The Neandertal-modern cultural synthesis

220px-Pointes_de_chatelperronA new paper in PNAS, Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne, weighs in the question of whether the Châtelperronian culture were Neandertals, with an answer in the affirmative in this case:

The displacement of Neandertals by anatomically modern humans (AMHs) 50,000–40,000 y ago in Europe has considerable biological and behavioral implications. The Châtelperronian at the Grotte du Renne (France) takes a central role in models explaining the transition, but the association of hominin fossils at this site with the Châtelperronian is debated. Here we identify additional hominin specimens at the site through proteomic zooarchaeology by mass spectrometry screening and obtain molecular (ancient DNA, ancient proteins) and chronometric data to demonstrate that these represent Neandertals that date to the Châtelperronian. The identification of an amino acid sequence specific to a clade within the genus Homo demonstrates the potential of palaeoproteomic analysis in the study of hominin taxonomy in the Late Pleistocene and warrants further exploration.

The details about stratigraphy are beyond me. But the protein and mtDNA evidence is pretty conclusive in my opinion that there are Neandertal individuals in this assemblage. Therefore, assuming their stratigraphy is correct, what you see in the Châtelperronian may be a cultural influence upon Neandertals by anatomically modern humans who were pushing into Europe at this time.

51r8Ph-vcaL._SY344_BO1,204,203,200_But cultural influence may not be the only dynamic at work. In The 10,000 Year Explosion: How Civilization Accelerated Human Evolution Greg Cochran hypothesized that Châtelperronian culture may have been a vector for Neandertal genes coming into modern human populations. And now we know that this isn’t always one directional. That is, just as modern humans absorbed genes from “archaic” populations, so archaic groups absorbed ancestry from modern populations (or at least humans closer to the main stem of modern humanity).

51dw0Uce+XL._SX330_BO1,204,203,200_In The Third Chimpanzee Jared Diamond posited that the Châtelperronian Neandertals were analogous to native peoples in the New World such as the Cherokee, who adopted many aspects of European settler culture in their attempt to resist cultural absorption and marginalization. But one dynamic we need to remember about these tribes is that they also had a lot of European ancestry, in part because of the rapidly unbalanced population sizes. It seems entirely likely, as some have posited, that the last “Neandertal” populations were also substantially admixed. Therefore, it is not entirely surprising that they would also tend to exhibit cultural features more commonly found among modern humans.

My prediction is that when whole genomes of Châtelperronian Neandertals are available it is highly likely that they often show evidence of modern human ancestry.

Note: Diamond’s The Third Chimpanzee is in my opinion a very underrated work. It is a bit dated today, but I still think it is quite worth reading.

Open Thread, 9/18/2016

What’s going on?

51I89uOM0AL._SX331_BO1,204,203,200_Very busy, so haven’t gotten much further in The Dialectical Imagination, but I do have to say that the distinction between “positive freedom” and “negative freedom” is a useful one to highlight at this point. The comments below make me unsure about the influence of the Frankfurt School on modern socio-political movements, but the ideal of a utopian end state for society which enshrine a vision of the good definitely seems to be one of the things that moderns have lost. Rather, a lot of identity politics talk seems to be about positional games and status competition. The perpetual revolution.

At the suggestion of a reader I purchased Explaining Postmodernism. The Kindle version is $4.99.

There was an ancient DNA convention in England. It turns out that the original Polynesians may not have had much Melanesian ancestry, implying multiple migrations into Far Oceania.

The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives.

The genetic structure of Denmark with SNP data


We live in an age when we have a lot of SNP data on a lot of populations. This allows for a very fine level of granularity in terms of analysis. To illustrate, Genetics recently published Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity, which analyzes hundreds of Danes with hundreds of thousands of SNPs. In The History and Geography of Human Genes, published twenty years ago, most of the analysis was grounded in pairwise comparisons between populations using hundreds of markers. Not only do we have much greater resources in terms of data, but we have various analytic frameworks which in concert allow for richer, more precise, inferences. Today we can actually assign ancestry regions of an individual’s genome!

