# On the precipice of the Kali Yuga

The idea of decline is an old one. See The Idea of Decline in Western History for a culturally delimited view. But whether it is Pandora opening her box or Eve biting the apple, the concept of an idyllic past and the ripeness of imminent decline seems baked into the cake of human cultural cognition. It was always better in the good old days.

Of course there is the flip side of those who presume that the Eternal City will continue as it always was unto the end of time. Meanwhile, cornucopian optimists of our modern era, such as Steve Pinker, are the historical aberration. But they are influential in our age.

Tanner Greer has a profoundly pessimistic post up, Everything is Worse in China, which is getting some attention (as I’ve stated before Tanner’s blog in general is worth a read). Rod Dreher has two follow up posts in response. First, A: Confucius, Basically, which is somewhat an answer to Tanner. And then an email from Tanner himself. It is here that he suggests to Rod’s readers Xunzi: The Complete Text. That is all for the good (for a broader view, A Short History of Chinese Philosophy).

Readers can probably read between the lines that I have been gripped somewhat by Sinophilia of late. I am rather pessimistic about the state of American culture and the prospects for the American republic as we have known it. I don’t see any of the major political factions offering up a solution for the impending immiseration of the middle class.

So I look to the east. Much of the history of the world has been a history of Asia, and it seems we are going to go back in that direction. If we are pessimistic about China, to a great extent we are pessimistic about the world.

Perhaps then we need to abandon the idol of the nation-state, or in China’s case the nation-civilization. Rod Dreher has the Benedict Option for orthodox Christians* But we need to think bigger. Men and women of civilized inclinations may need to band together, and form secret societies shielded from the avarice of the institutional engines which channel human passions toward inexorable ends. We need a strategy for living as civilized people in an anarchic world, an archipelago of oligarchy in the sea of barbarism. Sooner, rather than later.

History comes at you fast.

* I mean here Trinitarian Christians of a traditionalist bent, not Eastern or Oriental Orthodox Christians.

# Ancient Europeans: isolated, always on the edge of extinction

A few years ago I suggested to the paleoanthropologist Chris Stringer that the first modern humans who arrived in Europe did not contribute appreciable ancestry to modern populations in the continent (appreciable as in 1% or more of the genome).* It seems I may have been right according to results from a 2016 paper, The genetic history of Ice Age Europe. The very oldest European ancient genome samples “failed to contribute appreciably to the current European gene pool.”

Why did I make this claim? Two reasons:

1) 40,000 years is a long time, and there was already substantial evidence of major population turnovers across northern Eurasia by this point. You go far enough into the future and it’s not likely that a local population leaves any descendants. So just work that logic backward.

2) There was already evidence of low population sizes and high isolation levels between groups in Pleistocene and Mesolithic/Neolithic Europe. This would again argue in favor of a high likelihood of local extinctions give enough time.

This does not only apply to just modern humans, descendants of southern, likely African, populations. Neanderthals themselves show evidence of high homogeneity, and expansions through bottlenecks over the ~600,000 years of their flourishing.

The reason that these dynamics characterized modern humans and earlier hominins in northern Eurasia is what ecologists would term an abiotic factor: the Ice Age. Obviously humans could make a go of it on the margins of the tundra (the Neanderthals seem less adept at penetrating the very coldest of terrain in comparison to their modern human successors; they likely frequented the wooded fringes, see The Humans Who Went Extinct). We have the evidence of several million years of continuous habitation by our lineage. But many of the ancient genomes from these areas, whether they be Denisovan, Neanderthal, or Mesolithic European hunter-gatherer, show indications of being characterized by very low effective population sizes. Things only change with the arrival of farming and agro-pastoralism.

