Razib Khan One-stop-shopping for all of my content

June 24, 2017

Indian genetics, part n of many

Filed under: ancient india,History,Indo-Europeans — Razib Khan @ 2:59 pm

I put up close to definitive piece for me in relation to South Asian historical population genetics. At least until new research is published. I did leave out some stuff about my own vague thoughts…but I think the takeover of Hattian and Hurrian cultures by the Nesha (Hittites) and Haryannu (Mitanni) have something to teach us….

Indian genetic history: before the storm

Filed under: Genetics,History,India — Razib Khan @ 2:52 pm

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 misinterpreted by those who Google you, and watch how much you value the objective “truth-telling” power of the press.

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 further 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 Indian 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 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 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 divers 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 one they are supporting within the paper.

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 most “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 expands 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 haven’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).

June 18, 2017

The Finnic peoples emerged in Baltic after the Bronze Age

Filed under: Finland,History — Razib Khan @ 10:07 am


A reader in the comments reminds me there has been a preprint which is relevant to the population structure of Baltic Europe which came out a few months ago, Extensive farming in Estonia started through a sex-biased migration from the Steppe:

…Here we present the analyses of low coverage whole genome sequence data from five hunter-gatherers and five farmers of Estonia dated to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic Culture are closest to Eastern hunter-gatherers. The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with Steppe Belt Late Neolithic/Bronze Age individuals, Caucasus hunter-gatherers and Iranian farmers while their X chromosomes are most closely related with the European Early Farmers of Anatolian descent…

As you can see in the PCA plot above the Comb Ceramic Culture and the Corded Ware culture in Estonia are modeled well by the three ancestral populations hypothesis for Europe. The problem with this is that Finns and Russians with Finnic background do not fit with this model. There has been clear later gene flow.

From the text:

Interestingly, modern Estonians showed a bigger proportion of the blue component [associated with European hunter-gatherers] than CWC individuals. Comparing to CCC individuals, modern Estonians lack the red component [Eastern Siberian]. This, together with the absence of Y chromosome hg N in CCC and CWC, points to further influx and change of genetic material after the arrival of CWC.

The sample sizes are small. Additionally these are from Estonia, not Finland. But the Comb Ceramic Culture was widespread throughout the region.

Also, from a 2015 paper (supplements):

Among the northern Europeans, the Finnish (finni3) show evidence of an admixture event involving a minority source most similar to contemporary North Siberians (469CE (213BCE-1011CE)). Finns are thought to have originated from the northward migration, and subsequent contact, between Central Europeans and indigenous Scandinavian hunter-gatherers closely related to the Saami [S33]. The Saami are closely related to the individuals that make up the North Siberian world region, and whilst our confidence in this admixture date is low because of the small size of the cluster, the event we see is likely to represent this key period in Finnish history.

The “North Siberia” cluster are: Selkup, Chukchi, Dolgan, Ket, Koryak, Nganassan, Yakut and Yukagir. The admixture is very recent. I suspect too recent. But it gets us to the qualitative point that the Siberian admixture into Finns is probably not that old.

Related: The Origin of the Finnic Peoples.

June 17, 2017

The origin of the Finnic peoples

Filed under: Finland,History — Razib Khan @ 8:13 pm

 

One of the very first things I wrote about in relation to historical population genetics was in on the origins of the Finnic peoples. The reasons are two fold:

– first, the Finns and Estonians speak language is rather peculiar in a Europe dominated by Indo-European tongues (I suspect one reason that Tolkien based Quenya, the high elvish language, on Finnish is that it is so otherworldy to the Germanic ear. The Sindarin language, which was the common tongue of elves in Middle Earth, was based on Welsh). Rather, the distribution to the Uralic languages extends to the east, as far as Siberia. Even the closest affinities to Finnish and Estonian extend eastward, as there are Karelians who live deep in northwest Russia.

– second, there were peculiarities in the genetics of the Finns which date back to the 20th century that have always been notable.

Some of the distinctiveness of the Finns clearly has to do with the demographic isolation of the recent past, and the range expansion into the north and east. I will ignore this aspect of recent drift, and focus on their deep history and phylogenetic relationships.

New molecular genetic techniques in the 1980s and 1990s which enabled the genotyping of Y and mtDNA lineages immediately yielded the fact that the paternal heritage of the Finns is very unique in comparison to their neighbors, and erstwhile hegemons, the Scandinavians. While Swedes tend to be haplogroup I (indigenous to Western Europe dating to the late Pleistocene) or one of the two R1 lineages (intrusive from the Eurasian steppe during the Bronze Age), Finns tend to be haplogroup N3, with a substantial minority of I. While 63 percent of Finns are N3, only 3 percent of Swedens are. Due through the reality of migration of Finns to Sweden, as well as the prevalence of Saami all across Northern Sweden until the early modern period, Swedish N3 may be due to gene flow in the last thousand years. The two R1 lineages are ~10% of the Finnish paternal gene pool, they’re strongly skewed toward R1a, while the ~40% of Swedish R1 lineages are balanced.

In contrast the mtDNA profiles of Finns are very similar to their neighbors. Like Sweden the dominant haplogroup is a branch of H, with the reduced fraction accountable for the fact that Finns have a higher percentage of U5, which has been associated with European hunter-gatherers. The various haplogroups (e.g., T) associated with Early European Farmers are at somewhat lower frequency in Finland than Sweden.

A simple explanation then presents itself to us: the Finns have been subjected to male mediated admixture into a “conventional” European substrate. But there has been long been controversy as to whether the Finnish N3 haplogroup was indigenous to Europe, or its presence in Northeast Europe was due to migration. If it was indigenous than the admixture model does not make as much sense. But as with many things we’ve moved very far in comparison to where we were when I first began to look at this issue in 2002.

If you read Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families the likelihood than the Y chromsomal structure of Finland is old seems low. First, Finnish N3 lineages are very young and underwent rapid expansion beginning 4 to 6 thousand years ago (this is evident in their whole genome variation pattern). Second, the most diversity of N seems to be in Western Siberia. Third, N exists in higher frequencies in parts of Siberia than even in Finland. Fourth, the range of N pushes it all the way to the Pacific Ocean. It is not implausible that it expanded from one rim of Eurasia to the other, but the most likely scenario is that it came from somewhere in the middle.

Also, it is likely that there has been admixture into Finns from an East Eurasian population. To give some examples, a derived SNP at EDAR is at very high frequency in Northeast Asians. The ancestral variant is dominant outside of East Asia and the New World. In Europe among modern Europeans the derived variant of EDAR is not present in indigenous populations. A quick check in the 10000 Genomes data shows that it’s at ~6% in Finns (in contrast, the ancestral variant of SLC24A5 is present at frequencies of ~1; this could be random, but I suspect in situ selection….). You can see that the derived variant is absent in a rather large sampling of other Europeans.

Running ADMIXTURE unsupervised it’s immediately obvious that Finnic peoples have a minority component of East Eurasian admixture. This dark blue element is absent in most of the Swedes. Not surprisingly the Russians exhibit structure depending on where you sample. Some Russian populations are clearly Slavicized relatively recently, and exhibit a genetic profile rather like Finnic peoples (this northern Russian regions also have high frequencies of haplogroup N, which is much rarer in the south or among Ukrainians).

There’s a cline that runs east to west in relation to this component. The Finn’s neighbors immediately to the east, Karelians and Veps, have a higher fraction than the Finns proper. Additionally, some Finns in the data seem to lack it totally. One might speculate that these are people of Swedish origin who eventually assimilated to the Finnish identity. This is not impossible. In the 19th century Finnish nationalism was sparked in large part by middle class activists, many of whom were Swedish ethno-linguistically due to the connections between class and language at that time. But these individuals may be evidence of older structure in Finland. More on that later.

I also ran some Treemix on a subset of the data. You see there is gene flow coming into the Finns from a Siberian group. I used Nenets (a group of Samoyeds) and Yakut because the former have more linguistically in common with the Finns, while the latter are used by companies like 23andMe (Yakuts are the most northeasterly Turkic people). Strangely the Karelians and Veps get gene flow from Nenets, while the Finns get it from Yakuts (I pruned with PCA and ADMIXTURE to remove individuals with recent European ancestry).

But the model of a single pulse admixture is probably wrong anyhow. Rather, the spread of Finnic hunters and gatherers may have gradual, and/or occurred in several pulses. On the fringe of Northern Eurasia local extinctions were probably common. The landscape of Northern Eurasia, from the Baltic to Siberia, may long have been rather dynamic, with interactions between Uralic, Indo-European and Altaic peoples.

At this point I am at a loss. The archaeology of Finland is not something I know well, and the academic literature is hard for me to track down. Some scholars believe that the Comb Ceramic Culture plays a major role in the ethnogenesis of the people we call Finns. During the Bronze Age the Corded Ware zone spread into southern Finland, bringing agriculture. The fusion between the Comb Ceramic and Corded Ware led up to the societies which are first mentioned by Classical authors.

Finland was always liminal to early agriculture, and the Corded Ware Indo-Europeans may eventually have given away to the forest Finns as the climate turned more difficult. The predominance of N3 haplogroups may be a function of the nature of patriarchal societies, where certain lineages maintain powerful long term advantages.