The first author of the Genetics paper, Yorgos Athanasiadis, has put up a post where does a walk-through of the various methods step-by-step. It’s useful for anyone who has an inclination to do something similar for another data set.

This portion jumped out at me:

The six Danish regions showed highest affinity with a cluster that we call BRI(tish), because it’s mostly made up by British samples, followed by the NOR(wegian) and SWE(dish) clusters. This is not to say that Danes are about 40% made up by British DNA, as some enthusiastic twitters have mentioned. The BRI cluster also includes German, Belgian and Dutch samples, meaning that it might as well be reflecting some other ethnic component; in lack of a better name, we called it BRI. Another interesting fact is that because of the presence of this cluster, haplotype sharing with other Scandinavians was about 40%….

I think the implications of this are something I’m going to have to chew on for a while. Some of these genetics results aren’t straightforward in terms of what they mean in a vacuum, though the historical inference is obvious.

Anyway, read the whole thing, On the genetic structure of Denmark.

What little we know about megafauna


Ewen Callaway reports from a conference in England, Elephant history rewritten by ancient genomes:

Modern elephants are classified into three species: the Asian elephant (Elephas maximus) and two African elephants — the forest-dwellers (Loxodonta cyclotis) and those that live in the savannah (Loxodonta africana). The division of the African elephants, originally considered a single species, was confirmed only in 2010.

Scientists had assumed from fossil evidence that an ancient predecessor called the straight-tusked elephant (Paleoloxodon antiquus), which lived in European forests until around 100,000 years ago, was a close relative of Asian elephants.

In fact, this ancient species is most closely related to African forest elephants, a genetic analysis now reveals. Even more surprising, living forest elephants in the Congo Basin are closer kin to the extinct species than they are to today’s African savannah-dwellers. And, together with newly announced genomes from ancient mammoths, the analysis also reveals that many different elephant and mammoth species interbred in the past.

Palkopoulou and her colleagues also revealed the genomes of other animals, including four woolly mammoths (Mammuthus primigenius) and, for the first time, the whole-genome sequences of a Columbian mammoth (Mammuthus columbi) from North America and two North American mastodons (Mammut americanum).

The researchers found evidence that many of the different elephant and mammoth species had interbred. Straight-tusked elephants mated with both Asian elephants and woolly mammoths. And African savannah and forest elephants, who are known to interbreed today — hybrids of the two species live in some parts of the Democratic Republic of Congo and elsewhere — also seem to have interbred in the distant past. Palkopoulou hopes to work out when these interbreeding episodes happened.

15x coverage. This is awesome. And incredible.

The genetic legacy of Greater India

Screenshot 2016-09-15 16.38.46

51gumWkW0TLA new paper in Quaternary International, Western Eurasian genetic influences in the Indonesian archipelago, confirms what has long been suspected by smaller batch data:

…To locate the primary areas of Western Eurasian genetic influence in Indonesia, we have assembled published uniparental genetic data from ∼2900 Indonesian individuals. Frequency distributions show that Western Eurasian paternal lineages are found more commonly than Western Eurasian maternal lineages. Furthermore, the origins of these paternal lineages are more diverse than the corresponding maternal lineages, predominantly tracing back to South West and South Asia, and the Indian sub-continent, respectively. Indianized kingdoms in the Indonesian archipelago likely played a major role in dispersing Western Eurasian lineages, as these kingdoms overlap geographically with the current distribution of individuals carrying Western Eurasian genetic markers. Our data highlight the important role of these Western Eurasian migrants in contributing to the complexity of genetic diversity across the Indonesian archipelago today.

The table above highlights the distribution of paternal Indian lineages in several parts of Indonesia. These Y chromosomal haplotypes are found in the core of what was Majapahit. Some of these haplotypes might be due to shared ancient ancestry, but the presence of R1a means that it is more recently than the past 4,000 years, as I believe R1a is relatively intrusive into South Asia. Many of the other haplogroups are a diverse cross-section of those typical for South Asia.

The further question then is whether these date to the period of European colonialization, or to the first millennium A.D., when the first “Indianized kingdoms” arose in Southeast Asia. The fact that there is compelling evidence of old and even admixture in Cambodia, where colonialism was not as pervasive or longstanding as in maritime Southeast Asia, suggests that it can’t be chalked up to the Dutch presence, and their role as mediators for migration (more plainly, they enslaved many South Asians and moved them around the Indian ocean basin).

