Ancient Irish genomes confirm Bronze Age steppe incursion

Press release: First ancient Irish human genomes sequenced.

BBC: Ancient DNA sheds light on Irish origins.

Guardian: Origins of the Irish down to mass migration, ancient DNA confirms.

These settlers were followed by people, initially from the Pontic steppe of southern Russia, who knew how to mine for copper and work with gold, and who carried the genetic variant for a blood disorder called haemochromatosis, a hereditary genetic condition so common in Ireland that it is sometimes called Celtic disease.

These people also brought with them the inherited variation that permits the digestion of milk in maturity – much of the world becomes intolerant to the milk sugar lactose after infancy – and they may even have brought the language that became what is now Irish. Some of them, too, had blue eyes.

“There was a great wave of genome change that swept into Europe from above the Black Sea into Bronze Age Europe and we now know it washed all the way to the shores of its most westerly island,” said Dan Bradley, professor of population genetics at Trinity College Dublin.

“And this degree of genetic change invites the possibility of other associated changes, perhaps even the introduction of language ancestral to western Celtic tongues.”

The Dublin team and colleagues from Queens University Belfast report in the Proceedings of the National Academy of Sciences that the two great changes in European prehistory – the emergence of agriculture and the advance of metallurgy – were not just culture shifts: they came with new blood. An earlier population of hunter gatherers was successively overwhelmed by new arrivals. And in Ireland, these new settlers began to define a nation.

But the latest study throws more light on the birth of a nation. All three dead men from Rathlin Island carried what is now the most common type of Irish Y chromosome, inherited only from male forebears. [. . .]

And Lara Cassidy, a researcher in genetics at Trinity College Dublin and another co-author, said “Genetic affinity is strongest between Bronze Age genomes and modern Irish, Scottish and Welsh, suggesting establishment of central attributes of the insular Celtic genome 4,000 years ago.”

The PNAS paper: Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

Ancient DNA: Late Upper Paleolithic Swiss and Caucasus hunter-gatherers sequenced

Upper Palaeolithic genomes reveal deep roots of modern Eurasians (open access):

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Press release: 'Fourth strand' of European ancestry originated with hunter-gatherers isolated by Ice Age

Selection against Neanderthal introgression (two biorxiv preprints)

The Strength of Selection Against Neanderthal Introgression

Ivan Juric, Simon Aeschbacher, Graham Coop
doi: http://dx.doi.org/10.1101/030148

Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that there are systematically lower levels of initial introgression on the X chromosome, a finding consistent with a strong sex bias in the initial matings between the populations. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.

The Genetic Cost of Neanderthal Introgression

Kelley Harris, Rasmus Nielsen
doi: http://dx.doi.org/10.1101/030387

Approximately 2-4% of the human genome is in non-Africans comprised of DNA intro- gressed from Neanderthals. Recent studies have shown that there is a paucity of introgressed DNA around functional regions, presumably caused by selection after introgression. This observation has been suggested to be a possible consequence of the accumulation of a large amount of Dobzhansky-Muller incompatibilities, i.e. epistatic effects between human and Neanderthal specific mutations, since the divergence of humans and Neanderthals approx. 400-600 kya. However, using previously published estimates of inbreeding in Neanderthals, and of the distribution of fitness effects from human protein coding genes, we show that the average Neanderthal would have had at least 40% lower fitness than the average human due to higher levels of inbreeding and an increased mutational load, regardless of the dominance coefficients of new mutations. Using simulations, we show that under the assumption of additive dominance effects, early Neanderthal/human hybrids would have experienced strong negative selection, though not so strong that it would prevent Neanderthal DNA from entering the human population. In fact, the increased mutational load in Neanderthals predicts the observed reduction in Neanderthal introgressed segments around protein coding genes, without any need to invoke epistasis. The simulations also predict that there is a residual Neanderthal derived mutational load in non-African humans, leading to an average fitness reduction of at least 0.5%. Although there has been much previous debate about the effects of the out-of-Africa bottleneck on mutational loads in non-Africans, the significant deleterious effects of Neanderthal introgression have hitherto been left out of this discussion, but might be just as important for understanding fitness differences among human populations. We also show that if deleterious mutations are recessive, the Neanderthal admixture fraction would gradually increase over time due to selection for Neanderthal haplotypes that mask human deleterious mutations in the heterozygous state. This effect of dominance heterosis might partially explain why adaptive introgression appears to be widespread in nature.