For two obvious reasons we happen to have many ancient European genomes. First, many of the researchers are located in Europe, and the continent has a well developed archaeological profession which can provide well preserved samples with provenance and dates. And second, Europe is cool enough that degradation rates are going to be lower than if the climate was warmer. But if Europe, as part of northern Eurasia, is subject to peculiar exceptional demographic dynamics we need to be cautious about generalizing in terms of the inferences we make about human population genetic history. Remember that ancient Middle Eastern farmers already show evidence of having notably larger effective population sizes than European hunter-gatherers.

Two new preprints confirm the long term population dynamics typical of European hunter-gatherers, Assessing the relationship of ancient and modern populations and Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. The first preprint is rather methods heavy, and seems more of a pathfinder toward new ways to extract more analytic juice from ancient DNA results. Those who have worked with population genomic data are probably not surprised at the emphasis on collecting numbers of individuals as opposed to single genome quality. That is, for the questions population geneticists are interested in “two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage.”

I encourage readers (and “peer reviewers”) to dig into the appendix of Assessing the relationship of ancient and modern populations. I won’t pretend I have (yet). Rather, I want to highlight an interesting empirical finding when the method was applied to extant ancient genomic samples: “we found that no ancient samples represent direct ancestors of modern Europeans.”

This is not surprising. The ‘hunter-gatherer’ resurgence of the Middle Neolithic notwithstanding, Northern Europe was subject to two major population replacements, while Southern Europe was subject to one, but of a substantial nature. Recall that the Bell Beaker paper found that “spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain’s Neolithic gene pool within a few hundred years.” This means that less than 10% of modern Britons’ ancestry are a combination of hunter-gatherers and Neolithic farmers.

And yet if you look at various forms of model-based admixture analyses it seems as if modern Europeans have substantial dollops of hunter-gatherer ancestry (and hunter-gatherer U5 mtDNA and Y chromosomal lineage I1 and I2, associated with Pleistocene Europeans, is found at ~10% frequency in modern Europe in the aggregate; though I suspect this is a floor). What gives? Let’s look at the second preprint, which is more focused on new empirical results from ancient Scandinavian genomes, Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. From early on in the preprint:

Based on SF12’s high-coverage and high-quality genome, we estimate the number of single nucleotide polymorphisms (SNPs) hitherto unknown (that are not recorded in dbSNP (v142)) to be c. 10,600. This is almost twice the number of unique variants (c. 6,000) per Finnish individual (Supplementary Information 3) and close to the median per European individual in the 1000 Genomes Project (23) (c. 11,400, Supplementary Information 3). At least 17% of these SNPs that are not found in modern-day individuals, were in fact common among the Mesolithic Scandinavians (seen in the low coverage data conditional on the observation in SF12), suggesting that a substantial fraction of human variation has been lost in the past 9,000 years (Supplementary Information 3). In other words, the SHGs (as well as WHGs and EHGs) have no direct descendants, or a population that show direct continuity with the Mesolithic populations (Supplementary Information 6) (13–17). Thus, many genetic variants found in Mesolithic individuals have not been carried over to modern-day groups.

The gist of the paper in terms of archaeology and demographic history is that Scandinavian hunter-gatherers were a compound population. One component of their ancestry is what we term “Western hunter-gatherers” (WHG), who descended from the late  Pleistocene Villabruna cluster (see paper mentioned earlier). Samples from Belgium, Switzerland, and Spain all belong to this cluster. The second element are “Eastern hunter-gatherers” (EHG). These samples derive from the Karelia region, to the east of modern Finland, bound by the White Sea to the north. EHG populations exhibit affinities to both WHG as well as Siberian populations who contributed ancestry to Amerindians, the “Ancestral North Eurasians” (ANE). There is a question at this point whether EHG are the product of a pulse admixture between an ANE and WHG population, or whether there was a long existent ANE-WHG east-west cline which the EHG were situated upon. That is neither here nor there (the Tartu group has a paper addressing this leaning toward isolation-by-distance from what I recall).

Explicitly testing models to the genetic data the authors conclude that there was a migration of EHG populations with a specific archaeological culture around the north fringe of Scandinavia, down the Norwegian coast. Conversely, a WHG population presumably migrated up from the south and somewhat to the east (from the Norwegian perspective).