But the text of the paper makes some things rather clear:

…constant since the first contacts and exchanges between the Indian sub-continent and Indonesia in the late 1st millennium B.C.E., it is likely that this gene flow was particularly intense during the period of the Hindu kingdoms in Indonesia (7th to the 16th century AD). These assumptions, based on archaeological and historical data, are also in broad agreement with dating on unpublished genome-wide SNP markers from Island Southeast Asia (unpublished data).

Open thread, 9/12/2016

51I89uOM0AL._SX331_BO1,204,203,200_Reading The Dialectical Imagination: A History of the Frankfurt School and the Institute of Social Research, 1923-1950.

A good book. Dense. But it is clear (the author so admits) that it’s only a superficial exploration of the ideas of the Frankfurt School.

That being said, a lot of the abstruse and in my opinion wrong-headed tendencies of Critical Theory types does seem to get back to the roots. In relation to impenetrability, the influence of Heidegger on Marcuse makes a lot of sense.

The rise of the patriarchs: circumpolar edition

Screenshot 2016-09-05 12.27.38
For whatever reason I missed this paper which came out in July in AJHG, Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families. Basically it blows up sample size and utilizes NGS techniques (whole-genome) to resolve some questions around haplogroup N, and in particular the M46/TAT subclade which exhibits a peculiar geographic distribution, from the shores of the Baltic to easternmost Siberia.

Screenshot 2016-09-05 12.33.34I actually blogged about this as far back as 2003, so it’s a long term mystery. There’s no autosomal rhyme or reason to the frequency of this lineage. Yes, there is a vague Uralic affinity, but this Y chromosomal variant is higher in the Lithuanians than the Finns, and found in peoples as distant as the Koryaks. One of the major early questions was whether it was a marker that indicated east-west movement, or west-east movement. In other words, was it associated Siberian ancestry in Finns and affiliated people, or did it indicate European ancestry in Siberian people?

Rurik, carrier of N1c
Rurik, carrier of N1c
If the results in this paper are correct the likely answer is: none of the above. The core TAT lineage looks like it underwent an explosion ~5,000 years ago. This is around the same time as Northern Europeans and Siberians as we understand them were coming into being. So the TAT lineage didn’t come with a specific people, it was part of the process which made the people. I’ll quote from the discussion:

Overall, a considerable proportion of men inhabiting much of the Arctic and temperate zones of western and eastern Eurasia share N3a3’6 lineages that date back to the mid-Holocene (4.5–5.0 kya). This common patrilineal ancestry unites widely different linguistic phyla, including Indo-European, particularly Balto-Slavic, branches of the Altaic, such as the Mongolic, Turkic, Tungusic, and Chu- kotko-Kamchatkan branches, as well as the Balto-Finnic branch of the Finno-Ugric.

The autosomal genome-wide data is clear, pretty much all the Finnic peoples in Europe seem to have a small (to various degrees, with Finns proper the least), but clear, signal of admixture that is Siberian. It is tempting to associate this with the men who carried TAT into these populations, but observe that the Lithuanians seem to be lacking in this signature. Y chromosomes and autosomes are not always in alignment, but recall that many Siberians have some West Eurasian ancestry, some of it likely quite ancient, and carry R1a1a Y chromosomes. The past was more complex than we had assumed, and the relationship between movements of men and languages is likely not so straightforward in the inferences we can make. It may be that the Siberian admixture into Finnic peoples, and their linguistic identity, post-dates the arrival of TAT into the far north of Europe.

One of the aspects of the explosion of many Y chromosomal lineages 4-5,000 years ago is how much they don’t associate well with ethno-linguistic boundaries. The “Indo-Aryan” R1a1a in South Asia is very common in some low caste South Indian tribal populations. The R1b brought by the Corded-Ware culture, which presumably transmitted Indo-European languages, is at very high frequency among the non-Indo-European Basques, as well as groups such as Sardinians, who were Indo-Europeanized only in Classical Antiquity. The Y lineages seem to expanded far beyond the totality of the cultural unit.