"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 , Songül 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

"Male Homosexual Preference" and social stratification

I don't necessarily buy positive selection for genes predisposing to male homosexuality in stratified societies via pleiotropic effects in females. But I could easily believe that evolutionary mismatch leads to higher levels of homosexuality in denser (though population density is apparently not a significant predictor in their analysis) and/or more stratified societies, and that sexually antagonistic selection plays some role in slowing down selection against homosexuality.

Male Homosexual Preference: Where, When, Why? (PLoS ONE):

Male homosexual preference (MHP) has long been of interest to scholars studying the evolution of human sexuality. Indeed, MHP is partially heritable, induces a reproductive cost and is common. MHP has thus been considered a Darwinian paradox. Several questions arise when MHP is considered in an evolutionary context. At what point did MHP appear in the human evolutionary history? Is MHP present in all human groups? How has MHP evolved, given that MHP is a reproductively costly trait? These questions were addressed here, using data from the anthropological and archaeological literature. Our detailed analysis of the available data challenges the common view of MHP being a “virtually universal” trait present in humans since prehistory. The conditions under which it is possible to affirm that MHP was present in past societies are discussed. Furthermore, using anthropological reports, the presence or absence of MHP was documented for 107 societies, allowing us to conclude that evidence of the absence of MHP is available for some societies. A recent evolutionary hypothesis has argued that social stratification together with hypergyny (the hypergyny hypothesis) are necessary conditions for the evolution of MHP. Here, the link between the level of stratification and the probability of observing MHP was tested using an unprecedented large dataset. Furthermore, the test was performed for the first time by controlling for the phylogenetic non-independence between societies. A positive relationship was observed between the level of social stratification and the probability of observing MHP, supporting the hypergyny hypothesis. [. . .]

Minor sub-Saharan and substantial Levantine admixture in Southern Europe

According to "The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape", something like a third of Southern Italian and Tuscan genetic ancestry appears to derive from the Levant in Roman times:

Moorjani et al [S?], who use a method based on allele frequency comparisons, and not haplotypes (ROLLOFF), found evidence for sub-Saharan African admixture in Sardinia 71±28 generations ago, at a proportion of 3%. These are the same Sardinians included in our analysis. In the largest Sardinian (sardi13) cluster in our analysis we infer West African admixture 66 (53-82) generations ago at a proportion of 2%.

S5.2 Continuous low level African admixture in the Mediterranean and Anatolia

We infer West African admixture across broad date ranges, but at low admixture proportions (admixture α < 0.07; Figs. 2 and S3) in several Mediterranean groups, consistent with a long term movement be- tween sub-Saharan Africa and southern Europe [S?,S?]. Specific West African admixture dating to the Arabic conquest of the Mediterranean [S?] is seen in Spanish (spani27: 1042 (740-1201CE)), Southern Italian and Sicilian (sicil30: 1105 (882-1250CE)), and Basque (basqu24: 886 (283-1162CE)) clusters. Earlier African admixture at low admixture proportion is inferred in the Cypriots (cypri12: 427(107- 734CE)), and a Sardinian cluster (sardi13: 36 (458BCE-430CE); α = 0.02). This latter event is con- sistent with the occurrence of A3b2-M13 (0.6%) and E1a-M44 (0.4%) African Y chromosome lineages in Sardinia [S?]. and the dating is more compatible with documented exchanges between the island and Mauretania Cesariensis in Roman times (2 nd century BCE to 2 nd century CE) than later displacements of northern-African males to Sardinia at the time of the Vandals rule (5 th century CE) [S?]. [. . .]