June 15, 2017

The system of the world by William H. McNeill

Filed under: History — Razib Khan @ 9:13 pm

In the post below on book recommendations I forgot to mention William H. McNeill and John Robert McNeill’s The Human Web: A Bird’s-Eye View of World History. It’s arguably been one of the most influential works that has percolated in my mind throughout the years. It’s less than 400 pages, and illustrates in broad sketches that history has been through many random shocks, but that there are broad patterns that one can discern.

The elder McNeill is most famous for The Rise of the West and Plagues and Peoples. To a great extent he was Jared Diamond before there ever was Jared Diamond.

Unfortunately I did not notice that McNeill died last summer. From his obituary:

Refuting Francis Fukuyama’s premise in “The End of History and the Last Man” in 1992 that the American model of a liberal, capitalist democracy had become the paradigm for governance, Professor McNeill wrote in The New York Times Book Review: “I do not believe that human nature is uniform and unchanging. Rather, whatever penchants and capabilities we inherit with our genes are so malleable that their expression takes infinitely diverse forms.”

“When Asian models of social and economic efficiency seem to be gaining ground every day, and when millions of Muslims are at pains to sustain the differences, great and small, that distinguish them from Americans,” he continued, “it is hard to believe that all the world is destined to imitate us.”

June 12, 2017

Books I suggest you read so you won’t be misled as often

Filed under: History — Razib Khan @ 9:29 pm

People often ask me for history books on a very specific topics often, assuming I’ve read something on an issue because I exhibit some fluency discussing something that might seem abstruse or arcane. The thing is that I haven’t always read a monograph on a singular topic even if I know a fair amount on it. It’s just that I’ve read a larger number of history books, so the union of my knowledge set is quite wide and expansive.

For example, in reading The Myth of the Andalusian Paradise the author recounts with some tinge of outrage that North Africa, which is had been predominantly Christian since the early 4th century, was conquered by the Muslims in the late 7th century as a prequel to the conquest of the Visigothic kingdom in Iberia (I knew the loss of Carthage occurred between Justinian II’s two reigns thanks for the fine historical novel Justinian!). First, the tinge of taking sides is kind of adolescent in my opinion and detracts from the narrative, though that’s a matter of personal taste. Second, North Africa was not majority Christian in the early 4th century.

No, I’ve not read specifically about North Africa Christianity (aside from a few books here and there about St. Augustine, who was North African and a Christian). Rather, I have read The Making of the Christian Aristocracy, which addresses the religious change in the Roman Empire in the 4th century, as well as works such as Through the Eye of a Needle: Wealth, the Fall of Rome, and the Making of Christianity in the West, 350-550 AD, where religious change is a theme if not a central one (I would say that really it is a book with a greater focus on material culture and politics and economics than religion as such). Additionally, it is clear that many people confuse Constantine’s toleration and then later espousal of Christianity under a united Roman Empire in 325 as the point at which Christianity became the official religion of the state. An “official state religion” in a modern sense is an anachronism. It took decades for the customary subsidies to the pre-Christian traditional cults to cease (that really occurred in earnest under Gratian in the 380s), with elite public paganism’s coup de grace occurring under Theodosius in the 390s (paganism persisted as a counter-culture down to the early 6th century, and it seems very likely that some pagan philosophers were still present in Alexandria up to the Arab conquest, while the Syrian city of Haran maintained a pagan religious culture with an appreciation for Hellenic religious values down to the 10th century A.D.).

In any case, what books should you read? It’s useful to read big general surveys because they allow you to frame and interpret narrower monographs. Long-time readers are aware that I am a big fan of Warren Treadgold’s History of Byzantine State and Society. This survey is expansive. And, it touches upon many of the different peoples who interacted with Byzantium. You should read it.

Next I would recommend Albert Hourani’s A History of the Arab Peoples. To a great extent this is a history of Islamic civilization. If you want more specificity on early Islam, try Hugh Kennedy’s When Baghdad Ruled the Muslim World. For later Islam, Osman’s Dream. But really should read some survey first before drilling down to a specific epoch or region.

For China it has to be John King Fairbank and his China: A New History. If you want something more accessible, John Keay’s China: A History is where you want to go. Division by periods is important in China though. For a little more specificity, The Early Chinese Empires: Qin and Han is good. Obviously there are books which cover the later dynasties, but the Qin and Han are really the hinges of Chinese history, and essential supplements to any survey. For a book which explores how China related to the rest of the world with a light theoretical touch I’d suggest Adshead’s China in World History.

For India I would recommend Romilla Thapar’s A History of India: v. 1. This recommendation will raise many peoples’ hackles because Thapar is accused of being biased and ideological, and she probably is. But if you keep that in mind usually you will survive. John Keay also has a book on this Asian civilization, India: A History. Again, it is really aimed at the general lay reader at a very middle-brow level. But if that’s where you think you need to start, that’s how it goes. If you want a very dramatic narrative focused on biography then The Peacock Throne does an OK job in relation to Mughal India, which is to a great extent a formative period to understanding modern India.

For Southeast Asia I don’t have any suggestion aside from Strange Parallels. This will leave a lacunae for maritime Southeast Asia, which is a pretty big blind spot. I did read The History of Indonesia about 10 years ago, but that book was strongly biased toward modern periods. Reader suggestions welcome.

At some point we need to loop back to Europe, and Rome before Byzantium. For this Michael Grant is really a good resource for surveys. His History of Rome is an A-Z review from legendary times to the fall. It’s old and probably out of print, but usually you can find library copies, or paperback used versions somewhere.

Speaking of the fall though, if you haven’t read The Fall of Rome: And the End of Civilization, please do so. I know many of you have already read this book, but it’s really a major work. I can’t emphasize this enough. It makes history more than just interpretation because of its utilization to material metrics.

When it comes to Greece, I’m in a peculiar position. Much of my reading of ancient Greece was done in my elementary school years. So a lot of it is fuzzy and I don’t recall specific books, though I know enough about the travesty of the Sicilian expedition or the futile resistance against Philip of Macedon to follow broad sketches. Honestly I need to read something about this topic, in fact several books, as a grown ass adult.

I’ll recommend Grant again, with The Classical Greeks.

For the Hellenistic period that spans the gap between the rise of Rome and the decline of Classical Greece, Alexander to Actium should do the trick. But that’s a long book, and the same author has more recently published The Hellenistic Age: A Short History. That’s probably a better bet for many readers.

One book I am somewhat partial to is Robin Lane Fox’s The Classical World, which is a really broad work which has many topics it doesn’t touch. But Fox is a really great historical writer, so with consideration for its shortcomings (it’s not a straight ahead survey), I think some readers might enjoy it.

Since I’ve hit Athens, what about Jerusalem? Norman Cantor’s The Sacred Chain is a history of the Jewish people. I read it in 1995, so I don’t know exactly that it’s the most up to date work, but there is surely goodness in it still.

If you want to focus on the cultural tension between Jew and gentile, then Rome and Jerusalem might be of interest. It’s probably too narrow focus for what I’m recommending here…but it’s a good book so I thought I had to mention it.

In regards to post-Rome but the proto-West, Europe in the High Middle Ages is good. Chris Wickham’s Medieval Europe is a bit too focused on the author’s materialist hobby-horses in my opinion for the naive reader (e.g., not enough about the Cluniac Reforms).

A little earlier than that, I think Peter Heather’s work is probably sufficient. First, Empires and Barbarians, and then the Restoration of RomeEmpires and Barbarians is easily the better book if you had to pick one.

Perhaps you want to jump back to the edge of history, A History of the Ancient Near East is pretty good. Then there is the The Rise and Fall of Ancient Egypt, highly recommended. For later in the Bronze Age 1177 B.C. covers a lot of the states and the several centuries before the collapse.

Japan is pretty important in many ways to understanding the evolution of civilizations and cultural exchange. I would recommend A History of Japan by Mason and Caiger. But those who want a somewhat more contemporary skew might want to check out The Making of Modern Japan.

And as long as we’re going to talk about islands, readers know I’m a fan of The Isles. Norman Davies does not give short shrift to the Celtic fringe.

Moving back to the heart of Eurasia, Grousset’s The Empire of the Steppes: A History of Central Asia is old, but I think it’s a decent survey.

Empires of the Silk Road: A History of Central Eurasia from the Bronze Age to the Present is probably a little too in the weeds for many readers, but if you are interested in the topic I recommend it. Like Thapar this is an author with a perspective…just keep that in mind. Where Empires of the Silk Road is panoramic, Lost Enlightenment: Central Asia’s Golden Age from the Arab Conquest to Tamerlane takes a narrower focus, following a particular thread over seven hundred years.

Taking a 50,000 foot view again, Africa: biography of a continent is definitely worth your time. I read it twice.

We’re now venturing in territory where there is less history conventionally defined. That is, based on writing. But some parts of the world don’t really have that, but you should probably know something about them.

1491: New Revelations of the Americas Before Columbus is not a survey like some of the ones above, but it does reflect what I think is the new orthodoxy (which is being subject to its own revisionism). I’m broadly persuaded that the revisionists-turned-mainstream viewpoint that is presented by Charles C. Man in 1491 has a lot going for it (ancient DNA adds broadly the likelihood in my opinion, perhaps more on that in some other post). Our knowledge of peoples like the Aztecs and Inca are to a great extent happenstance; they flourished when Europeans arrived. We don’t know the history of the peoples who came before. But we do know the history of the Maya because of the decipherment their hieroglyphs. In A Forest of Kings you’ll read about warlords like 18-Rabbit (a name I’ll never forget).

