have had a lower fraction of “Basal Eurasian” (BEu) than those populations further to the east. But already 15,000 years ago BEu populations were mixed with more generic West Eurasians to generate the back-migration to Africa. If BEu diverged from other Eurasians >50,000 years ago, then it may have merged back into the “Out-of-Africa” populations around or before the Last Glacial Maximum, ~20,000 years ago.

Finally, the authors looked at some pigmentation genes. Curiously the Taforalt and IAM individuals did not carry the derived variants for pigmentation found in many West and South Eurasians, but the KEB did. This confirms results from Europe, and population genomic inference in modern samples, that selection for derived pigmentation variants is relatively recent in the Holocene.

I do want to add that one possibility about the Sub-Saharan ancestry in the Taforalt, and probably all modern North Africans to a lesser extent, is that it is ancient and local. We now know proto-modern humans were present in the region >300,000 years ago. Northwest Africa may have been part of the multi-regional metapopulation of H. sapiens, as opposed to the Eurasian biogeographic zone that it is often placed, before a post-LGM back migration of Eurasians.

Open Thread, 5/07/2018

Longtime readers are well aware that A History of the Byzantine State and Society is one of my favorite books. To understand the Middle East right before the arrival of the Mongols and the emergence of the Crusader states, one has to understand the expansion of Byzantium in the early 11th century, and its subsequent regression in the late 11th and 12th centuries. In 2005 I actually did a 10 questions with the author, Warren Treadgold.

So I’m very excited to be reviewing his new book, The University We Need: Reforming American Higher Education, for NRO.

Had a chance to read Matt Hahn’s Molecular Population Genetics. The con is that it’s an $80 book that’s 350 pages. This is not a replacement for Principles of Population Genetics or Introduction to Quantitative Genetics. Rather, as alluded to by the title there’s a lot of focus on molecular evolutionary and population genetics. Imagine a population genetics book written with an assumption that you know what a SNP-chip is and have access to genome-wide sequence data. In some ways, it’s similar to Rasmus Nielsen’s (and Slatkin) An Introduction to Population Genetics. But these books reflect the authors.

For example, if you look up “site frequency spectrum” in An Introduction to Population Genetics there are seven pages. In Molecular Population Genetics there is one page on this topic. Anyone familiar with the work of these researchers would totally expect this. If you are a pop-gen nerd, there’s really no debate. You need to get Molecular Population Genetics or steal it from a friend. But a bigger question is why I recommend seemingly esoteric books to my readers. I say seemingly because understanding population genetics in the generality makes a lot of the detailed more specifically interesting stuff much more comprehensible.

The readership of this weblog is small but self-selected. If you consider yourself an intellectual person and have some disposable income and leisure you should be developing yourself in various ways outside of the professional sense.  If you are reading this weblog you are likely to be the type of person who wants to understand things not just because one gets paid to understand things, but because understanding things is an end unto itself.

I am privileged to be paid to explore various topics related to certain intellectual interests (human population genomics), but I believe that something would be seriously wrong with me if I limited my inquiries to this narrow topic. Therefore I read a fair amount of history, and take an interest in topics like cognitive science and Biblical scholarship. Part of my attempt on this weblog to is to add population genetics to the list of interests of people who are professionally not engaged with the topic, whether they be in closely related fields (e.g., a theoretical ecologist) or in a totally different line of work (union organizer).

The Neutral Theory in Light of Natural Selection. This review is free. One of the great things about this is that it kind of revived a corner of science Twitter which had started to go into senescence (Patrick Phillips has been at the center of several of these discussions).

Related to our podcast topic from this week, Doc Edge and Graham Coop have the definitive formal take, How lucky was the genetic investigation in the Golden State Killer case? The TL;DR version is not that lucky. They show formally that with a database of ~1 million individuals with SNP-data it’s likely that you’ll get relative matches that might be useful. More precisely, a database of ~1 million means that there is a ~90% chance of at least one 3rd cousin match. There’s even a 25% chance of a 2nd cousin match! A database of ~5 million gives a 75% chance of a 2nd cousin match, and ~10 million gives a 90% chance of a 2nd cousin match. These are around the range of the databases of 23andMe and Ancestry right now.

As the authors say: “it’s a question of deciding the circumstances under which we as a society want these familial searches to be used.”

Tales of Human Migration, Admixture, and Selection in Africa.