S5.3 A key role for the Levant in the genetic history of the Mediterranean

Early admixture involving source groups most similar to contemporary populations from in and around the Levant (which we define as the World Region containing individuals from Syria, Palestine, Lebanon, Jordan, Saudi, Yemen and Egypt) is seen at high proportions in several clusters from Italy dating to the first half of the first millennium CE, from Southern Italy (itali8: 295CE (72BCE-604CE); α = 0.34), Tuscany (tsi23: 400CE(30BCE-686); α = 0.29), and Sardinia, as well as in a large cluster from Armenia at an early date (armen27: 363BCE(1085BCE-383CE)). [. . .] these events loosely coincide with the formation of the pan-Mediterranean Roman Empire [S?], which may also have allowed increased gene flow from east to west Mediterranean. [. . .] We infer more recent Levant admixture in the French (frenc24: 728(424-1011CE)) and in a complex multiway event in a Spanish cluster (spani9: 668 (286-876CE)). The dates and sources of admixture in these cases are consistent with movements of Middle Eastern and North African individuals during the Islamic Conquest of Spain [S?], and suggest a legacy of this key moment in southern European history in the genomes of French as well as Spanish populations.

Autosomal DNA from Atapuerca pre- or proto-Neanderthals

DNA from Neandertal relative may shake up human family tree

The Sima people, who lived before Neandertals, were thought to have emerged in Europe. Yet their teeth, jaws, and large nasal cavities were among the traits that closely resembled those of Neandertals, according to a team led by paleontologist Juan-Luis Arsuaga of the Complutense University of Madrid. As a result, his team classified the fossils as members of Homo heidelbergensis, a species that lived about 600,000 to 250,000 years ago in Europe, Africa, and Asia. Many researchers have thought H. heidelbergensis gave rise to Neandertals and perhaps also to our species, H. sapiens, in the past 400,000 years or so. [. . .]

After 2 years of intense effort, paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology has finally sequenced enough nuclear DNA from fossils of a tooth and a leg bone from the pit to solve the mystery. [. . .] They scanned this DNA for unique markers found only in Neandertals or Denisovans or modern humans, and found that the two Sima fossils shared far more alleles—different nucleotides at the same address in the genome—with Neandertals than Denisovans or modern humans. “Indeed, the Sima de los Huesos specimens are early Neandertals or related to early Neandertals,” suggesting that the split of Denisovans and Neandertals should be moved back in time, Meyer reported at the meeting. [. . .]

“It resolves one controversy—that they’re in the Neandertal clade,” says paleoanthropologist Chris Stringer of the Natural History Museum in London. “But it’s not all good news: From my point of view, it pushes back the origin of H. sapiens from the Neandertals and Denisovans.” The possibility that humans were a distinct group so early shakes up the human family tree, promising to lead to new debate about when and where the branches belong.

Darren Curnoe points out:

What are the broader implications of the research for understanding the evolution of living humans?

First, the finding pushes the age of the shared human-Neanderthal ancestor well beyond 400,000 years ago, suggesting our species, H. sapiens, might also be at least this old.

Also, with the Atapuerca group living in Europe, it’s even possible that our species evolved in this or an adjacent region of Eurasia, and later migrated back into Africa.

And being close to the common ancestor, the Atapuerca fossils give us real insights into what it must have looked like and the ancestral body form of our own species.

The fossils from Europe, Asia and Africa from around this time are physically very diverse, with some researchers thinking they represent multiple species, only one of which could be the ancestor of living humans.

Question is, which one?

This new research suggests the European branch is closest among them all and deserves much more attention in this regard.

In contrast, we don’t know, and will doubtless ever know, whether Homo naledi had anything to do with the evolution of living humans, least of all whether its brain, mind or behaviour were anything like our own.

ASHG 2015: growth rate estimates from whole Y chromosome sequences

Estimation of growth rates for populations and haplogroups using full Y chromosome sequences.