And yet the distinctiveness of the very high quality genome as inferred from unique SNPs they have suggests to them that very little of the ancestry of modern Scandinavians (and Finns to be sure) derives from these ancient populations. Very little does not mean all. There is a lot of functional analysis in the paper and supplements which I will not discuss in this post, and one aspect is that it seems some adaptive alleles for high latitudes might persist down to the present in Nordic populations as a gift from these ancient forebears. This is no surprise, not all regions of the genome are created equal (a more extreme case is the Denisovan derived high altitude adaptation haplotype in modern Tibetans).

Nevertheless, there was a great disruption. First, the arrival of farmers whose ultimate origins were Anatolia ~6,000 years ago to the southern third of Scandinavia introduced a new element which came in force (agriculture spread over the south in a few centuries). A bit over a thousand years later the Corded Ware people, who were likely Indo-European speakers, arrived. These Indo-European speakers brought with them a substantial proportion of ancestry related to the hunter-gatherers because they descended in major fraction from the EHG (and later accrued more European hunter-gatherer ancestry from both the early farmers and likely some residual hunter-gatherer populations who switched to agro-pastoralism**).

For several years I’ve had discussions with researchers whose daily bread & butter are the ancient DNA data sets of Europe. I’ve gotten some impressions implicitly, and also from things they’ve said directly. It strikes me that the Bantu expansion may not be a bad analogy in regards to the expansion of farming in Europe (and later agro-pastoralism). Though the expanding farmers initial mixed with hunter-gatherers on the frontier, once they got a head of steam they likely replaced small hunter-gatherer groups in totality, except in areas like Scandinavia and along the maritime fringe where ecological conditions were such hunter-gatherers were at advantage (War Before Civilization seems to describe a massive farmer vs. coastal forager war on the North Sea).

But this is not the end of the story for Norden. At SMBE I saw some ancient genome analysis from Finland on a poster. Combined with ancient genomic analysis from the Baltic, along with deeper analysis of modern Finnish mtDNA, it seems likely that the expansion of Finno-Samic languages occurred on the order of ~2,000 years ago. After the initial expansion of Corded Ware agro-pastoralists.

The Sami in particular seem to have followed the same path along the northern fringe of Scandinavia that the EHG blazed. Though they herd reindeer, they were also Europe’s last indigenous hunter-gatherers. Genetically they exhibit the same minority eastern affinities in their ancestry that the Finns do, though to a greater extent. But their mtDNA harbors some distinctive lineages, which might be evidence of absorption of ancient Scandinavian substate.

I’ll leave it to someone else to explain how and why the Finns and Sami came to occupy the areas where they currently dominate (note that historically Sami were present much further south in Norway and Sweden than they are today). But note that in Latvia and Lithuania the N1c Y chromosomal lineage is very common, despite no language shift, indicating that there was a great deal of reciprocal mixing on the Baltic.

Overall the story is of both population and cultural turnover. This should not surprise when one considers that northern Eurasia is on the frontier of the human range. And perhaps it should temper the inferences we make about other areas of the world.

* You may notice that this threshold is lower than the Neanderthal admixture proportions in the non-African genome. Why is this old admixture still detectable while modern human lineages go extinct? Because it seems to have occurred with non-African humans had a very small effective population, and was mixed thoroughly. Because of the even genomic distribution this ancestry has not been lost in any of the daughter populations.

** Haplogroup I1, which descends from European late Pleistocene populations, exhibits a star phylogeny of similar time depth as R1b and R1a.

Finished The Enigma of Reason. The basic thesis that reasoning is a way to convince people after you’ve already come to a conclusion, that is, rationalization, was already one I shared. That makes sense since one of the coauthors, Dan Sperber, has been influential in the “naturalistic” school of anthropology. If you’ve read books like In Gods We Trust The Enigma of Reason goes fast. But it is important to note that the cognitive anthropology perspective is useful in things besides religion. I’m thinking in particular of politics.