For Oceania all I’ve really only read is Richard Broome’s Aboriginal Australians. I don’t know of any primer, as such, about the history of Austronesians, though someone should write one. After all, these are a people who settled from Madagascar, off the coast of Mozambique, to Eastern Island to the west of Chile.

There are two nations which occupy roles in history which are somehow both liminal and central which like Japan, India, and China, deserve their own treatments. Russia is one. Gregory L. Freeze’s Russia: A History is pretty good. A history of Russia is essential because it is weird to see prominent pundits (I will not name, but it shocked me) not understand that Russia’s identification as a Western nation is substantively problematic.

There’s a whole historiography that covers the tension between Westernizers and Slavophiles (or their prototypes). Strangely this is another case where Western liberals and white nationalists are well aligned, they only see race, as the Russians are white, therefore they are Western (and another alignment, this racial essentialism to Western identity disappears for Southeast European Muslims like Albanians, Pomaks and Bonsiaks, who are often treated like “people of color”). The Russian Moment in World History is a short little book which outlines just now non-Western, and oppositional to the West, in many ways Russia has been.

Then we have Iran: Empire of the Mind. The conceit of the subtitle is a little annoying, but it reflects the role of Persian culture as hegemonic from Istanbul to Delhi to Samarkand. And, as you know if you read this weblog, a huge disproportionate number of scholars and intellectuals during the “Arab Islamic” intellectual Golden Age were ethno-linguistically of Iranian background (although many hailed from Turan, the Central Asian Iranian regions, and many of the non-Persians, like Thabit ibn Qurra, were non-Muslims).

Excuse my Eurocentrism, but Europe did conquer the world recently. So The Pursuit of Glory: The Five Revolutions that Made Modern Europe: 1648-1815. It’s a page turner (and you see how Russia reintegrated itself into Europe, at least its elites). The Reformation by Diarmaid MacCulloch is still the best sweeping history on the topic I’ve ever read (I’ve read probably a dozen big tomes on this period and subject?). World Goods: A New History of the Renaissance. We’ll miss the author, Lisa Jardine. At least I will.

As we move into the 19th and 20th century there is so much out there. Books like The Vertigo Years: Europe 1900-1914 are useful and very interesting, but there are so many on these sorts of topics, and we’re all more familiar with the era, so I’ll forgo giving you recommendations aside from one: After Tamerlane: The Rise and Fall of Global Empires, 1400-2000. It’s close enough to many thinks people talk about that it’s useful. For the rest, you can find documentaries.

I’ve focused on surveys which zoom in on a region and skim over a time period purposely. Traditional histories if you will. But I’ll finish out with some more unconventional stuff that I think would be useful. A Concise Economic History of the World: From Paleolithic Times to the Present covers all the bases. Power and Plenty: Trade, War, and the World Economy in the Second Millennium has a narrower time frame. The Ascent of Money: A Financial History of the World is self-explanatory, but Niall Ferguson is a great writer for all his faults.

Yes, read Guns, Germs and Steel. Not so much for the detailed assertions of fact, but for the way to think about historical processes and the forces that shape them. Reach Peter Turchin’s War Peace and War because it gives you a framework for decomposing patterns (some of the models in War Peace and War I have actually applied to books I read years before it, as I still have the “data” in my head).

Finally, read books like Life and Leisure in Ancient Rome. Social history is important, though many of the books above actually cover society and culture in great depth. There are so many “daily life in….” that you can take your pick. But remember that for most of history most people were peasants, and peasants had a lot in common in their daily life, with differences being relatively trivial (e.g., gruel of barely vs. gruel of wheat or a porridge of rice).

The list above is not exhaustive. It is limited by the fact that I read on some periods of history (e.g., Classical Greece) as far back as the 1980s, so I’m not up to date on the latest survey books. Reader suggestions are welcome.

What is my goal with providing you this list? I want you to be able to iterate through historical assertions people in the media and politics make against your internal data set. See if they are full of shit. They often are.

There are two classes of bullshit. The first class are the nakedly mendacious. This is more common in the political class, where lying is a form of art. The second class are just ignorant and don’t know any better. This is more common in the pundit class.

One trick that the pundit class pulls sincerely because they are often ignorant is that they cite a historian to buttress an assertion, even getting a quote from that historian. But quite often the historian is clearly misleading the audience…the historian may not utter a lie, but in their presentation they allow the reader to have a takeaway that aligns with the normative bias of the pundit, and the historian that has prostituted themselves to some cause. Obviously you will never master a specific area of history like an academic with a command of another language, but if you know enough you can easily smell bullshit when it’s being injected into the information stream.

June 6, 2017

St. Augustine knew of the Buddha!

Filed under: Culture,History,St. Augustine — Razib Khan @ 12:04 am

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

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

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

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

June 2, 2017

The nadir of genetics in the Soviet Union

Filed under: Genetics,History — Razib Khan @ 8:05 pm

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

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

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

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

May 30, 2017

The material over the ideological

Filed under: Economic History,Economics,History,Max Weber — Razib Khan @ 11:42 pm

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

And here we are!

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

Ancient Egyptians: black or white?

Filed under: Egypt,Genetics,Historical Genetics,History — Razib Khan @ 9:20 pm

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

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

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

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

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

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

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

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

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

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

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

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

I actually recomputed the haplogroups to a finer granularity from the supplements for readers who know this stuff well. Here they are:

 

Haplogroup Count
H 2
H13c1 2
H5 2
H6b 2
HV 3
HV1a’b’c 4
HV1a2a 3
HV1b2 2
HV21 2
I 5
J1d 2
J2a1a1 2
J2a2b 2
J2a2c 4
J2a2e 3
K 16T 2
K1a 2
K1a4 2
L3 2
M1a1 4
M1a1e 2
M1a1i 2
M1a2a 2
N 2
N1’5 2
N1a1a2 2
R 3
R0 2
R0a 2
R0a1 2
R0a1a 3
R0a2 3
R0a2f 2
R2’JT 2
T 3
T1a 3
T1a2 2
T1a5 4
T1a7 7
T1a8a 2
T2 3
T2c1 2
T2c1c 2
T2e 2
U 2
U1a1 2
U1a1a3 2
U3b 3
U5a 2
U6a 2
U6a2 2
U6a3 2
U7 4
U8b1a1 3
U8b1b1 2
W3a1 2
W6 2
W8 2
X 2
X1 2
X1c 2

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

May 26, 2017

The Canaanites walk among us: ancient DNA edition

Filed under: Ancient DNA,Bronze Age,History — Razib Khan @ 2:09 pm

Ancient DNA from here to there:

Ancient DNA has illuminated many things, but there is a logic as to what topics and questions it tackles. The focus on northern Eurasia is clearly a function of the probability of preservation, though techniques of extraction are getting better and better. I can’t imagine how we’d ever get a sample out of a moist tropical environment, but I won’t be surprised if something is obtained from a cave in southern Africa or high in the Tibesti in the near future.

But another parameter is time since the demographic events in question. Too ancient, and the probability of success is too low(ok, time is a parameter in much of science!). It seems plausible that in idealized circumstances we’re going to push beyond the one million year barrier. And yet too recent is also a problem (or not a problem!). For humans and even non-humans we have lots of corroboration about questions we might ask about the recent past. You could use “ancient DNA” to trace the migration of Mormons across the Intermontane West, but why would you?

So you see the earliest ancient DNA work on humans was biased toward testing models about gene flow and ancestry tens of thousands of years in the past, between modern humans and archaic lineages. Obviously we don’t have oral history or written texts from this period, and archaeology will only get us so far.

More recently the time depth has been getting shallower and shallower. Both David Reich and Eske Willerslev’s work on European prehistory is liminally historical. By this, I mean that what is prehistory in Europe is a historical period in the Near East. We may not have written records from the Corded Ware or Bell Beaker cultures, but we do have plenty of them from contemporaneous Near Eastern groups.

The Cauldron of Peoples:

There are still questions to be asked about European prehistory, but the gaps are getting narrower and narrower. Scholars are finally devoting resources to other regions of the world. Last year Iosif Lazaridis’ The genetic structure of the world’s first farmers finally opened up the box that was the prehistory of the Near East. This was important, because much of prehistory and history began in the Near East. Farmers from this region seem to have moved into Europe, South Asia, Central Eurasia, and Africa. To understand the population histories of these areas one needs to understand the population history of the Near East.

What Lazaridis et al. found this that there were at least two major groups of very genetically distinct Near Eastern farmers at the dawn of agriculture. Once group faced the eastern Mediterranean, while the other seems to have flourished on the slopes of the Zagros. Western and eastern farmers respectively. It is important to note that these two groups were very genetically distinct. If we sampled these two groups of farmers, who faced each other across northern Mesopotamia, in any modern population survey we’d assume that the genetic distance meant that they were sampled from different continents or very distant regions of Eurasia.

This finding suggest that the clinal patterns of variation in much of today’s world may be a consequence of massive population admixture between groups which had heretofore exhibited deep population structure. Why such deep structure existed and persisted is an interesting question, but at this point it is important to note descriptively that the past 10,000 years have seen a massive reduction of this structure due to gene flow between populations.

In the Near East Lazaridis et al. found that there was significant reciprocal gene flow between the western and eastern regions of the Near East after the emergence of farming, down to the historical period. This is one reason that estimates of “farmer” ancestry in modern Europeans always gave very low estimates: the reference populations no longer existed in unmixed form in the Near East. The peoples who brought agriculture to Southern Europe were related exclusively to the western farmers of the Near East, a population which no longer exists in unmixed form in that region of the world (ergo, among modern groups Sardinians are the closest proxies we have).