The evolutionary history of human populations in Europe. Preprint by Iosif Lazaridis.

There are a certain number of traditional liberals with a libertarian bent who I’ve always admired. Nadine Strossen is one of those (Wendy Kaminer is another). Strossen is out with a new book, HATE: Why We Should Resist It with Free Speech, Not Censorship (Inalienable Rights). It strikes me this is conservative in the literal sense in that she is attempting to defend a late 20th-century liberalism which is now on the wane.

The Liberal Media Can Have Ideological Diversity Without Conservatives. Two sections jump out at me. First, “the social conservative’s view on fetal personhood is unfalsifiable — and does boast a significant constituency — but it doesn’t generally lend itself to novel or engaging debates.” The issue with abortion is not about debating, as much as it is important to not always put forward writers who implicitly assume that the pro-choice position is the only view that one might entertain. I’m skeptical of some of the leaps that pro-life writers make based on their political position…but then, I’m not pro-life. It’s important to at least know the views of other people.

Second, the author suggests that Left-wing socialists who believe that the people should control the means of production (as opposed to simply redistributive socialism as is the case in Scandinavia) should be given a fair hearing, though they observe “concentrating financial power in the state apparatus has often been an invitation to tyranny.” Yeah. That.

Pretty straightforward establishment liberals, such as Matt Yglesias, are starting to assert that publications like The Atlantic and The New York Times are equivalent to National Review, in their ideological valence (the argument being that they shouldn’t have to hire conservatives since they’re liberal publications). Conservative critics have long asserted this, but now liberals are agreeing.

Conservatives have lost the universities and the press. Both these institutions don’t even make a pretense at evenhandedness at this point. The broadly liberal center is eroding. I suspect that people like Nadine Strossen will be viewed in the future like Cato the Younger.

Stuff You Missed in History Class podcast, Mohenjo Daro. People don’t really know much.

Interviewing Carl Zimmer for the podcast this week. Taking suggestions for questions to ask him (we have a finite time so might not get it in….)

 

The Insight, Episode 19: Roberta Estes, the Golden State Killer, and forensic genetics


Last week Spencer & I took a break from The Insight. We’re at 71 iTunes ratings. I would appreciate it if readers of this weblog could help us make it to 100 (then I’ll stop pestering you). Also, we only have 5 reviews on Stitcher.

This week we’re talking to Roberta Estes about the arrest of the suspect in the “Golden State Killings”. We kind put this together really quickly since it seemed relevant, and Roberta, Spencer and I have some competency in this area (we’ve all been talking to science journalists). The biggest takeaway from our conversation is that we were a little surprised that it took this long to apply 21st century genomics to forensics.

When I first heard about the arrest I told my wife that it probably was due to a relative match on something like GEDMatch. After the media reported that it was a “new method” I dismissed my supposition because relative matches aren’t a new or novel thing. Well, it turned out that’s exactly what they were talking about!

A lot of the story here is how law enforcement snapped a bunch of pieces together that were out there. The horse has left the barn, and everyone is trying to figure out how to deal with it.

Hui have a lot of West Eurasian Y chromosomes

O C R1a R1b R2 E1b G H I1 I2 J1 J2 L N Q T Total N
Han 258 12 2 2 2 1 1 2 1 1 7 9 2 300
Hui 24 7 21 1 9 1 3 1 1 4 1 11 1 3 14 4 106
Tibetan 49 11 18 1 1 3 3 3 3 7 1 100

It’s been a while since I checked in on the genetics of the Hui people. I found the paper, Analysis of 17 Y‐STR loci haplotype and Y‐chromosome haplogroup distribution in five Chinese ethnic groups. About 50% of the Y chromosomal haplogroups are normally classified as “West Eurasian” (R, E, G, I and J). But curious a fraction of the Han have these too, as do some Tibetans.

Additionally, know that some Mongols also have R1a1a. It’s hard to differentiate different periods of admixture. But to me the presence of R2 and J2 point to a Central/South Asian origin of a lot of the Hui R1a as well.

Is American genetic diversity enough?


In the nearly 20 years since the draft of the human genome was complete,* we’ve moved on to bigger and better things. In particular, researchers are looking to diversify their panels of human genetic diversity, because of differences between groups matter. You can’t just substitute them for each other genetically.