F. L. Mendez; G. D. Poznik; C. D. Bustamante; 1000 Genomes Project Consortium

Department of Genetics, Stanford University, Stanford, CA.

Evolutionary processes affecting a population influence gene genealogies across the genome. Coalescent theory provides the mathematical framework to connect realized genealogies to the underlying evolutionary processes. However, in most cases, information about the genealogies is obtained only indirectly through the observation of genetic variation. Therefore, in general, very limited information about any individual locus is available. As the longest non-recombining portion of the human genome, the Y chromosome accumulates mutations relatively quickly. When large amounts of sequence are used, the Y chromosome provides an unparalleled ability to resolve the structure and coalescence times of its genealogy. Because patterns of variation in the Y chromosome are only influenced by processes affecting men, they can be used to study both demographic and social phenomena. The 1000 Genomes Project includes whole Y-chromosome data from more than 1000 men and has an extensive representation of most lineages that have experienced recent massive expansions in size. Though the dynamics of population growth have likely changed over time, we are more interested in the growth rates at the times of these rapid expansions than on an average effect. To study this, we have developed a new method that takes advantage of the temporal resolution provided by Y-chromosome data and of historical data, while accounting for the uncertainties associated with the coalescent and mutational processes. We estimate the growth rates for several branches of the Y-chromosome tree, including those in Europe, sub-Saharan Africa and South Asia. We estimate that several lineages within the European R1b, sub-Saharan African E1b, and South Asian R1a haplogroups experienced growth rates of at least 20-60% per generation at the onset of their massive expansions, some 3-5 thousand years ago. These high growth rates are comparable to those experienced by human populations during the 20th century. However, we find that most observed genealogies are unlikely to be the result of whole population expansion or of natural selection.

ASHG 2015: Population differentiation analysis of 54,734 European Americans

Population differentiation analysis of 54,734 European Americans reveals independent evolution of ADH1Bgene in Europe and East Asia.

K. J. Galinsky1,2 ; G. Bhatia2,3 ; P. Loh2,3 ; S. Georgiev4 ; S. Mukherjee5 ; N. J. Patterson2 ; A. L. Price1,2,3

Population differentiation is a widely used approach to detect the action of natural selection. Existing methods search for unusual differentiation in allele frequencies across discrete populations, e.g. using FST. Loci that are unusually differentiated with respect to the genome-wide FST or with respect to a null distribution of F­ST are reported as signals of selection. These approaches are particularly powerful for closely related populations with large sample sizes.However, population genetic data often is not naturally partitioned into discrete populations. We developed a test for selection that uses SNP loadings from principal components analysis (PCA). For a given PC reflecting geographic ancestry, under the null hypothesis of no selection, the square of the SNP loadings, rescaled by a scaling factor derived from the eigenvalue of the PC, follows a chi-square (1 d.o.f.) distribution. This statistic is able to infer selection with genome-wide significance, a key consideration in genome scans for selection. We confirmed via simulations that this statistic has correct null calibration under a wide range of demographies and is well-powered to detect selection at large sample sizes.We applied the method to a cohort of 54,734 European Americans genotyped on genome-wide arrays. PCs were inferred using our FastPCA software (running time: 57 minutes). The top 4 PCs corresponded to clines of Irish, Eastern European, Northern European, Southeast European and Ashkenazi Jewish ancestry, validated via PCA projection of samples of known ancestry. We detected genome-wide significant signals of selection at 4 known selected loci (LCT, HLA, OCA2 and IRF4) and 3 novel loci: ADH1B, IGFBP3 and IGH. 2 of the 3 novel loci could not be detected using discrete-population tests (or other existing tests). The ADH1B gene is associated with alcoholism (via the same coding SNP rs1229984 producing a signal in our selection scan) and has been shown to be under recent selection in East Asians (via a haplotype-based test for recent selection); we show here that it is a rare example of independent evolution on two continents. The IGFBP3 gene and IGH locus have been implicated in breast cancer and multiple sclerosis, respectively. Our results show that application of our PC-based selection statistic to large data sets can infer novel, genome-wide significant signals of selection at loci linked to disease traits.