The Age of Bronze:

But there is much that occurred after prehistory in the Near East. We know this because we have extensive records going back 4,500 years, and even earlier. And though put into written form in the first millennium before Christ, the Hebrew Bible also records the deeds and names of people who have come and gone well before the Classical Age.

A new preprint on biorxiv sheds some light on a critical transitory period, Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences:

The Canaanites inhabited the Levant region during the Bronze Age and established a culture which became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole-genomes from ~3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalogue modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600-3,550 years ago, coinciding with massive population movements in the mid-Holocene triggered by aridification ~4,200 years ago. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate this Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive conquests by distant populations such as the Persians and Macedonians.

The period between 1700 and 1800 BCE in the Near East saw many changes and was a sort of nexus. Sumer had fallen, the Hittites had not emerged as a superpower, while Egypt was not heavily involve in the game of kings as of yet. The system of international relationships described in Brotherhood of Kings had not crystallized. That was for the late Bronze Age.

But some of the pieces we were to recognize were already in place. An Amorite Babylon under Hammurabi established the contours of the culture and polity we’d recognize down to the Persian conquest. In Egypt the Middle Kingdom was going into decline, and the Hyksos interregnum would give rise to the New Kingdom, which would become a major player in the Levant (and probably is the model for much of the Egypt we see described in the Bible).

The admixture plot above reflects the five individuals from Sidon dating to about ~1750 BCE. They are about a 50:50 mix of western and eastern farmer. Though they seem to be genetically rather similar to modern Lebanese (the authors sampled Lebanese Christians in particular), there have been some changes between the Bronze Age and the modern period. In particular, a genetic component that seems to be related to the Eurasian steppe is present in modern Lebanese. Explicit admixture estimates give a range of 5-10% mixing into a ~90-95% Bronze Age ancestral background.

This seems to establish basic continuity between the Bronze Age and the modern period. Totally unsurprising. Remember that Italy exhibits deep population structure that dates back to at least 2,000 years ago, and probably earlier. It is likely that much of the same applies to the Near East. Though looking at Muslim populations one can see minor and non-trivial contributions of populations which moved in after Islam (Sub-Saharan and East Asia segments are clear signs of slavery impacting Muslims that would not apply to ethno-religious minorities), most of the ancestry broadly is deeply rooted back to antiquity.

Because of sampling issues one can’t estimate admixture between eastern and western farmers just from looking at ancient DNA transects. We don’t have the density that we have in Europe (yet). So the authors used a more classic inference technique looking at decays of linkage disequilibrium in the genome. In short you can see how many generations that a pulse admixture between two populations occurred by looking at correlations of variants across the genome. The authors arrive at the intervals above, and in particular focus on the period that seems to overlap with the rise and fall of the empire of Sargon of Akkad and correlated with a climatic disruption.

I suspect they are wrong here. First, it seems pretty clear to me that LD based admixtures assuming a pulse event have a bias toward underestimating values. There are theoretical reasons for this. So usually I pad the mid-point value across the interval on these estimates.

One thing that ancient DNA has told us is that often the less complex the society, the more demographic turnover you have. All things equal then we would expect turnover to be an older event, as simple societies are succeeded by complex ones. The succession of complex societies by other complex societies is often less disruptive for the masses because this transformation is more a matter of elite replacement.

By ~2200 BCE the Near East was already quite complex. I believe that the massive western-eastern farmer admixture occurred between 3600 and 3100 BCE, during the Uruk Expansion. The evidence of lower Mesopotamian influence and demographic settlement in places as far afield as Anatolia, the Caucasus, and Syria, are well attested from the archaeology of this period. This was was a time when a very complex and sophisticated civilization emerged almost de novo across much of the Near East. I believe that a prehistoric expansion of Sumerian civilization mediated the merging of eastern and western farmers, though some of the mixing pre-dates and post-dates the Uruk Expansion and collapse (e.g., the movement of western farmer ancestry into Mesopotamia seems certain to have occurred through the arrival of groups like the Amorites).

Additionally, buried in this preprint is evidence of major Y chromosomal turnover. We’ve seen this  before. The prominence of haplogroup J in Bronze Age and modern Levantines seems to be due to eastern farmer migration. In fact, adding haplogroup J and R together we get the inference that more than half the paternal lineages of Lebanese today are not from western farmers native to the area.

Beyond the Bronze Age:

What about the second ancestral component? Drilling down on the Y chromosomes of the Levant, R1b seems to far outnumber R1a, though the R1a clades are all of the Asian/Scythian Z-93 branch which is dominant in Central Asia and the Levant. The R1a may have come with the Persians, but in region of the western Levant for several hundred years after the period of the Bronze Age Sidon samples there was a state, the Mitanni, which clearly had an Indo-Aryan ruling class.

An Aegean influence occurred multiple times. First, at the end of the Bronze Age many of the “Sea Peoples” were clearly of Aegean origin, and so may have brought steppe-like ancestry. Second, there was the long period under Hellenistic and Roman rule, when Greek and non-Greek ethnic identity existed side by side, and movement occurred in both directions. I think only ancient DNA will answer this question, and it may be that there were multiple post-Bronze Age inputs of genes which shaped modern Levantines.

After Babel:

The curious thing that many of these studies are telling us is two-fold:

  1. Most of the population genetic structure we see around us dates to the Bronze Age, on the borderlands between history and prehistory. I think we can start to set this as a strong prior. It holds true for the Near East, Africa, South Asia, Japan and Southeast Asia. We’ll see about core East Asia, but I think probably it is true there too.
  2. Selection has continued, so that alleles for lactose tolerance and lighter skin have changed in frequency even since that period. The derived allele for SLC45A2 is found at about 2/3 frequency in modern Lebanon, but was absent in these five Sidonians. Though the sample size is small, this was somewhat surprising, and suggests that they were a swarthier people than modern Lebanese.

Addendum: I have said little here about Afro-Asiatic languages, as I don’t know enough about this topic.

May 25, 2017

At an inflection point of archaeology and genetics

Filed under: Genetics,History — Razib Khan @ 1:54 pm

People always ask me what to read in relation to the field of historical population genetics. In the 2000s there were a series of books which focused on the mtDNA and Y results from modern phylogeographic analysis. Journey of Man, Seven Daughters of Eve, The Real Eve, and Mapping Human History. But there hasn’t been much equivalent in the 2010s.

Why? I think part of the issue is that the rate of change has been so fast that scholars and journalists haven’t been able to keep up. And, the change is happening right now, so it would likely mean that any book written over a year would be moderately out of date by publication.

I noticed today that Jean Manco has an updated and revised version of her book, Ancestral Journeys: The Peopling of Europe from the First Venturers to the Vikings. This was needed, because the original book was written before some major recent findings, though after some preliminary ones. As Manco has observed herself it was feasible to replace speculations with facts.

Since it seems likely that George R. R. Martin’s next book will be published before David Reich’s, I think that’s all you got. Any suggestions would be welcome.

As for the flip side for history that might be useful to understanding the genetics results, J. M. Roberts The History of the World is the best cliff notes I can think of. It’s obviously a high level survey, but frankly that would improve the interpretation I see in some papers. The fact that much of the history has no contemporary relevance is pretty unimportant, since you want to focus on the older stuff, which is where ancient DNA really shows its metal.

At some point ancient DNA will start to exhibit diminishing returns. Then the long hard slog of interpretation and synthesis will have to begin in earnest.

May 19, 2017

The eternal Axial Age

Filed under: History — Razib Khan @ 11:17 pm

As I have noted before one of the most interesting aspects of ancient Greek history is that in many ways the socio-political identities and outlook of the Hellenic people before and after the Bronze Age were probably as distinct as that between hunter-gatherers and agriculturalists. That is, the citadel culture of the Mycenaeans was constructed out of recognizable elements. Take one dollop Near Eastern autocracy, add a dash of semi-civilized barbarian warlord, and finish off with the tincture of brutalist post-Minoan aesthetic, and you have the pirate kings of Achaea, who so plagued the kings of the Hittites and later transformed themselves into the “Sea Peoples.”

The story of what happened after the end of the Bronze Age is somewhat well known to us, because the roots of our civilizations are clear in the ideas which emerged in the period between 1000 BCE and 0 CE. The basis of the institutional religions which we see around us date to the Axial Age. Judaism, Christianity, Islam, Hinduism, and arguably Daoism, Confucianism, Buddhism and Zoroastrianism, either arose or ripened in the one thousand years after the birth of Christ, but from a naturalistic perspective the bases of these traditions are present in the early Iron Age. To be concrete about what I’m getting at, Judaism over its history truly takes shape in the centuries leading up to, and subsequent to, the compilation of the Babylonian Talmud. But the disparate threads of Rabbinical Judaism were already there in the centuries before Christ; they were simply synthesized and extended later on.

Much the same can be said about science. On the one hand, a narrow view of science is that it is the cultural product of a group of individuals who began collectively exploring aspects of the natural world in the 17th century. Eventually this contingent cultural enterprise spread across the whole world. But the roots of the scientific enterprise can also be seen in the Pre-Socratic philosophies. It was already there 2,500 years ago. But the victory of Platonism, and later the rise of Hellenistic ethical systems, and finally the ideological uniformity imposed by Christianity, dampened the efflorescence of heterodox speculations which flourished for the few centuries around 450 BCE. The steam went out of the scientific enterprise, and it never truly became science as we understand it in the modern world. But pieces of it that came together later on were familiar to us of old.