There have been efforts to diversify the population panels recently, but that prompts the question whether American population coverage is sufficient. My first thought is that the genetic diversity in the USA is probably getting us 90% of the way there. Consider Spencer’s comment about Queens, it’s the most ethnically diverse large conurbation in the country.

There are some gaps though. In Who We Are David Reich points out the distinctiveness of Indian population genetics. The subcontinent has lots of large census populations which have drifted upward deleterious alleles due to long-term endogamy. And, many of these populations don’t have a strong representation in the Diaspora.

In contrast, much of the rest of the world is panmictic enough that an American panel can pick up most of the variation. American Chinese are skewed toward Guandong and Fujian, but a substantial number of people from other parts of China have arrived in the last generation. Regional structure is not so strong that you’ll miss out on too much, aside from very rare variants which are more extended pedigree scale rather than population scale.

There are small populations such as Hadza, Khoikhoi, and Pygmies in Africa which are probably going to be missed by American population panels, but the total census size of these groups is pretty low (for comparison, there are 1 million Pulayar Dalits in the state of Kerala alone). Much of the rest of Africa is West African variation well represented in African Americans, and Bantu and Nilotic variation probably captured my immigrant communities.

I’d propose supplementing American genetic diversity with sampling Cape Coloureds in South Africa.

* No discussions about how the genome isn’t totally complete. I know that.

Open Thread, 04/29/2018

One of the strange things about getting old is that your friends start to become kind of a big deal. Matthew Hahn has a new book out, Molecular Population Genetics. If there is one single reason I keep blogging, it’s to get awareness of the field of population genetics to spread beyond the small circle who are “in the know.” I joked on Twitter that buying this textbook is like spending money to talk to Matt about pop-gen, and that’s surely worth it.

Another one for the stack!

Speaking of worth it, Kyle Harper’s The Fate of Rome: Climate, Disease, and the End of an Empire is definitely worth a read. Not done, and I’m not sure it’s better than The Fall of Rome: And the End of Civilization. Perhaps my issue is that exogenous shocks are to be expected in my view of the world. Though the details in The Fate of Rome are novel, the general thesis and framework were what I’d assumed were taken for granted.

What Happens When Geneticists Talk Sloppily About Race. I don’t think that David Reich was sloppy…though the op-ed was edited in a way that was confusing. That being said I’ve heard through the grapevine that some prominent human population geneticists may write a response to David’s op-ed, which is something I want to see. Part of me still thinks that these vigorous public discussions are important (another part of me just thinks that when Sulla or Marius take over all this old-fashioned fixation on truth will be irrelevant).

One thing stated in the piece above is that regular people have a Platonic model of race. This is true. But it is also a fact that geneticists have not done a good job of explaining to the educated public what population structure is, and why it’s not trivial or arbitrary. I know this from personal experience over 15 years interacting with people about genetics online (some of the funniest interactions are on Facebook where a person of professional class background/status “genetics-splains” me about how I don’t understand the extent [lack] of human genetic variation and how arbitrary population cluster identity is).

With The Genomic Formation of South and Central Asia I obviously think we have the broad outlines of the peopling of South Asia in hand. There will be lots of detailed elaborations of how/what happened, but I think the big picture is nailed down.

That being said some of the objections remind me a lot of Creationist tendencies. Creationists often focus on weak points and hammer in on them over and over.

One of the weird things about Indian genetics is that a lot of people think new research will overturn Hindu nationalism. But I know several Hindu nationalists, and privately they tell me that most Hindu nationalists don’t care about these abstruse issues, and many of the more intellectual ones don’t have a major problem with the science.

GEDmatch, Ysearch and the Golden State Killer.

Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.

Bracketing phenotypic limits of mammalian hybridization.

A few people have asked about the podcast. We skipped a week, but we’ll be back. Taking some feedback in relation to various aspects of the show. A common issue seems to be that my voice is too quiet though Spencer’s is “just right.”

Again, if you use Stitcher or iTunes please remember to give us positive reviews and 5-stars!

If you have ideas for shows, we’re game.

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.