I haven’t been blogging much since I was abroad on a business trip. Specifically to the Persian Gulf. I’ll say more later, though I am going to be vague on geography since I’d rather not mix these two streams of my life (also, to be clear, this is not related to my day job).

One Family, Many Revolutions: From Black Panthers, to Silicon Valley, to Trump. I had known of this connection before, between Ben Horowitz, the Silicon Valley VC guy, and David Horowitz, the right-wing provocateur. The elder Horowitz’s contention that one needs to play dirty to get anywhere is a position that I believe has more support today than it did ten years ago. The culture has come to him.

Don’t Believe in God? Maybe You’ll Try U.F.O.s. No surprise.

43 Senators Want to Make It a Federal Crime to Boycott Israeli Settlements. Here are the sponsors. I’ve never felt so sympathetic toward BDS….

My piece in India Today on South Asian genetics is hitting the printing press this week.

# Castes are not just of mind

Before Nicholas Dirks was a controversial chancellor of UC Berkeley, he was a well regarded historian of South Asia. He wrote Castes of Mind: Colonialism and the Making of Modern India. I read it, along with other books on the topic in the middle 2000s.

Here is Amazon summary from Library Journal:

Is India’s caste system the remnant of ancient India’s social practices or the result of the historical relationship between India and British colonial rule? Dirks (history and anthropology, Columbia Univ.) elects to support the latter view. Adhering to the school of Orientalist thought promulgated by Edward Said and Bernard Cohn, Dirks argues that British colonial control of India for 200 years pivoted on its manipulation of the caste system. He hypothesizes that caste was used to organize India’s diverse social groups for the benefit of British control. His thesis embraces substantial and powerfully argued evidence. It suffers, however, from its restricted focus to mainly southern India and its near polemic and obsessive assertions. Authors with differing views on India’s ethnology suffer near-peremptory dismissal. Nevertheless, this groundbreaking work of interpretation demands a careful scholarly reading and response.

The condensation is too reductive. Dirks does not assert that caste structures (and jati) date to the British period, but the thrust of the book clearly leaves the impression that this particular identity’s formative shape on the modern landscape derives from the colonial experience. The British did not invent caste, but the modern relevance seems to date to the British period.

This is in keeping with a mode of thought flourishing today under the rubric of postcolonialism, with roots back to Edward Said’s Orientalism. As a scholar of literature Said’s historical analysis suffered from the lack of deep knowledge. A cursory reading of Orientalism picks up all sorts of errors of fact. But compared to his heirs Said was actually a paragon of analytical rigor. I say this after reading some contemporary postcolonial works, and going back and re-reading Orientalism.

To not put too fine a point on it postcolonialism is more about a rhetorical posture which aims to destroy what it perceives as Western hegemonic culture. In the process it transforms the modern West into the causal root of almost all social and cultural phenomenon, especially those that are not egalitarian. Anyone with a casual grasp of world history can see this, which basically means very few can, since so few actually care about details of fact.

Castes of Mind is an interesting book, and a denser piece of scholarship than Orientalism. Its perspective is clear, and though it is not without qualification, many people read it to mean that caste was socially constructed by the British.

This seems false. It has become quite evident that even the classical varna categories seem to correlate with genome-wide patterns of relatedness. And the Indian jatis have been endogamous for on the order of two thousand years. From The New York Times, In South Asian Social Castes, a Living Lab for Genetic Disease:

The Vysya may have other medical predispositions that have yet to be characterized — as may hundreds of other subpopulations across South Asia, according to a study published in Nature Genetics on Monday. The researchers suspect that many such medical conditions are related to how these groups have stayed genetically separate while living side by side for thousands of years.

This is not really a new finding. It was clear in 2009’s Reconstructing Indian Population History. It’s more clear now in The promise of disease gene discovery in South Asia.

