"Eight thousand years of natural selection in Europe" preprint - updated with Anatolian Neolithic and other data

Eight thousand years of natural selection in Europe

The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. [. . .]

Our sample of 26 Anatolian Neolithic individuals represents the first genome-wide ancient DNA data from the eastern Mediterranean. Our success at analyzing such a large number of samples is likely due to the fact that at the Barcin site–the source of 21 of the working samples–we sampled from the cochlea of the petrous bone 9 , which has been shown to increase the amount of DNA obtained by up to two orders of magnitude relative to teeth (the next-most-promising tissue) 3 . Principal component (PCA) and ADMIXTURE 10 analysis, shows that the Anatolian Neolithic samples do not resemble any present-day Near Eastern populations but are shifted towards Europe, clustering with Neolithic European farmers (EEF) from Germany, Hungary, and Spain 7 (Fig. 1b, Extended Data Fig. 2). Further evidence that the Anatolian Neolithic and EEF were related comes from the high frequency (47%; n=15) of Y-chromosome haplogroup G2a typical of ancient EEF samples 7 (Supplementary Data Table 1), and the low F ST (0.005-0.016) between Neolithic Anatolians and EEF (Supplementary Data Table 2). These results support the hypothesis 7 of a common ancestral population of EEF prior to their dispersal along distinct inland/central European and coastal/Mediterranean routes. The EEF are slightly more shifted to Europe in the PCA than are the Anatolian Neolithic (Fig. 1b) and have significantly more admixture from Western hunter-gatherers (WHG), shown by f 4 -statistics (|Z|>6 standard errors from 0) and negative f 3 -statistics (|Z|>4) 11 (Extended Data Table 3). We estimate that the EEF have 7- 11% more WHG admixture than their Anatolian relatives (Extended Data Fig. 2, Supplementary Information section 2).

On the presence of the "East Asian" EDAR variant in Scandinavian hunter-gatherers:
We find a surprise in six Scandinavian hunter-gatherers (SHG) from the Motala site in southern Sweden. In three out of six samples, we observe the haplotype carrying the derived allele of rs3827760 in the EDAR gene (Extended Data Fig. 5), which affects tooth morphology and hair thickness and has been the subject of a selective sweep in East Asia 24 , and today is at high frequency in East Asians and Native Americans. The EDAR derived allele is largely absent in present-day Europe except in Scandinavia, plausibly due to Siberian movements into the region millennia after the date of the Motala samples. The SHG have no evidence of East Asian ancestry 4,7 , suggesting that the EDAR derived allele may not have originated not in East Asians as previously suggested 24 . A second surprise is that, unlike closely related western hunter-gatherers, the Motala samples have predominantly derived pigmentation alleles at SLC45A2 and SLC24A5.
Polygenic selection on height in Europe:

We also tested for selection on complex traits. The best-documented example of this process in humans is height, for which the differences between Northern and Southern Europe have driven by selection 25 . To test for this signal in our data, we used a statistic that tests whether trait-affecting alleles are both highly correlated and more differentiated, compared to randomly sampled alleles 26 . We predicted genetic heights for each population and applied the test to all populations together, as well as to pairs of populations (Fig. 4). Using 180 height-associated SNPs 27 (restricted to 169 where we successfully targeted at least two chromosomes in each population), we detect a significant signal of directional selection on height (p=0.002). Applying this to pairs of populations allows us to detect two independent signals. First, the Iberian Neolithic and Chalcolithic samples show selection for reduced height relative to both the Anatolian Neolithic (p=0.042) and the Central European Early and Middle Neolithic (p=0.003). Second, we detect a signal for increased height in the steppe populations (p=0.030 relative to the Central European Early and Middle Neolithic). These results suggest that the modern South-North gradient in height across Europe is due to both increased steppe ancestry in northern populations, and selection for decreased height in Early Neolithic migrants to southern Europe. We do not observe any other significant signals of polygenetic selection in five other complex traits we tested: body mass index 28 (p=0.20), waist-to-hip ratio 29 (p=0.51), type 2 diabetes 30 (p=0.37), inflammatory bowel disease 21 (p=0.17) and lipid levels 16 (p=0.50).

Political background and identification of US professors circa 1969

Previously, we've seen that upper income Jews in Boston voted much further left than Protestant Bostonians in the middle of the 20th century; that "Boston Brahmins" were a relatively conservative group; that Jewish billionaires are further left than non-Jewish billionaires; etc.

It should not come as much of a surprise to anyone passingly familiar with non-Moldbuggist American history that in a 1969 survey of professors, Jews reported themselves more leftist in parental background, personal identification, voting behavior, and their children's activism than Protestants.