Genetics is giving us lots of data. But there are no theoretical bones to scaffold this flesh.

Living in the age of structure

Screenshot 2016-09-05 04.14.05

Jonathan Novembre and Benjamin Peter have posted a preprint of a review, Recent advances in the study of fine-scale population structure in humans, which readers will find useful. In particular, the citations are a gold-mine for anyone attempting to navigate this literature.

The figure above from their preprint illustrates the number of markers needed to differentiate populations in Europe. Recall that genetic variation within Europe, especially Northern Europe, is rather low. It’s pretty clear that if you sample 100 SNPs from the human genome you can’t differentiate much. At 1,000 SNPs structure begins to appear, and this is starting to be well resolved by 10,000 SNPs. By 100,000 SNPs you are pretty much going to hit diminishing returns for regional diversity on Europe level scales. The pattern differs by method. PCA for example does much better with 10,000 SNPs in Europe than the model-based clustering (e.g., ADMIXTURE) in my experience, but the two are comparable as you near 100,000 SNPs. Beyond 100,000 SNPs there is not that much increase in resolution for genome-wide methods that rely on genotypes at this level of genetic diversity.

51qciM4cBhL._AC_UL320_SR242,320_Of course, if you want really fine-scale differences, between villages for examples, more markers, and perhaps whole-genome sequencing that can pick up rare variants, are useful. In other words, there are cases one can imagine where more data than is normally available on SNP-chips ps useful. But these are definite boundary conditions. Once you get to the point of distinguishing branches of extended families you really can’t collapse the genealogies any further.

Another instance where more marker density, or the power of high coverage whole-genome sequencing, might be useful is for local ancestry deconvolution. If you’re assigning ancestry to windows of the genome then your marker density is going to be a limiting factor, as you might be slicing the 100,000 SNPs into 1,000 subunits.

Finally, there’s the issue of the models being tested. Novembre and Peter allude to the fact that many of these models posit stylized discrete pulse admixtures. As it turns out in some cases ancient DNA seems to have confirmed that something like this went on. That is, long periods of local stability and panmixia, followed by genetic turnover and admixture. But they note that there isn’t a good simulation framework where demographic scenarios are allowed to generate in silico data for testing new models. In other words, biologists are currently having to rely on “natural experiments.”

Range restriction always looms

Scatterplot_r=-.76The correlation between medical school GPA and career outcomes is low. The correlation between height and number of all-star appearances in the NBA is low. The correlation between SAT score and performance as a Google engineer is low.

Actually, I don’t know if all of these are strictly true. But I think you’ve seen the general form of the fact. So, for example, a professor I knew once recounted that at his graduate institution they once looked at correlation between GRE scores and future positions at tenure track institutions. They didn’t find any association.

51sdHZvYfTL._SX334_BO1,204,203,200_ (1)But there was a problem here: the institution was one of the top 10 graduate programs in the country in the biological sciences. The GRE scores were likely to be very high already. The result reported is certainly correct. But the inference given toward a general audience is often misleading. The correct inferences is within a particular range of the independent variable the correlation between the variable (here, GRE score) and an outcome (here, a tenure track position) is low. But what is often inferred is that there is no relationship between a variable and an outcome. Period. This is usually an incorrect inference.

One reason I’m putting this post up is a blogpost I noticed, Google Finds That Successful Teams Are About Norms Not Just Smarts. It links to The New York Times Magazine article which outlined how Google had attempted to find the “perfect” makeup of a team. The title is key here: not just. Most people who get to interview at Google are very bright. They aren’t arbitrary people pulled off the street. That’s one reason that the old Google system might have been counter-productive, since you already knew that the people you were testing were good at taking tests, as opposed to gauging them on other personal characteristics (e.g., do they have social skills which might allow them to work well on a team?).

Norms matter a lot. Isaac Newton’s father was an unlettered (if prosperous) farmer. If Newton had been born a few hundred years earlier he would not have flourished as he did. Norms matter. Culture matters. But not all men are born Isaac Newtons. Aptitude matters too. When we observe that norms and culture matters in the context of genius we are often engaging in range restriction. The individuals who illustrate the power of culture are not arbitrarily selected from the whole population.