Rakhigarhi sample doesn’t have steppe ancestry (probably “Indus Periphery”)

We’ve been waiting for two years now, and it looks like they’re about to pull the trigger, Indus Valley People Did Not Have Genetic Contribution From The Steppes: Head Of Ancient DNA Lab Testing Rakhigarhi Samples:

Niraj Rai, the head of the Ancient DNA Laboratory at Lucknow’s Birbal Sahni Institute of Palaeosciences (BSIP), where the DNA samples from the Harappan site of Rakhigarhi in Haryana are being analysed, has revealed that a forthcoming paper on the work will show that there is no steppe contribution to the DNA of the Harappan people….

“It will show that there is no steppe contribution to the Indus Valley DNA,” Rai said. “The Indus Valley people were indigenous, but in the sense that their DNA had contributions from near eastern Iranian farmers mixed with the Indian hunter-gatherer DNA, that is still reflected in the DNA of the people of the Andaman islands.” He added that the paper based on the examination of the Rakhigarhi samples would soon be published on bioRxiv (pronounced “bio-archive”), a preprint repository of papers in the life sciences.

At this point none of this is surprising. I also wonder if this preprint was hastened by the release of The Genomic Formation of South and Central Asia. It seems that the results here are totally consonant with what came before. My expectation is that the lone sample that they got genetic material out of will be similar to the “Indus Periphery” (InPe) individuals in the earlier preprint: a mix of West Asian with ancestry strongly shifted toward eastern Iran, and indigenous South Asian “hunter-gatherer.”  That’s pretty much what Niraj Rai states in the piece. I think genetically the individual won’t be that different from the Chamars of modern day Punjab.

In fact, Rai, the lead researcher, ends by twisting the knife:

In other words, the preprint observes that the migration from the steppes to South Asia was the source of the Indo-European languages in the subcontinent. Commenting on this, Rai said, “any model of migration of Indo-Europeans from South Asia simply cannot fit the data that is now available.”

A major caveat here is that we’re talking about one sample from the eastern edge of the Indus Valley Civilization (IVC). I’m not sure that this should adjust our probabilities that much. From all the other things we know, as well as copious ancient DNA from Central Asia, our probability for the model which the Rakhigarhi result aligns with should already be quite high.

Again, since it’s one sample, we need to be cautious…but I bet once we have more samples from the IVC the Rakhigarhi individual will probably be enriched for AASI relative to other samples from the IVC. The InPe samples in The Genomic Formation of South and Central Asia exhibited some variation, and it’s likely that the IVC region was genetically heterogeneous.

But, this is going to be a DNA sample from an individual who lived 4,600 years ago within the orbit of the IVC when it was in its mature phase. That’s still a big deal. As most of you know the IVC is prehistory because we haven’t deciphered the seals which are associated with this civilization. But, the IVC clearly had relationships with West Asia and Central Asia, with parts of eastern Iran and the BMAC culture both being influenced and interaction with it. Traders who were likely from the IVC seem to be mentioned in Mesopotamian records.

Additionally, the genetics of one individual can be highly informative if it’s high-quality whole-genome data (I’m skeptical of that in this case). One could possibly even identify the time period that admixture between West Asian and AASI components occurred from a single genome, by looking at ancestry tract lengths.

A single sample isn’t going to falsify the idea held by some that steppe peoples were long present within the IVC. Perhaps they’ll show up in other samples? That’s possible, and it’s what I would argue if I held their position, but I think the constellation of evidence on the balance now does suggest that a relatively late incursion into South Asia is likely. The steppe ancestry with Northern European affinities shows up in BMAC only around 4,000 years ago. It is hard to imagine it was in South Asia before it was in Central Asia.

As I’ve been saying for a while it seems that though there will be more genetic work written on India in the near future, the real analysis is going to have to come out of archaeology and mythology.

It’s pretty clear that in Northern Europe the arrival of the Corded Ware peoples from the steppe zone resulted in great tumult. A linguistic analysis suggests that the languages of Northern Europe have words related to agriculture with a non-Indo-European origin, of common provenance.  But we don’t have much in the way of mythos about the arrival of the Corded Ware.

In contrast, India has a rich mythos which seems to date to the early period of the arrival of the Indo-Aryans. One interpretation has been that since these myths seem to take as a given that Indo-Aryans were autochtonous to India, they were. But the genetic data seem to be strongly suggesting that the arrival of pastoralists occurred in South Asia concomitant with their arrival in West Asia, and somewhat after their expansion westward into Europe. Indian tradition and mythos could actually be a window into the general process of how these pastoralists dealt with native peoples and an illustration of the sort of cultural synthesis that often occurred.