ASHG 2015: The lingering load of archaic admixture in modern human populations

The lingering load of archaic admixture in modern human populations.

K. Harris1,2 ; R. Nielsen2,3

1) Stanford University, Stanford, CA; 2) University of California Berkeley, Berkeley, CA; 3) Center for Bioinformatics, University of Copenhagen, Copenhagen, Denmark.

Founder effects and bottlenecks can damage fitness by letting deleterious alleles drift to high frequencies. This almost certainly imposed a burden on Neanderthals and Denisovans, archaic hominid populations whose genetic diversity was less than a quarter of the level seen in humans today. A more controversial question is whether the out-of-Africa bottleneck created differences in genetic load between modern human populations. Some previous studies concluded that this bottleneck saddled non-Africans with potentially damaging genetic variants that could affect disease incidence across the globe today (e.g. Lohmueller, et al. 2009; Fu, et al. 2014), while other studies have concluded that there is little difference in genetic load between Africans and non-Africans (e.g. Simons, et al. 2014; Do, et al. 2015). Although previous studies have devoted considerable attention to simulating the accumulation of deleterious mutations during the out-of-Africa bottleneck, none to our knowledge have incorporated the fitness effects of introgression from Neanderthals into non-Africans. We present simulations showing that archaic introgression may have had a greater fitness effect than the out-of-Africa bottleneck itself, saddling non-Africans with weakly deleterious alleles that accumulated as nearly neutral variants in Neanderthals. Assuming that the exome experiences deleterious mutations with additive fitness effects drawn from a previously inferred gamma distribution, we predict that the fitness of the average Neanderthal was about 50% lower than the fitness of the average human, implying the existence of strong selection against early Neanderthal-human hybrids. This is a direct consequence of mutation accumulation during a period of low Neanderthal population size that is thought to have lasted ten times longer than the out-of-Africa bottleneck (Pruefer, et al. 2014). Although our model predicts some transmission of deleterious Neanderthal variation to present-day non-Africans, it also predicts that many Neanderthal alleles have been purged away, depleting conserved genomic regions of Neanderthal ancestry as observed empirically by Sankararaman, et al. (2014). Our results imply that the deficit of Neanderthal DNA from functional genomic regions can be explained without the action of epistatic reproductive incompatibilities between human and Neanderthal alleles.

ASHG 2015: The genetic structure of the Saudi Arabian population

The genetic structure of the Saudi Arabian population.

H. Al-Saud1 ; SM. Wakil1 ; BF. Meyer1 ; M. Falchi2 ; N. Dzimiri1

1) Genetics Department, King Faisal Hospital and Research Centre, Riyadh, Saudi Arabia; 2) Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom.

Saudi Arabia is the largest Gulf Cooperation Council (GCC) country. Its population consists of different tribes that originated in the northern, western, eastern, middle and south regions of Saudi Arabia, respectively. Due to political and cultural reasons, there has historically been very limited admixture between different tribes. People from the different Saudi tribes then migrated from Saudi Arabia, contributing to foundation of the populations now inhabiting other Gulf countries. Few population genetics research projects have been conducted on this highly consanguineous population that has been shown to have one of the highest prevalence in the world of recessive disorders and common metabolic diseases, especially diabetes. It is therefore important to identify the genetic substructures of the Saudi population, both to help in tracing the migratory genetic flows that contributed to other Gulf populations, and to permit designing of efficient genetic studies aimed at the identification of risk factors underlying common and rare diseases in the GCC countries. We carried out the largest population genetic study in Saudi Arabia to date, by genotyping 2,150 Saudi nationals sampled from different regions of Saudi Arabia using Axiom GWH-96 Array (Affymetrix) arrays. Model-based and model-free clustering were applied to these data, including in our analyses data on eight populations (encompassing Europe, America, Oceana, East Asia, Central South Asia, Middle East, Africa and Qatari populations) from the Human Genetic Diversity Project (HGDP) data set. We identified clear clustering of the Saudi samples into different subgroups, with some tribes showing similarity with both Central East Asian (Kalash Pakistan, Balochi Pakistan, Sindhi Pakistan, Makrani Pakistan and Brahui Pakistan subpopulations) European (Orkney Islands Europe, Russian Europe and Russian Caucasus subpopulations) and Qatari populations, while other tribes appear to show specificity of background.These data strongly support the presence of genetic stratification within the Saudi population, and suggest the presence of subgroups that are characterized by a unique genetic background different from other Arabian populations. Our findings constitute a valuable resource for the investigation of both general and population-specific genetic risk variants associated with different disorders in this population.