In "Jewish academics in the United States", Lipset reports:

The extent to which the political background of Jewish academics differs from that of others may be seen in the responses to the Carnegie survey question: "What were your father's politics while you were grow- ing up?" Forty-six per cent of the Jews, as contrasted to 19 per cent of the Catholics and but 14 per cent of the Protestant majority, reported fathers who were "left" or "liberal" in their views. Conversely, less than 20 per cent of the Jewish professors had "conservative" fathers, while 63 per cent of the Protestant academics indicated such a background (Table 19).

Family political-intellectual tradition affects the behavior of the chil- dren of academics. Among those faculty with children of college age, a majority (56 per cent) of the Jews report that their children have "been active in civil rights, anti-Vietnam, or other demonstrations," as con- trasted with little more than one-fifth (22 per cent) of the Gentile pro- fessors. The reason, of course, is that the children of liberal academics participate much, much more in demonstrations than children of con- servative academics, and Jewish faculty are disproportionately liberal. That the correlation is between parental politics and participation is made clear by Table 20, which shows that 68 per cent of the left faculty having children of the right age—regardless of religion—said their children had been active in demonstrations, compared to just 4 per cent of the strongly conservative professors.

The contribution of faculty of Jewish background to liberal and left political groups has been stressed in a number of surveys preceding our own. Almost all earlier studies found that close to 90 per cent of Jewish academics regularly voted Democratic in presidential elections. 45 Jewish faculty also were found to contribute heavily to the backing of leftist third parties. Thus, according to a 1948 study, fully 30 per cent of the Jewish professors voted for Henry Wallace. 46 The same proclivity can be seen in Britain, where a faculty opinion study reported that the Jews were "the most left-wing of all." 47 Recent studies of American college professors conclude that Jews have been much more heavily opposed to the Vietnam war, and stronger supporters of student activism, than their Gentile colleagues. 48

The Carnegie Commission's national survey yielded the same strong relationships. The Jewish faculty were much more inclined to identify their politics as "left" or "liberal" than Protestants and Catholics (Table 21 ). 49 Jews contributed disproportionately to the small group who backed left-wing third party presidential candidates in 1968; they were much more likely to have been for the nomination of Eugene McCarthy than of Hubert Humphrey at the Democratic convention, and gave Richard Nixon an exceptionally low vote in the election. In 1964 only 2 per cent of the Jewish faculty voted for Barry Goldwater, compared to 24 per cent of those of Protestant parentage (Tables 22, 23, and 24).

The Jews, as a group, took much more liberal positions on such issues as the use of force at the Chicago Democratic convention in 1968, the Vietnam war, student activism, the treatment of blacks in both the university and the larger society, and the legalization of marijuana (Tables 25, 26 and 27). The gap between Jews and Christians on these issues is very large, while among Christians, Protestants are usually slightly more conservative than Catholics. For example, 59 per cent of the Jews gave general approval to "the emergence of radical student activism in recent years," compared to 44 per cent of the Catholics and 40 per cent of the Protestants. The proportion of Jews favoring immediate United States withdrawal from Vietnam is twice that of non-Jews. Three- fifths of the Jews favored the legalization of marijuana (59 per cent), compared to 33 per cent of the Catholics and 29 per cent of the Protestants.

Religious backgrounds of US professors circa 1969

This data comes from "a large national sample (60,000) of faculty who filled out questionnaires for the Carnegie Commission on Higher Education in 1969", as reported in "JEWISH ACADEMICS IN THE UNITED STATES: THEIR ACHIEVEMENTS, CULTURE AND POLITICS" by Seymour Martin Lipset and a co-author (pdf).

Jewish overrepresentation was even greater among faculty of elite colleges and universities, and Protestants were reduced to a bare-majority of under-30 professors at elite schools by this time.

Lipset:

The considerable presence of Jews in social science departments (and schools of social work), in comparison to most of the humanities and natural sciences, may be related to the disposition of secularized Western Jews for reform-oriented politics, to be discussed later. A variety of studies of undergraduate career choices indicate that the more left- disposed students are more inclined than others to an academic career, particularly in the politically relevant social sciences. 14 As the newest group of disciplines, the social sciences have been less discriminatory, more committed to universalistic principles than the humanities. The latter, as the oldest and least "practical" fields, have tended to be identified with high status, and hence were more restrictive in their admission policies.