And then there are the political innovations. The Greeks gave us all their different varieties; democracy, oligarchy, the mixed monarchy-oligarchy of Sparta. The Romans had their republic, and even during the imperial period rejected the institution of ‘kinship,’ though all the powers of a king were eventually accrued to the emperors.

But political debate existed outside of Greece and Rome. In China political and ethical philosophy were intertwined, the tension between Legalism and Confucianism would continue down through the ages after the official ascendancy of the latter during the Former Han. In India there was a variety of forms of governance characterized by differing levels of centrality before the conquest of the Mauryas set the horizons and template for much of the rest of South Asian history.

Democracy and republics faded. Republican governments eventually made periodic revivals. During the period of the American Revolution many were skeptical of the idea of such a geographically expansive state such as the United States being able to maintain a republican form of governance. The shift toward a more democratic self-identity in the early 19th century with the rise of Jacksonian populism was even more shocking, because for much of history democracy was seen as a failed Greek experiment which often devolved into illiberal mob rule.

I recall 15 years ago Steven Pinker observing that one reason philosophy has made little progress is that what one could not make progress in was consigned to philosophy, while the natural and social sciences waxed in their ability to model and explain the world around us. This is uncharitable to philosophy in many ways, but it gets at something real: we haven’t pushed much further beyond the Greeks on foundational questions. Similarly, Islam is the last major religion to have emerged, and the theology of Christian churches and the metaphysics of Buddhism and Hinduism are all one to two thousand years old. Instead of progress we’ve seen shifts back and forth in fashion. Reworking of templates, not the creation of new things.

Over the past few centuries we have witnessed something different than this. The birth of the modern. The explosion of democracy and liberalism, and economic well being through massive gains to welfare and well being to the non-elites. Between 1800 and 1970 the wage gap between the skilled and unskilled in Western societies shrank. Seen from the first half of the 1960s the future was shiny, infectious disease was going to be unknown, and robots would allow us a life of leisure.

Though we do have iPhones and other shiny devices, and nerds like me can consume lots information on the web, things have not quite worked out in exactly the way predicted. Yes, China and much of the developing world has improved in terms of vital statistics. And it looks like space commerce may finally arrive in the next decade. But we do not have a Mars colony in 2017, let alone a Moon colony.

Economic productivity combined with a demographic transition mean that extreme deprivation is slowly being strangled. But inequality flourishes, and the wage gap between the skilled and unskilled began to increase after 1970 in the developed world. Whereas at one point the Whiggish perception that history was progressive, and that it would end in some quasi-utopian terminus, was self-evident, today many are not as certain. The unipolar geopolitics of the 1990s has given way to a new farcical world of the “Great Game,” while secular Arab nationalism has faded to irrelevance in the face of a resurgence Islamic identity.

History does not move in cycles where the future reenacts the past. But much of the modular furniture of existence seems to be 2,000 years old. The Salafi movements the world over are fundamentally products of modernity, or the reaction to various elements of European modernity. Their roots pre-date the 20th century, and go back to revivals in the Arabian peninsula in the 18th century which parallel a reconstruction of self conscious orthodox Islam in India as the Mughal order was collapsing. But ultimately they are refurbishing the furniture put together by Ibn Hanbal in the 9th century, who himself might have been comfortable among Judaean Zealots. The Taliban are simply the Maccabees of our age.

From an American perspective the reality, the necessity, of the spread of democracy and the expansion of liberalism seem self-evident. Inevitable. Along with technology and science, it all seemed to hang together. In the 1990s the future was arriving as scheduled.

In 2017 the Russian experiment with Western democratic forms has not turned out how we wanted. Though China is economically liberal, it is not democratic. The global capitalist elite were as surprised as everyone else by 2008, and in the wake of that shock they have persuaded themselves that there is no need for a fundamental rethink of the institutions that they’ve developed over the past 70 years since the Bretton Woods Agreement.

As the Western economic elite continues to persist in denial, the cultural elite has been making a broad push to sweep post-1960s social liberalism throughout the world. This, all the while that Western societies have been demographically stagnant, and Western economic power has been declining in relative terms.

We are in the late stages of the long 20th century. The institutions and mores of the post-World War II are still with us, like Zeitgeist zombies. But the combination of global capitalism, individualism, democratic values always constrained by oligarchic preferences, and the universal acid of Critical Theory infused identity politics, does not hang together in a robust fashion. In most of the world if people have to pick between their ‘sexual identity’ and their ‘religious identity’, I think it will be the latter (assuming they concede that a sexual identity is a thing). In the early 20th century Marxists had to confront the fact that internationalism was not capable of overcoming nationalism. In the 21st century the identity politics of individual self-actualization and self-definition will likely confront 2,000 year old identities.

Ideologues dream of final victories. Of ideologies sweep through the world, from sea to sea. Global Communism. A world-wide capitalist order defined by free trade and free movement of peoples. China and India converting to Christianity and finally ending the civilizational conflict between Christendom and Islam, as Muslim MENA is constricted between Christian Europe, Africa, and Asia.

But pluralism has defined the last few thousand years. The final victory has been elusive. The old ideologies and religions do not die, they evolve, they reinvent, they repurpose. The stories are different in each age, but they live in a shared universe of characters who also repeat similar plot elements.

The second century BC was a strange time for the Roman republic. It was an empire in all but name. The ancient enemy Carthage was no more. But destitution was also coming to some of the Roman people. This resulted in reformers attempting to right the ship of state. The brothers Gracchi attempted to help the plight of the Roman poor with redistribution.  Marcus Livius Drusus expanded the franchise to non-Roman Italians. Political redistribution if you will. Gaius Marius began as a necessary general, but ended as a chaotic autocrat. The social cohesion of the Roman republic was breaking down. Faction began to dominate all of public life.

Into situation stepped Sulla. Sulla is not a contingent man. Sulla is a type. A reaction, usually a vain and futile attempt to hold the past together, and push it into the future, by brutal means. Sulla arises when social elites lose faith in the present, and attempt to recreate institutions from an idealized past.

Sulla is efficient. Cruel, but certain in his rightness. Sulla is not a clown. He is not narcissistic, for Sulla does have ideals, even if you hold that those ideals are cruel or callous. Sulla is a piece of furniture, found in many places at many times. The United States of America has not seen Sulla yet. I believe it will.

May 11, 2017

Dramatization of the arrival of the Beaker people

Filed under: Bell Beakers,History — Razib Khan @ 8:29 pm


Normally a conference or a talk related to the Bell Beakers and their spread across Western Europe would involve a few presentation slides with pictures of beakers and shaded maps, and result in the production of a scholarly compendium such as The Bell Beaker Transition in Europe: Mobility and local evolution during the 3rd millennium BC. From the description on Amazon in relation to this book:

Could the circulation of objects or ideas and the mobility of artisans explain the unprecedented uniformity of the material culture observed throughout the whole of Europe? The 17 papers presented here offer a range of new and different perspectives on the Beaker phenomenon across Europe. The focus is not on Bell Beaker pottery but on social groups (craft specialists, warriors, chiefs, extended or nuclear families), using technological studies and physical anthropology to understand mobility patterns during the 3rd millennium BC. Chronological evolution is used to reconstruct the rhythm of Bell Beaker diffusion and the environmental background that could explain this mobility and the socioeconomic changes observed during this period of transition toward Bronze Age societies. The chapters are mainly organized geographically, covering Eastern Europe, the Mediterranean shores and the Atlantic coast of the Iberian Peninsula, includes some areas that are traditionally studied and well known, such as France, the British Isles or Central Europe, but also others that have so far been considered peripheral, such as Norway, Denmark or Galicia. This journey not only offers a complex and diverse image of Bell Beaker societies but also of a supra-regional structure that articulated a new type of society on an unprecedented scale.

Pretty dry. But thankfully in lieu of PowerPoint slides some researchers have gotten more clever, and in light of new findings I present a short film depicting the Bell Beaker arrival in what became Britain. Pretty quick turnaround, no?

Related: The Bronze Age Demographic Transformation Of Britain.

When conquered pre-Greece took captive her rude Hellene conqueror

Filed under: Genetics,Genomics,Greece,History,Migration — Razib Khan @ 12:22 am


When I was a child in the 1980s I was captivated by Michael Wood’s documentary In Search of the Trojan War (he also wrote a book with the same name). I had read a fair amount of Greek mythology, prose translations of the Iliad, as well as ancient history. The contrast between the Classical Greeks, the strangeness of their mythology was always something that on the surface of my mind. The reality that Bronze Age Greeks were very different from Classical Greeks resolved this issue to some extent.

Though Classical Greeks were very different from us, to some extent Western civilization began with them, and they are very familiar to us. Rebecca Goldstein’s Plato at the Googleplex was predicated on the thesis that the ancient Greek philosopher had something to tell us, and that if he was alive today he would be a prominent public speaker.

I’m going to dodge the issue of Julian Jaynes’ bicameral mind, and just assert that people of the Bronze Age were fundamentally different from us. And that difference is preserved in aspects of Greek mythology. Though it is fashionable, and correct, to assert that Homer’s world was not that of Mycenaeans, but the barbarian period of the Greek Dark Age, it is not entirely true. Homer clearly preserved traditions where citadels such as Mycenae and Pylos were preeminent, and details such as the boar’s tusk helmets are also present in the Iliad.