ASHG 2015: Reconstructing genetic history of Siberian and Northeastern European populations

Reconstructing genetic history of Siberian and Northeastern European populations.

E. Wong1 ; A. Khrunin2 ; L. Nichols2 ; D. Pushkarev3 ; D. Khokhrin2 ; D. Verbenko2 ; O. Evgradov4 ; J. Knowles4 ; J. Novembre5; S. Limborska2 ; A. Valouev1

Siberia and Western Russia are home to some of the least studied ethnic groups in the world, and their genetic history holds keys to understanding peopling of the world. We present whole-genome sequencing data from 28 individuals belonging to 14 distinct indigenous populations from that region. We used these datasets together with an additional 32 modern-day and 15 ancient human genomes to build and compare autosomal, Y-DNA and mtDNA trees and delineate genetic history. Our analyses uncover complex migratory processes that shaped the genetic landscapes in Asia and Europe. Admixture events between ancient Siberian groups resulted in distinct ancestries of nowadays Western and Eastern Siberians. Western Siberians share genetic affinity with modern Europeans. Both can trace their ancestry to the lineage of a 24,000-year-old Siberian Mal’ta boy. For Eastern Siberians, they have much weaker genetic affinity with Europeans and their ancestor separated from East Asians much later (approximately 10,000 years ago). Major migration wave from Eastern Siberians into Western Siberian groups occurred approximately 7,000 years ago, and it extended into Northeastern Europe. This is based on the admixtures we observed between Siberians and lineages represented by the 5,000-year-old hunter-gatherer Ire8 from Pitted Ware Culture excavated in Sweden, the 2,900-year-old Iron age Hungarian IR1 from the Mezocsat Culture, and modern-day northeastern Europeans. Our whole-genome data based on a broad sample of populations in Siberia and Western Russia provides new insights at a high-resolution into the genetic history of Eurasians.

Population genetic differentiation of height and body mass index across Europe

From Visscher and colleagues:

Population genetic differentiation of height and body mass index across Europe

Across-nation differences in the mean values for complex traits are common1, 2, 3, 4, 5, 6, 7, 8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58).

ASHG 2015: ancient Anatolians similar to European Neolithic farmers and distinct from modern Near Easterners

Genome-wide data on 34 ancient Anatolians identifies the founding population of the European Neolithic.

I. Lazaridis1,2 ; D. Fernandes3 ; N. Rohland1,2 ; S. Mallick1,2,4 ; K. Stewardson1,4 ; S. Alpaslan5 ; N. Patterson2 ; R. Pinhasi*3 ; D. Reich*1,2,4

1) Department of Genetics, Harvard Medical School, Boston, MA USA; 2) Broad Institute of MIT and Harvard, Cambridge, MA USA; 3) Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland; 4) Howard Hughes Medical Institute, Harvard Medical School, Boston, MA USA; 5) Independent physical anthropologist, Netherlands.