The underrepresentation of Jews in the humanities and history may reflect the continuation of a distinction frequently made in Wilhelminian and even Weimar Germany. Some who supported the appointment of Jews to professorships in the sciences and social sciences argued that they could not be professors of German literature or history. These subjects were at the heart of the Volkswesen, the national essence, while the Jews (obviously) were wesenfremd, alien to the national essence. Suspicions about the Volkswesen suitability of Jews in English and history have not completely vanished in the U.S. In his presidential address to the American Historical Association, in 1962, Carl Bridenbaugh lamented that "many of the younger practitioners of our craft . . . are products of lower middle-class or foreign origins and . . . find themselves in a real sense outsiders to our past and feel themselves shut out. This is certainly not their fault, but it is true." By "products of . . . foreign origins," we would hazard the guess, Professor Bridenbaugh was not thinking primarily of Albanians. 15

Moldbug's sources: Forrest McDonald, "Celtic Southernism", and the Lew Rockwell school of late 20th C. PC anti-Yankeeism

As he himself eventually confirmed, moldbug's ideology was formed by mashing up a variety of vaguely rightist and libertarian ideas and filtering them through the lens of what he perceived to be "good for the Jews".

Similarly, moldbug's school of pseudo-history arose from moldbug latching on to a convenient thread and running with it to outlandish extremes, the overriding goal not being to promote understanding but to absolve Jews (and moldbug's Communist grandparents, in particular) of any agency in their radical political activity.

Moldbug picked up the initial inspiration for moldbuggist history from the anti-Yankeeism of lewrockwell.com contributors like Clyde Wilson, Jimmy Cantrell, and Thomas "Abraham Lincoln was the real racist" DiLorenzo, some of which was outlandish enough to begin with. They, in turn, were influenced by Forrest McDonald.

Linguistics, Archaeology & Genetics conference abstracts

This conference, aimed at "integrating new evidence for the origin and spread of the Indo-European languages", will take place next week. Some abstracts (pdf):

Close genetic relationship of Neolithic Anatolians to early European farmers

Iosif Lazaridis 1,2 , Song├╝l Alpaslan 3 , Daniel Fernandes 4 , Mario Nowak 4 , Kendra Sirak 4 , Nadin Rohland 1,2 , Swapan Mallick 1,2,5 , Kristin Stewardson 1,5 , Fokke Gerritsen 6 , Nick Patterson 2 , Ron Pinhasi 4, *, David Reich 1,2,5, *

We study 1.2 million genome-wide single nucleotide polymorphisms on a sample of 26 Neolithic individuals (~6,300 years BCE) from northwestern Anatolia. Our analysis reveals a homogeneous population that was genetically similar to early farmers from Europe (F ST =0.004±0.0003 and frequency of 60% of Y-chromosome haplogroup G2a). We model Early Neolithic farmers from central Europe and Iberia as a genetic mixture of ~90% Anatolians and ~10% European hunter-gatherers, suggesting little influence by Mesolithic Europeans prior to the dispersal of European farmers into the interior of the continent. Neolithic Anatolians differ from all present-day populations of western Asia, suggesting genetic changes have occurred in parts of this region since the Neolithic period. We suggest that the language spoken by the homogeneous Anatolian-European Neolithic farmers is unlikely to have been the same as that spoken by the Yamnaya steppe pastoralists whose ancestry was derived from eastern Europe and a different population from the Caucasus/Near East [Haak et al. 2015], and discuss implications for alternative models of Indo-European dispersals.

The Genetic History and Structure of Britain

Nick Patterson, Broad Institute, Boston and David Reich, Harvard Medical School and Broad Institute, Boston

The recently published paper on the genetic structure of Britain (Leslie et al. Nature 2015) has shown subtle genetic variation correlating with geography. Here we reexamine the evidence in the light of our understanding of the genetics of Ancient Europe and comment on some implications for how Indo-Europeans spread into Europe.

In search for initial Indo-European gene pool from genome-wide data on IE popula- tions as compared with their non-IE neighbors

Oleg Balanovsky, Vavilow Institue of General Genetics, Russian Academy of Sci- ences, Moscow

From Yamnaya to Bell Beakers: Mechanisms of Transmission in an Interconnected Europe, 3500–2000 BC

Volker Heyd, Universtiy Bristol, Bistol and University of Helsinki, Helsinki

Yamnaya Peoples in the East and Bell Beakers Users in the West are rightly seen as the apogees in a long-term process of individualisation, gender differentiation, warrior display and internationalisation/unification that fundamentally change the face of the European Continent from the mid fourth and throughout the third millennium BC. We can only approach the reasons why prehistoric peoples and cultures from regions across Europe, which were no more than marginally in touch before, join in the same emblematic pottery, new drinking habits, similar burial customs, anthropomorphic stelae, ostentatious display of weapons and other paraphernalia, and thus common values. However rather than seeing this development as an internal European progress I want to point to the importance of the Pontic-Caspian steppes, and a 2000 years lasting interaction scenario of infiltrating Suvorovo-Novodanilovka, Nizhnemikhailovka-Kvityana and Yamnaya peoples and populations with their more sedentary contemporaries in southeast Europe, the Carpathian basin and northeast of the Carpathian bow. A crucial part of this interaction –besides migrations and the exchange of genes and goods as recently highlighted in several publications not only in Nature and Science– is the forwarding of innovations in the sphere of subsistence economy. We see this archaeologically in a further importance of animal husbandry, with larger herds, specialised breeding and new forms of herding management in particular for cattle. This obviously sets in motion a substantial shift in general mobility patterns and of communication networks.