Unfortunately though science is not well known in any depth among the general public. The ascendency of social constructionism is such that a garbled and debased view that “caste was invented by the British” will continue to be the “smart” and fashionable view among many intellectual elites.

I know that Game of Thrones is premiering tonight, but just wanted to remind readers that R. Scott Bakker’s The Unholy Consult will be out in a week. The author, R. Scott Bakker, has a blog, Three Pound Brain. He has some strange ideas…much of which I can’t make heads or tails of. But that’s OK, I enjoy his fiction, I don’t worship his philosophy.

I’m traveling, so not much time to comment. But let me say that I’m sad to see that Maryam Mirzakhani has died.

If you want to get a sense of the historical background of the framework within which I write much of this blog, you might find Will Provine’s The Origins of Theoretical Population Genetics of interest.

Tucker Carlson Goes to War Against the Neocons. I know that most people on the Left don’t like Tucker Carlson now because of his recent political postures, but back in the 2000s he was known as a quite heterodox (read: not partisan and boring) commentator. And I have to say that it is nice for someone to say what may of us, including former supporters of the Iraq invasion, think now and then when we recall the period before 2011.

# The past was not PG

The Week has published a screed against the low moral quality of Game of Thrones, Game of Thrones is bad — and bad for you. Obviously there is something to this insofar as one can see a coarsening of entertainment, or at least a decline in the stylized aspects of the depiction of reality.

But one of my initial reactions is that much of the narrative that we value from the past was not particularly PG. If you read The Harlot by the Side of the Road: Forbidden Tales of the Bible you see that the “Good Book”, in fact the only book many read front to back by many after the Reformation in Protestant Europe, has some quite unsavory tales. The story of Judah and Tamar in particular is hard to digest from a modern Western perspective because many of the elements are understated and workaday. Greek mythology is no better obviously. From Zeus raping Leda, Achilles throwing a fit because his sex-slave was taken away, to the tradition of Agamemnon sacrificing Iphigenia.

In some cases the shocking aspect of ancient stories is because moderns have different values. Slavery and concubinage were taken for granted during the period that the Hebrew Bible and Classical mythology crystallized into the forms which came down to us. In other cases I presume that it was unlikely that small children were going to ever read the original stories themselves, so sexual elements that might confuse were probably omitted in some oral tellings.

This is not to say that Game of Thrones is a modern masterpiece. But some of the disquieting, and frankly perverse, aspects of the narrative are only shocking if your standard is the relatively antiseptic literary fiction which one finds between the Regency and the cultural revolution of the 1960s. That is the aberration in human history, while gritty genre fiction much closer to primal human storytelling.

# When white people were “ethnic”

In the period between 2005 and 2010 I spent a fair amount of time reading about American history. And one aspect which interested me was the nature of the assimilation of white Americans of non-Protestant background, in particular Roman Catholics and Jews. This was triggered by reading The Impossibility of Religious Freedom, where the author argues that the modern American conception of church-state separation is difficult to understand in practice unless religion is defined as something similar to low church American Protestantism

Though the American founding was famously eclectic and tolerant, as befitted a republic designed by men with elite Enlightenment sensibilities, it was culturally without a doubt Protestant in heritage, if not belief. The American Revolutionary Zeitgeist was steeped in British-influenced anti-Catholicism. In keeping with the same sort of Protestant populism which inspired the Gordon riots a broad swath of American colonial opinion was critical of the Quebec Act for giving French speaking Catholics a modicum of religious liberty and equality before the law.

Despite this historical context the relationship between the Roman Catholic population and the American republic in the early years was relatively amicable. Most of the priests were French Canadians, and Catholic population was highly assimilated and integrated. The great change occurred with the arrival of large numbers of Roman Catholic Irish, as well as a Irish American clerical ascendency which drew upon a revival in the Church in Ireland.

John T. McGreevy’s Catholicism and American Freedom is probably the best history of the religion in the United States that I read during that period. Not because it’s comprehensive, it’s not. Rather, because it focuses on the tension between the Church and the American republic and society, and how it resolved itself, and how that resolution unravelled.