But aesthetic details or geopolitics are not what struck me about Greek mythology, but events such as the sacrifice of Iphigenia. Like Abraham’s near sacrifice of his son, this plot element strikes moderns as cruel, barbaric, and unthinking. And though the Classical Greeks did not have our conception of human rights, they had turned against human sacrifice (and the Romans suppressed the practice when they conquered the Celts) on the whole, but it seems to have occurred in earlier periods.

The rupture between the world of the Classical Greeks and the strange edifices of Mycenaean Greece were such that scholars were shocked that the Linear B tablets of the Bronze Age were written in Greek when they were finally deciphered. In fact many of the names and deities on these tablets would be familiar to us today; the name Alexander and the goddess Athena are both attested to in Mycenaean tablets.

Preceding the Mycenaeans, who  emerge in the period between 1400-1600 BCE, are the Minoans, who seem to have developed organically in the Aegean in the 3rd millennium. This culture had relations with Egypt and the Near East, their own system of writing, and deeply influenced the motifs of the successor Mycenaean Greek civilization. The aesthetic similarities between Mycenaeans and Minoans is one reason that many were surprised that the former were Greek, because the Minoan language was likely not.

Mycenaean civilization seems to have been a highly militarized and stratified society. There is a reason that this is sometimes referred to as the “age of citadels.” Allusions to the Greeks, or Achaeans, in the diplomatic missives of the Egyptians and Hittites suggests that the lords of the Hellenes were reaver kings. In 1177 B.C. Eric Cline repeats the contention that a fair portion of the “sea peoples” who ravaged Egypt in the late Bronze Age were actually Greeks.

So when did these Greeks arrive to the shores of Hellas? In The Coming of the Greeks Robert Drews argued that the Greeks were part of a broader movement of mobile charioteers who toppled antique polities and turned them into their own. The Hittites and Mitanni were two examples of Indo-European ruling elites who took over a much more advanced civilizational superstructure and made it their own. While the Hittites and other Indo-Europeans, such as the Luwians and Armenians, slowly absorbed the non-Indo-European substrate of Anatolia, the Indo-Aryan Mitanni elite were linguistically absorbed by their non-Indo-European Hurrian subjects. Indo-Aryan elements persisted only their names, their gods, and tellingly, in a treatise on training horses for charioteers.

Drews’ thesis is that the Greek language percolated down from the warlords of the citadels and their retinues over the Bronze Age, with the relics who did not speak Greek persisting into the Classical period as the Pelasgians. Set against this is the thesis of Colin Renfrew that Greece was one of the first Indo-European languages, as Indo-European languages began in Anatolia.

The most recent genetic data suggest to me that both theses are likely to be wrong. The data are presented in two preprints The Population Genomics Of Archaeological Transition In West Iberia and The Genomic History Of Southeastern Europe. The two papers cover lots of different topics. But I want to focus on one aspect: gene flow from steppe populations into Southern Europe.

We know that in the centuries after 2900 BCE there was a massive eruption of individuals from the steppe fringe of Eastern Europe, and Northern Europe from Ireland to to Poland was genetically transformed. Though there was some assimilation of indigenous elements, it looks to be that the majority element in Northern Europe were descended from migrants.

For various reasons this was always less plausible for Southern Europe. The first reason is that Southern Europeans shared a lot of genetic similarities to Sardinians, who resembled Neolithic farmers. Admixture models generally suggested that in the peninsulas of Southern Europe the steppe-like ancestry was the minority component, not the majority, as was the case in Northern Europe.

These data confirm it. The Bronze Age in Portugal saw a shift toward steppe-inflected populations, but it was not a large shift. There seems to have been later gene flow too. But by and large the Iberian populations exhibit some continuity with late Neolithic populations.  This is not the case in Northern Europe.

In The Genomic History Of Southeastern Europe the authors note that steppe-like ancestry could be found sporadically during early periods, but that there was a notable increase in the Bronze Age, and later individuals in the Bronze Age had a higher fraction. Nevertheless, by and large it looks as if the steppe-like gene flow in the southerly Balkans (focusing on Bulgarian samples) was modest in comparison to the northern regions of Europe. Unfortunately I do not see any Greece Bronze Age samples, but it seems likely that steppe-like influence came into these groups after they arrived in Bulgaria, which is more northerly.

Down to the present day a non-Indo-European language, Basque, is spoken in Spain. Paleo-Sardinian survived down to the Classical period, and it too was not Indo-European. Similarly, non-Indo-European Pelasgian communities continued down to the period of city-states in Greece.

These long periods of coexistence point to the demographic equality (or even superiority) of the non-Indo-European populations. The dry climate of the Mediterranean peninsulas are not as suitable for cattle based agro-pastoralism. This may have limited the spread and dominance of Indo-Europeans. Additionally, the Mediterranean peninsulas were likely touched by Indo-European migrations relatively late. Much of the early zeal for expansion may have already dissipated by them. The high frequency of likely Indo-European R1b lineages among the Basques is curious, and may point to the spreading of male patronization networks, and their assimilation into non-Indo-European substrates where necessary. R1b is also found in Sardinia, and in high frequencies in much of Italy.

The interaction and synthesis between native and newcomer was likely intensive in the Mediterranean. For example, of the gods of the Greek pantheon only Zeus is indubitably of Indo-European origin. Some, such as Artemis, have clear Near Eastern antecedents. But other Greek gods may come down from the pre-Greek inhabitants of what became Greece.

Ultimately these copious interactions and transformations should not be a great surprise. The sunny lands of the Mediterranean attracted Northern European tribes during Classical antiquity. The Cimbri invasion of Italy, Galatians in Thrace and Anatolia, the folk wandering of Vandals and Goths into Iberia, are all instances of population movements southward. These likely moved the needle ever so slightly toward convergence between Northern and Southern Europe in terms of genetic content.

In relation to the more general spread of Indo-Europeans, I believe there are a few areas like Northern Europe, where replacement was preponderant (e.g., the Tarim basin). But I also believe there were many more which presented a Southern European model of synthesis and accommodation.

When conquered pre-Greece took captive her rude Hellene conqueror

Filed under: Genetics,Genomics,Greece,History,Migration — Razib Khan @ 12:22 am


When I was a child in the 1980s I was captivated by Michael Wood’s documentary In Search of the Trojan War (he also wrote a book with the same name). I had read a fair amount of Greek mythology, prose translations of the Iliad, as well as ancient history. The contrast between the Classical Greeks, the strangeness of their mythology was always something that on the surface of my mind. The reality that Bronze Age Greeks were very different from Classical Greeks resolved this issue to some extent.

Though Classical Greeks were very different from us, to some extent Western civilization began with them, and they are very familiar to us. Rebecca Goldstein’s Plato at the Googleplex was predicated on the thesis that the ancient Greek philosopher had something to tell us, and that if he was alive today he would be a prominent public speaker.

I’m going to dodge the issue of Julian Jaynes’ bicameral mind, and just assert that people of the Bronze Age were fundamentally different from us. And that difference is preserved in aspects of Greek mythology. Though it is fashionable, and correct, to assert that Homer’s world was not that of Mycenaeans, but the barbarian period of the Greek Dark Age, it is not entirely true. Homer clearly preserved traditions where citadels such as Mycenae and Pylos were preeminent, and details such as the boar’s tusk helmets are also present in the Iliad.

But aesthetic details or geopolitics are not what struck me about Greek mythology, but events such as the sacrifice of Iphigenia. Like Abraham’s near sacrifice of his son, this plot element strikes moderns as cruel, barbaric, and unthinking. And though the Classical Greeks did not have our conception of human rights, they had turned against human sacrifice (and the Romans suppressed the practice when they conquered the Celts) on the whole, but it seems to have occurred in earlier periods.

The rupture between the world of the Classical Greeks and the strange edifices of Mycenaean Greece were such that scholars were shocked that the Linear B tablets of the Bronze Age were written in Greek when they were finally deciphered. In fact many of the names and deities on these tablets would be familiar to us today; the name Alexander and the goddess Athena are both attested to in Mycenaean tablets.

Preceding the Mycenaeans, who  emerge in the period between 1400-1600 BCE, are the Minoans, who seem to have developed organically in the Aegean in the 3rd millennium. This culture had relations with Egypt and the Near East, their own system of writing, and deeply influenced the motifs of the successor Mycenaean Greek civilization. The aesthetic similarities between Mycenaeans and Minoans is one reason that many were surprised that the former were Greek, because the Minoan language was likely not.

Mycenaean civilization seems to have been a highly militarized and stratified society. There is a reason that this is sometimes referred to as the “age of citadels.” Allusions to the Greeks, or Achaeans, in the diplomatic missives of the Egyptians and Hittites suggests that the lords of the Hellenes were reaver kings. In 1177 B.C. Eric Cline repeats the contention that a fair portion of the “sea peoples” who ravaged Egypt in the late Bronze Age were actually Greeks.

So when did these Greeks arrive to the shores of Hellas? In The Coming of the Greeks Robert Drews argued that the Greeks were part of a broader movement of mobile charioteers who toppled antique polities and turned them into their own. The Hittites and Mitanni were two examples of Indo-European ruling elites who took over a much more advanced civilizational superstructure and made it their own. While the Hittites and other Indo-Europeans, such as the Luwians and Armenians, slowly absorbed the non-Indo-European substrate of Anatolia, the Indo-Aryan Mitanni elite were linguistically absorbed by their non-Indo-European Hurrian subjects. Indo-Aryan elements persisted only their names, their gods, and tellingly, in a treatise on training horses for charioteers.