It is easily conceivable that this interaction must also have had a profound impact on the whole settlement organisation and people’s way-of-life, in consequence probably fundamentally affecting the basics of societies and thus challenging the whole system of ideas, imaginations, morale, symbols and terms – a new world-view and ultimately the base for a new language.

Pre-Indo-European speech carrying a Neolithic signature emanating from the Aegean

Guus Kroonen, Institute for Nordic Studies and Linguistics, Copenhagen University, Copenhagen

When different Indo-European speaking groups settled Europe, they did not arrive in terra nullius. Both from the perspective of the Anatolian hypothesis 1,2,3 and the Steppe hypothesis, 4,5,6 the carriers of Indo-European speech likely encountered existing populations that spoke dissimilar, unrelated languages. Relatively little is known about the Pre-Indo-European linguistic landscape of Europe, as the Indo-Europeanization of the continent caused a largely unrecorded, massive linguistic extinction event. However, when the different Indo-European groups entered Europe, they incorporated lexical material from Europe’s original languages into their own vocabularies. 7 By integrating these “natural samples” of Pre-Indo-European speech, the original European linguistic and cultural landscape can partly be reconstructed and matched against the Anatolia and the Steppe hypotheses. My results reveal that Pre-Indo-European speech contains a clear Neolithic signature emanating from the Aegean, 8 and thus patterns with the prehistoric migration of Europe’s first farming populations. 9,10,11 These results also imply that Indo-European speech came to Europe following a later migration wave, and therefore favor the Steppe Hypothesis as a likely scenario for the spread of the Proto-Indo-Europeans. 12

More carriers of deeply diverged Y lineage (haplogroup A00) found in Cameroon

This possibly archaic African Y lineage was discovered a few years ago by hobbyists, and a project run and funded by hobbyists to collect and test additional A00 samples has started to report results:
There are some striking patterns in the results already. 85% of the A00 so far are from the Bangwa (Nweh) people, and 15% from the Nkongho-Mbo. This is despite the fact that nearly 57% of the samples collected were from Mbo, and only 37% were from Bangwa. Once all the results have been fully tabulated, we can provide more complete statistics. It will take a while to transcribe all the rich data from those handwritten sheets into electronic spreadsheets. [. . .]

What's next? Matthew would like to head back to the field quite soon, in the second half of October, when the school where he teaches has a break. Our current plan is for him to visit the region of the Bamileke people. Matthew, an ethno-historian, has said "The similarity in names, language, dancing style and all other aspects of life suggest that the Bangwa are 90 percent Bamileke." By testing a good number of Bamileke, we'll be able to see whether the heritage they share includes A00, or not. It is possible that the A00 among the Bangwa comes from the indigenous people who originally inhabited the hills, before they arrived several centuries ago, or it could also have been present among the Bamileke earlier. Our results should give strong evidence to answer that question.

The next field trips should be even more exciting. One of our goals is to collect the most diverse samples of A00 possible, to uncover its internal structure. By sequencing the Y-DNA of A00 lines that have diverged and settled in different parts of Cameroon, we should be able to get a good idea of when those different lineages had a common ancestor, and understand better how the peoples among whom it's found are related.

One trip will take Matthew westward into the lowland regions close to Nigeria, where the Banyangi and Ejagham peoples live, toward the Cross River, home of the endangered Cross River Gorilla. These villages are also on the roads that led to the old Nigerian port of Calabar, where captives from Cameroon's highlands, including some Bangwa, were sold into slavery in the past. He has never before sampled in the western regions, and only 16 Banyangi have been tested in his past research, but there are versions of Bangwa history which say that these peoples make up a significant element of their founders. Members of the A0 haplogroup have been found in Nigeria, but we have no idea yet whether A00 are also found in that direction. The famed Iwo Eleru cave is in southern Nigeria, where a skull with archaic features has been found that dates to only 13,000 years ago, suggesting long survival of diverse humans in that region.

In his other trip, he'll seek to sample members of several of the different Pygmy communities of Cameroon, who live to the South and East. Among the Pygmy peoples, Matthew collected 53 samples in 2006, and two of them belonged to A00! These communities are far from the highlands where the Bangwa and Mbo live, so we can expect that their A00 will be quite distinct. This should be extremely interesting!

1000 Genomes phase 3 papers

Both papers are freely accessible:

A global reference for human genetic variation

An integrated map of structural variation in 2,504 human genomes