The filament across Eurasia

silkroad51u0BtDlYJL._SX329_BO1,204,203,200_Several people have asked me about this article in Foreign Policy, Does Chinese Civilization Come From Ancient Egypt? It’s interesting in terms of cultural commentary, and what it say about open-mindedness among the Chinese public and academy. In many ways the Chinese are much less open-minded than Westerners after decades of Marxism…but in other ways, they are surprisingly liberal in the classical sense. Willing to entertain crazy ideas out of left field.

The hypothesis that the roots of Chinese civilization diffused from ancient Egypt via the vector of a Hyksos migration is definitely a bridge too far. There’s no strong evidence for it from what I’ve seen. But there are different forms of diffusion. As highlighted in the article itself there is good evidence of cultural diffusion of specific elements of Shang technology, such as chariots. The chariot was the weapon of mass destruction of the Bronze Age. Once invented, it spread rapidly from one end of Eurasia to the other (and, into Egypt as well).

But there are still elements of uncertainty as to how it spread. One model is that it was transmitted from one society to another, in a process akin to how guns or influenza might have spread among Native Americans. Then, there is the leapfrog model, whereby long distance migration and travel serve to facilitate diffusion of culture (and genes).

k8882In the late 2000s I read Empires of the Silk Road: A History of Central Eurasia from the Bronze Age to the Present Reprint Edition, a sprawling and idiosyncratic book which makes the case for the centrality of the Eurasian “Heartland” to world history. The author suggests as an aside that the progenitors of the Shang themselves may have been from the steppe, perhaps Indo-Europeans. At the time I dismissed that as lacking evidence.

But the past half a decade or more has shown us that populations moved a long more in the past 10,000 years than we’d have been led to believe. I am probably more open to an Indo-European influence on early Chinese civilization than I was in the late 2000s. This is where Y chromosomes are helpful. Below are Y chromosomal distributions of some ethnic minorities from northern and western China today:

Screenshot 2016-09-04 19.31.00

And here’s a table of a more diverse set of East Asian groups:

Screenshot 2016-09-04 19.32.30

The question of timescale is important. The Chinese Tatars arrived only in the last few hundred years from the Volga region of Russia. They have a lot of haplogroup I, which seems to be carried over from Pleistocene era West Eurasian populations. In contrast, we know that haplgroup R1a1a, and in particular the Z93 subclade common among South and Central Asians, was present in the Altai region during the Bronze Age because of ancient DNA. And we see R1a1a across many populations in these data. Unfortunately though there isn’t a breakdown between European and Asian subclades, because there has been a long movement back and forth on the steppe in the last 4,000 years (the Uyghurs also carry H, which is typical more of South Asian groups, indicating movement across the Pamirs, as has been historically attested). But the high frequency among the Uyghurs, the low frequency of other West Eurasian Y haplogroups, such as R1b and I (as well as the presence of J), are suggestive (along with autosomal work) of pre-Mongol West Eurasian heritage.

This is obvious to anyone who knows the history of the Silk Road and the European features of the mummies of Xinjiang (not to mention the cave paintings). The ancient DNA and history indicate that very early on a mixed population of western and eastern origins emerged in the heart of Eurasia. The question then is what role did they play in Chinese history? Almost certainly at minimum they were the vector by which the knowledge of the construction of chariots and other aspects of the West Eurasian military-industrial system were transmitted (just as later they were instrumental in the transmission of Buddhism). At maximum, they may have been the seeds around which chariot elites emerged in the Shang period.

The genetic data suggest that if there was a demographic impact, it was very small. The Han Chinese in the data which carry West Eurasian haplogroups are invariably sampled from the far north and west. Regions where assimilation of non-Han minorities to a Han identity has been common. Unlike Europe and South Asia, and like the Middle East, the Y chromosomes in East Asia do not as a whole seem star-shaped. This suggests that the demographic basis of the elites probably dates to the Neolithic, and was indigenous, as opposed to migrants from elsewhere. The role of Indo-Europeans was probably stimulative, rather than directive.