Drews’ thesis is that the Greek language percolated down from the warlords of the citadels and their retinues over the Bronze Age, with the relics who did not speak Greek persisting into the Classical period as the Pelasgians. Set against this is the thesis of Colin Renfrew that Greece was one of the first Indo-European languages, as Indo-European languages began in Anatolia.

The most recent genetic data suggest to me that both theses are likely to be wrong. The data are presented in two preprints The Population Genomics Of Archaeological Transition In West Iberia and The Genomic History Of Southeastern Europe. The two papers cover lots of different topics. But I want to focus on one aspect: gene flow from steppe populations into Southern Europe.

We know that in the centuries after 2900 BCE there was a massive eruption of individuals from the steppe fringe of Eastern Europe, and Northern Europe from Ireland to to Poland was genetically transformed. Though there was some assimilation of indigenous elements, it looks to be that the majority element in Northern Europe were descended from migrants.

For various reasons this was always less plausible for Southern Europe. The first reason is that Southern Europeans shared a lot of genetic similarities to Sardinians, who resembled Neolithic farmers. Admixture models generally suggested that in the peninsulas of Southern Europe the steppe-like ancestry was the minority component, not the majority, as was the case in Northern Europe.

These data confirm it. The Bronze Age in Portugal saw a shift toward steppe-inflected populations, but it was not a large shift. There seems to have been later gene flow too. But by and large the Iberian populations exhibit some continuity with late Neolithic populations.  This is not the case in Northern Europe.

In The Genomic History Of Southeastern Europe the authors note that steppe-like ancestry could be found sporadically during early periods, but that there was a notable increase in the Bronze Age, and later individuals in the Bronze Age had a higher fraction. Nevertheless, by and large it looks as if the steppe-like gene flow in the southerly Balkans (focusing on Bulgarian samples) was modest in comparison to the northern regions of Europe. Unfortunately I do not see any Greece Bronze Age samples, but it seems likely that steppe-like influence came into these groups after they arrived in Bulgaria, which is more northerly.

Down to the present day a non-Indo-European language, Basque, is spoken in Spain. Paleo-Sardinian survived down to the Classical period, and it too was not Indo-European. Similarly, non-Indo-European Pelasgian communities continued down to the period of city-states in Greece.

These long periods of coexistence point to the demographic equality (or even superiority) of the non-Indo-European populations. The dry climate of the Mediterranean peninsulas are not as suitable for cattle based agro-pastoralism. This may have limited the spread and dominance of Indo-Europeans. Additionally, the Mediterranean peninsulas were likely touched by Indo-European migrations relatively late. Much of the early zeal for expansion may have already dissipated by them. The high frequency of likely Indo-European R1b lineages among the Basques is curious, and may point to the spreading of male patronization networks, and their assimilation into non-Indo-European substrates where necessary. R1b is also found in Sardinia, and in high frequencies in much of Italy.

The interaction and synthesis between native and newcomer was likely intensive in the Mediterranean. For example, of the gods of the Greek pantheon only Zeus is indubitably of Indo-European origin. Some, such as Artemis, have clear Near Eastern antecedents. But other Greek gods may come down from the pre-Greek inhabitants of what became Greece.

Ultimately these copious interactions and transformations should not be a great surprise. The sunny lands of the Mediterranean attracted Northern European tribes during Classical antiquity. The Cimbri invasion of Italy, Galatians in Thrace and Anatolia, the folk wandering of Vandals and Goths into Iberia, are all instances of population movements southward. These likely moved the needle ever so slightly toward convergence between Northern and Southern Europe in terms of genetic content.

In relation to the more general spread of Indo-Europeans, I believe there are a few areas like Northern Europe, where replacement was preponderant (e.g., the Tarim basin). But I also believe there were many more which presented a Southern European model of synthesis and accommodation.

May 10, 2017

The Bronze age demographic transformation of Britiain

Filed under: Bell Beaker,Britain,Evolution,History,Human Genetics,Human Genomics — Razib Khan @ 8:52 am

In Norman Davies’ the excellent The Isles: A History, he mentions offhand that unlike the Irish the British to a great extent have forgotten their own mythology. This is one reason that J. R. R. Tolkien created Middle Earth, they gave the Anglo-Saxons the same sort of mythos that the Irish and Norse had.

But to some extent I think we can update our assessments. Science is bringing myth to life. The legendary “Bell Beaker paper” is now available in preprint form, The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe. The methods are not too abstruse if you have read earlier works on this vein (i.e., no Nick Patterson authored methodological supplement that I saw). And the results are straightforward.

And what are those results?

First, the Bell Beaker phenomenon was both cultural and demographic. Cultural in that it began in the Iberian peninsula, and was transmitted to Central Europe, without much gene flow from what they can see. Demographic in that its push west into what is today the Low Countries and France and the British Isles was accompanied by massive gene flow.

In their British samples they conclude that 90% of the ancestry of early Bronze Age populations derive from migrants from Central Europe with some steppe-like ancestry. In over words, in a few hundred years there was a 90% turnover of ancestry. The preponderance of the male European R1b lineage also dates to this period. It went from ~0% to ~75-90% in Britain over a few hundred years.

If most of the genetic-demographic character of modern Britain was established during the Bronze Age*, then there has been significant selection since the Bronze Age. The figure to the left shows ancient (Neolithic/Bronze age) frequencies of selected SNPs, with modern frequencies in the British in dashed read. The top-left SNP is for HERC2-OCA2, the region related to brown vs. blue eye color, and also associated with some more general depigmentation. The top-right SNP is in SLC45A2, the second largest effect skin color locus in Europeans. The bottom SNP is for a mutation on LCT, which allows for the digestion of milk sugar as adults.

The vast majority of the allele frequency change in Britons for digestion of milk sugar post-dates the demographic turnover. In other words, the modern allele frequency is a function of post-Bronze Age selection. This is not surprising, as it supports the result in Eight thousand years of natural selection.

1000 Genomes derived SLC45A2 SNP frequency

At least as interesting are the pigmentation loci. The fact that the derived frequency in HERC2-OCA2 is lower in both British and Central European Beaker people samples indicates that the lower proportion is not an artifact of sampling. Britons have gotten more blue-eyed over the last 4,000 years. Second, SLC45A2 is at shocking low proportions for modern European populations.

HGDP derived SLC45A2 SNP frequency

In the 1000 Genomes the 4% ancestral allele frequency is almost certainly a function of the Siberian (non-European) ancestry. In modern Iberians the ancestral frequency is 18% (and it is even higher in Sardinians last I checked), but in Tuscans it is ~2%. Though not diagnostic of Europeans in the way the derived SNP at SLC24A2 is, SLC452 derived variants are much more constrained to Europe. Individuals who are homozygote ancestral for SNPs atSLC45A2 rare in modern Northern Europeans (pretty much nonexistent actually). But even as late as the Bronze Age they would have been present at low but appreciable frequencies.

This particular result convinces me that the method in Field et al. which detected lots of recent (last 2,000 years) selection on pigmentation in British populations is not just a statistical artifact. Though these papers are solving much of European prehistory, they are also going to be essential windows into the trajectory of natural selection in human populations over the last 5,000 years.

* In the context of this paper the Anglo-Saxon migrations tackled by the PoBI paper are minor affairs because the two populations were already genetically rather close. Additionally, the PoBI paper found that the German migrations were significant demographic events, but most of the ancestry across Britain does date to the previous period.

May 9, 2017

The Beaker is breaking!

The link is up, The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe, but the paper is still processing:

I’ll update the post when I can read the paper.

May 8, 2017

The lesson of Erasmus: the center that could not hold

Filed under: Culture,Erasmus,History,Religion — Razib Khan @ 11:35 pm

The return of the civilian

“On the coming of evening, I return to my house and enter my study; and at the door I take off the day’s clothing, covered with mud and dust, and put on garments regal and courtly; and reclothed appropriately, I enter the ancient courts of ancient men, where, received by them with affection, I feed on that food which only is mine and which I was born for, where I am not ashamed to speak with them and to ask them the reason for their actions; and they in their kindness answer me; and for four hours of time I do not feel boredom, I forget every trouble, I do not dread poverty, I am not frightened by death; entirely I give myself over to them”
-Niccolò Machiavelli

The sentiments expressed above are typical of Renaissance men, prone to archaisms and love of ancient learning. As all stylized facts are, the dichotomy between a dark Middle Ages and a flourishing Renaissance are clearly overwrought, and an artifact in some ways of the reality that the victors write history. A passionate intellectual such as Abelard is clearly a familiar figure despite the reality that he flourished in the early part of the High Middle Ages. And the period described in Aristotle’s Children was not lacking in brilliance on the whole.

But generalizations also have a basis. Henry the VIII reputedly wrote Defence of the Seven Sacraments as a rebuke to the assaults from the nascent Protestant tradition. For his services the Pope gave the king the title Defender of the Faith. It is no surprise that Thomas More “aided” in the composition, but the point is that a Renaissance monarch was expected to be a cultured individual for whom writing a theological treatise was not ludicrous.