Periodically people in the media make allusions to the ability of the American republic and culture to assimilate Catholics and Jews, and how that might apply to Muslims today. The discussion really frustrates me because there is almost never an acknowledgement that Roman Catholics experienced various degrees of low-grade persecution during periods of the 19th century. The Ursuline Convent riots are just the most sensational incident, and the Know Nothing movement turned into a political party.

The expansion of public schooling in parts of this was country tied to anti-Catholicism. But the Catholics did not take this passively. The emergence of a whole counter-culture, and parochial schools, suggested that they were ready to fight back to maintain their identity. The powerful Irish clerics who served as de facto leaders of the Roman Catholic faithful seem to have wanted to establish a modus vivendi with the American government which recognized the Church’s corporate role in society. By and large American elites and culture rejected this attempt to import a European style model to the New World.

By the late 19th century a movement began in the American Roman Catholic Church which became labeled the Americanist heresy. Despite its official condemnation I would argue that “Americanism” eventually became the de facto ideology of most American Roman Catholics. As Catholics conceded and assimilated toward American liberal and democratic norms in their everyday life, the hostility from the general public declined, and by the middle of the 20th century Will Herberg’s Protestant, Catholic, Jew articulated a vision of religious harmony among white Americans.

It should be rather obvious from the above that I believe this religious harmony was achieved in large part through concessions that American Catholics made to the folkways of the United States. You see the same dynamic in Jonathan Sarna’s American Judaism. Second, in Catholicism and American Freedom McGreevy lays out the great unravelling of the Catholic hierarchy’s understanding with American society which occurred in the 1960s, as social liberalism went far beyond what even the most progressive Roman Catholic intellectuals were ready to countenance. And in this cultural revolution Catholics were shocked to find that their Jewish allies made common cause with mainline Protestants and post-Protestants.

The reason I am writing this is that the American landscape today is different in deep ways from that of the 19th and early 20th century. The lessons of Catholic and Jewish assimilation to a Protestant understanding of religion were achieved through bitter conflict, and the rejection of a corporatist accommodation between the American government and religious minorities, as was achieved in several European countries. The modern ideas of religious pluralism are fundamentally different from the explicit understanding of Protestant supremacy which ruled the day a century ago, and only slowly faded with assimilation of non-Protestants.

# 23andMe ancestry only is $49.99 for Prime Day 23andMe has gone below$50 for “Prime Day”! For those of us who bought kits (albeit more fully featured) at $399 or even more this is pretty incredible. But from what I’m to understand these sorts of SNP-chips are now possible to purchase from Illumina for well less than$50 so this isn’t charitable.

At minimum a way to get a raw genotype you can bank later.

# The sons of Ham and Shem

Recently I had the pleasure of having lunch with David Reich and he asked me about my opinions in relation to the Afro-Asiatic languages. I thought it was a strange question in that I get asked about that in the comments of this weblog too. Why would I have any particular insight? I gave him what I thought was the likely answer: Afro-Asiatic languages probably emerged from the western Levant. The ancient textual evidence indicates that to the north and east of Mesopotamia the languages were not Semitic. Though Akkadian, a Semitic language, was present at the dawn of civilization, Sumerian was the dominant language culturally in the land between two rivers, and it was not Semitic. As Lazaridis et al. did not detect noticeable Sub-Saharan African ancestry in Natufians, or later Near Easterners, I have become skeptical of any Sub-Saharan African origin for Afro-Asiatic.

But after the earlier post I made a few mental connections, and so I’ll put something up which pushes forward my confidence on a few issues. They lean predominantly on Y chromosomes. I understand that this sort of phylogeography has been shown to be not too powerful in the past, but in the scaffold of the ancient DNA framework it can resolve some issues.