Though one should not take the analogy too far, in some ways the polities of the medieval period in Western Europe exhibited a social structure not unlike that of the Bronze Age. Literacy was one of the hallmarks of Romanitas, and later of Christian civilization. But literacy was not broad-based in Western Europe, but rather concentrated in a particular caste, that of the priests. In the Bronze Age literacy was also defined by its caste association, that of the scribes. In contrast, kings fought. Their rule was by divine right, whether as living gods on earth, or as vice-reagents of the national deity. Similarly, monarchs during the medieval period ruled as representatives of the God on high.

During the Iron Age the antipodes of Eurasia were dominated by polities and civilizations which were predicated on military rule, but at whose peak civilian norms reigned supreme. Even as militaristic a figure as Julius Caesar was a cultural patron who also wrote The Gallic Wars. Similarly the Chinese emperors were manifestly civilian figures, who often also had personal skills in the arts which they cultivated. It wasn’t until the reign of the emperor Justin in the year 518 that Rome first had an illiterate ruler (and this is implausible enough that some historians attribute this claim as one intended to be scurrilous toward Justin and his successor and nephew, Justinian).

The fall of the Western Roman Empire ended this civilian ascendancy, which in any case was being eroded by the necessary rise of military emperors to defend the borders against barbarian incursions. Once the German tribes, Roman allies or not, took the reins of power there were deep fundamental transformations of the order of society. Though great rulers such as Charlemagne were patrons of learning and Roman civilization, he himself remained very much a barbarian warlord.

The ruling elite of medieval Europe were manifestly a military elite. The feudal system demanded that they provide service in the armies of their lords, and that service entailed outfitting themselves and a retinue. Martial skills were a necessity. The legacy of this physical aspect to being part of the ruling elite persists down to the present day. Both of the two young princes in the House of Windsor have had military careers, while hunting remained a major part of every nobleman’s life down to the early modern period (apparently Louis XVI’s diaries are filled with days which simply state “went hunting”).

The gun and the printing press

Events such as the Battle of Crecy, the rise of the Swiss infantry, and the ubiquity of the gun, heralded the end of the military elite as a necessity. Gentility of birth became a matter of mores and manners, and the reemergence of an almost classical model of education and cultivation took hold.

Along with the the rise of the gun, there was the printing press. The existence of ancient graffiti in Egypt and Rome tells us that we should be cautious about assuming that literacy was rare in antiquity, but we should also admit that it was not quite common (when men of the lower classes were allowed in the legions in the late republic there were accommodations made for the fact that many would be illiterate).

The printing press was a technology that made production of printed works much easier. And so Europe was indudated with pamphlets and books. This was not always due to the literate content, as illustrations were quite influential. But it is hard to deny that this spread of information technology probably triggered a blooming of the “republic of letters” not out of chance, but necessity. The intellectuals of the medieval period were by and large clerics, but now they were joined by newly emerged urban professionals and the leisured nobility.

The Age of the Princes and their Liberal Critic

As medieval Western Christendom entered into the final stages of putrefaction something new was ripening within it. I do not believe it is coincidental that the Iberian powers were pushing forward and exploring the world beyond Europe in the decades before Martin Luther, and during the same period new learning was overturning the long reigning scholasticism.

At the center of much of the cultural religious ferment was Desiderius Erasmus. Born in 1466, he was the illegitimate son of a priest, and became a priest himself. After a fashion he was man of the later medieval period, born of a cleric who violated his vows of chastity, in the decades after the papacy was riven between different claimants, and conciliarism attempted to throw the Western Church back to a more antiquated style of governance. This was the age of the Borgia and Medici popes.

Erasmus’ accomplishments are legion in the field of humanities. Today he would be a stellar public intellectual, as well as a productive research scholar. He was the prince of the republic of letters of his day.

Like many Catholic reformers Erasmus aimed to sweep the superstition from his faith, and mocked and criticized the corruptions that he saw in the Church. With his pen he attempted to reform Christian civilization in his own image, sincere of faith and theologically orthodox, shorn of the idolatrous excesses of the medieval Catholicism, with its cult of saints and Marian devotions, as well as contemptuous of the hypocrisy of the clerical class as a whole (though still reverential of its role in performing the sacraments).

Erasmus was instrumental in the rebirth of the liberal arts in Europe in his day. But it seems clear that Erasmus was also fundamentally a liberal person in his attitude toward deviation from what he himself thought was true and right. And, events at the end of his life also suggest that he was much more accepting of the imperfections of the institutions which he critiqued throughout his whole life than others would be.

The Age of the Zealot

The last 19 years of Erasmus’ life overlapped with the Reformation. At the peak of his fame and influence men such as Luther reached out to him, but Erasmus did not return their enthusiasm in kind. The Reformation unleashed atavistic passions, and much of the world Erasmus had known, that he had critiqued and chided, collapsed before him.

Where Erasmus inveighed against the corruption of the Catholic Church, zealous new converts to the Protestant cause destroyed church property and relics, and expelled priests from their territory. When the Jews did not convert to Luther’s form of Christianity, he attacked them. When the peasants rose up against their lords, analogizing their rebellion to that of Luther and his colleagues, he justified their slaughter. When Erasmus temporized Luther attacked him.

Though there were long periods of peace in the decades after Erasmus’ death, the St. Bartholomew’s Day massacre became emblematic of an age. The period of the Reformation is also one of the age of Wars of Religion. The whole map of Europe transformed due to religious disputes, and between 25 to 50 percent of the population of the German nation died during the Thirty Years War due to causes rooted in the war itself.

In Northern Europe they burned witches. In Southern Europe the inquisition was in full effect. In France Protestants and Catholics lived separate lives, until the French monarchy gave the Protestants a choice of conversion or emigration.

Ideas With Consequences

In Erasmus’ life and work we see the shadow of the future. Some figures just subsequent to him, such as Montaigne, echoed his liberality of spirit. But they were marginalized for centuries by the intolerance of Luther, the controlling character of Calvin, and the machinations of the Jesuits. The power of monarchs grew, as they dispossessed the Catholic Church, or claimed that the Catholic Church gave them divine right to rule.

Charity toward those with whom one disagreed with, a plea of Erasmus in his later  years, disappeared. And what reason had the Catholics to be generous to the Protestants after the iconoclastic attacks on their sacred sites and objects? Protestants when they were expelled or forcibly converted by Catholics? Reformed when they were driven out of Lutheran and Catholic lands? Baptists when they were oppressed everywhere?

The decline of the centrality of fighting as the primary task of nobles, and the rise of humanist and cultured values among the aristocracy, was coincident with wars which tore the fabric of Europe apart for generations, over and over.

The Exhausted Return

Of course as I write today in 2017 the figure of Erasmus strikes many moderns, whatever our religious inclinations, as an admirable one. His emphasis on heart, and the fact that his heart was in the right place, are appealing. His liberality of spirit, his low tolerance for hypocrisy and corruption, but acceptance of genuine disagreement due to human fallibility, are characteristics many of us would wish we could cultivate more.

But it’s nearly 500 years since he died, and it took about two centuries after he died for the long road to enlightenment to put us where we are now. Erasmus shows us that a moderate position, taking the middle path, speaking in the language of intellectuals, has difficulties with the zealots who spew the argot of the street. John Calvin had a humanist education, as did many of the Reformers were humanists, but that did not prevent him from burning a heretic and giving voice to his inner totalitarian (though I do understand that Geneva was not totalitarian in a way we would understand it today). Humanism became a tool, part of one’s education, as opposed to the broad liberal minded spirit with Erasmus exemplified.

When learning is instrumentalized, when it is reduced purely to a tool in the service of society, that enslavement saps something out of its spirit. The idea of truth, the valorization of it above other things, likely does have broader cultural consequences. Without truth, I believe that our species reverts to zero-sum and negative-sum “games.” That was our past. I believe it could be our future.

 

May 4, 2017

The great Han Empire in Africa

Filed under: Africa,Chinese,Chinese in Africa,Culture,History — Razib Khan @ 10:23 pm

Howard French’s China’s Second Continent: How a Million Migrants Are Building a New Empire in Africa is a bit cliche. Rather than a scholarly book it’s more an observational travelogue, and it suffers somewhat from the fact that it is focused on Chinese who live in Africa, but are never of it. Chinese are Chinese, and those who migrate to Africa have more commonalities than most. So French’s attempts to spin out distinct experiences was a bit stretched. Basically, the same thing is happening over and over across the African continent.

When I say this that it is cliche, I’m alluding to the fact that for many Chinese presence in Africa is rather well known. But the reality is not everyone knows about it. So I was happy to see The New York Times put this issue front and center, Is China the World’s New Colonial Power?

There are twists which are important to remember. First, China’s working age population has been declining since 2012. This is going to put a crimp in any “imperial” ambitions. Second, this Chinese “empire” is not going to be an explicitly political one, but rather one of influence, control, and tough soft power.

That being said, we should’t underestimate the will and need of the Chinese to have their “time in the sun.” Fifteen years ago Ross Terrill wrote The New Chinese Empire. In it be observed that for much of Chinese history there has long been a division between a moralistic/ideological camp and a more nationalist realpolitik element. He traces this division back to antiquity, with Confucianism and Legalism as the prototypes (I’m not sure I believe this). But Terrill observed that Deng Xiaoping and the leaders who he cultivated and promoted to succeed him were generally much more nakedly nationalistic than Mao ever was.

Just something to keep in mind as we look to the future….

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