About a decade ago study of Adolf Hitler’s paternal lineage (through male relatives) indicated that his haplogroup was E1b1b. Though reports that Hitler was non-European, because this is a very common lineage in non-Europeans, as well as Jews, were incorrect, it does turn out that Hitler’s paternal lineage is not associated with the Indo-European migrations. That is, unlike me, Adolf Hitler does not descend from the All-father, but rather one of the men who were conquered and assimilated by the steppe pastoralists.

But E1b1b is an interesting lineage. First, it is very common in much of Africa, especially the north. Second, it is common among the Natufian people according to Lazaridis et al. In contrast the Neolithic Iranian farmers seem to have harbored haplogroups J. Today the Near East is a mix of the two, which makes sense in light of the fact that reciprocal gene flow has occurred in the last 6,000 years.

Looking at E1b1b frequencies you notice a few things. The highest frequencies with large N’s are in the Cushitic and Berber languages. Haplogroup J has a different distribution, being skewed more to West Asia. In Ethiopia E1b1b is more common, but J is far more prevalent among the Semitic Amhara than the Cushitic Oromo. Though it is subtle autosomal DNA makes it clear that the Semitic speaking populations in Ethiopia-Somalia have more Eurasian ancestry than the Cushitic ones. I believe this is evidence of the multiple migration pattern discerned earlier.

If you go further south in East Africa and compare E1b1b and J you see a skew in the ratio. E1b1b declines in frequency, but J basically disappears. Among the Masai, who have a clear minor West Eurasian ancestral component, albeit far less than Ethiopians, 50% carry E1b1b. Among the Sandawe, who are a language isolate  with clicks, but exhibit Cushitic genetic affinities, 34% carry E1b1b. Among their Hadza hunter-gatherer neighbors, 15% do so. Among many Khoisan groups the frequency of E1b1b is 10%. Most of these groups exhibit no J haplogroup. This aligns easily with what Skoglund was reporting earlier: the first pastoralists had no “eastern farmer,” but did have “western farmer.” The Natufians were E1b1b. The wider reach of E1b1b in Africa in comparison to J is likely due to the fact that the admixed pastoralists were pushing into relatively virgin territories. Later Eurasian backflow events, which brought Semitic languages, encountered a much more densely populated Africa.

The hypothesis I present is that after the descendants of the Natufians made the transition to farming, some immediately pushed into areas of Africa suitable for farming and/or pastoralism. They quick diversified into the various Berber and Cushitic languages. The adoption of Nilo-Saharan languages, and later Khoisan ones, was simply the process of successive and serial admixture into local populations as these paternal lineages introduced their lifestyle. In the Near East many distinct Semitic languages persisted across the Fertile Crescent, and for whatever reason the various non-Semitic languages faded and Semitic ones flourished.

# The great Bantu expansion was massive

Lots of stuff at SMBE of interest to me. I went to the Evolution meeting last year, and it was a little thin on genetics for me. And I go to ASHG pretty much every year, but there’s a lot of medical stuff that is not to my taste. SMBE was really pretty much my style.

In any case one of the more interesting talks was given by Pontus Skoglund (soon of the Crick Institute). He had several novel African genomes to talk about, in particular from Malawi hunter-gatherers (I believe dated to 3,000 years before the present), and one from a pre-Bantu pastoralist.

At one point Skoglund presented a plot showing what looked like an isolation by distance dynamic between the ancient Ethiopian Mota genome and a modern day Khoisan sample, with the Malawi population about $\frac{2}{3}$ of the way toward the Khoisan from the Ethiopian sample. Some of my friends from a non-human genetics background were at the talk and were getting quite excited at this point, because there is a general feeling that the Reich lab emphasizes the stylized pulse admixture model a bit too much. Rather than expansion of proto-Ethiopian-like populations and proto-Khoisan-like populations they interpreted this as evidence of a continuum or cline across East Africa. I’m not sure if this is the right interpretation of the plot presented, but it’s a reasonable one.

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

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

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

Bringing all of this together it suggests to me two things

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

Skoglund will soon have the preprint out.