It has hitherto been difficult to obtain genome-wide data from the Near East. By targeting the inner ear region of the petrous bone for extraction [Pinhasi et al., PLoS One 2015] and using a genome-wide capture technology [Haak et al., Nature, 2015] we achieved unprecedented success in obtaining genome-wide data on more than 1.2 million single nucleotide polymorphism targets from 34 Neolithic individuals from Northwestern Anatolia (~6,300 years BCE), including 18 at greater than 1× coverage. Our analysis reveals a homogeneous population that is genetically a plausible source for the first farmers of Europe in the sense of (i) having a high frequency of Y-chromosome haplogroup G2a, and (ii) low Fst distances from early farmers of Germany (0.004 ± 0.0004) and Spain (0.014 ± 0.0009). Model-free principal components and model-based admixture analyses confirm a strong genetic relationship between Anatolian and European farmers. We model early European farmers as mixtures of Neolithic Anatolians and Mesolithic European hunter-gatherers, revealing very limited admixture with indigenous hunter-gatherers during the initial spread of Neolithic farmers into Europe. Our results therefore provide an overwhelming support to the migration of Near Eastern/Anatolian farmers into southeast and Central Europe around 7,000-6,500 BCE [Ammerman & Cavalli Sforza, 1984, Pinhasi et al., PLoS Biology, 2005]. Our results also show differences between early Anatolians and all present-day populations from the Near East, Anatolia, and Caucasus, showing that the early Anatolian farmers, just as their European relatives, were later demographically replaced to a substantial degree.

ASHG 2015: Moorish admixture in Spain

Fine scale population structure of Spain and the genetic impact of historical invasions and migrations.

C. Bycroft1 ; C. Fernandez-Rozadilla1,2 ; A. Carracedo2 ; C. Ruiz-Ponte2 ; I. Quintela-García3 ; P. Donnelly1,4 ; S. Myers1,4

As well as being linguistically and culturally diverse, the Iberian Peninsula is unusual among European regions in that its demographic history includes a prolonged and large-scale occupation by people of predominately north-west African origin. Therefore, the Iberian Peninsula provides a unique opportunity for studying fine-scale population structure and admixture, and to test cutting-edge methods of detecting complex or subtle population genetic patterns.Previous studies using Y-chromosome, mtDNA as well as autosomal data have detected limited genetic structure in Iberia. However, powerful new methods and larger datasets mean it has recently become possible to detect and characterise genetic differentiation at a sub-national level. We performed the largest and most comprehensive study of Spanish population structure to date by analysing a dataset of ~1,400 Spanish individuals typed at ~700,000 SNPs. Using the fineSTRUCTURE method we detected striking and rich patterns of population differentiation within Spain, at scales down to tens of kilometres. Strikingly, the major axis of genetic differentiation in Spain runs from west to east, while conversely there is remarkable genetic similarity in the north-south direction.To infer details of historical population movements into Spain, we analysed Spain alongside a sample of ~6,000 individuals from Europe, North Africa, and sub-Saharan Africa. Across Spanish groups, we identify varying genetic contributions from north-west African ancestral populations, at times that all fall within the period of Islamic occupation. We also identify Basque-like admixture within Spanish groups to the south of the Basque-speaking region, implying southerly gene flow from this region. This analysis has revealed details of the strengths and weaknesses of different approaches to investigating population genetic history, as well as providing important new insights into the complex genetic history of Spain.

ASHG 2015: Historical mating patterns in the U.S.

Historical mating patterns in the U.S. revealed through admixture and IBD patterns from genome-wide data from over 800,000 individuals.

J. M. Granka1 ; Y. Wang1 ; E. Han1 ; J. K. Byrnes1 ; A. Kermany1 ; R. E. Curtis2 ; P. Carbonetto1 ; K. Noto1 ; M. J. Barber1 ; N. M. Myres2 ; C. A. Ball1 ; K. G. Chahine2

1) AncestryDNA, San Francisco, CA; 2) AncestryDNA, Provo, UT.

Within a diverse population like the United States, many individuals are admixed, with ancestry from many worldwide regions. Non-random mating and migration can result in non-random combinations of ancestries within ad­­­mixed individuals (i.e., certain sets of ancestries may be common, and others may be rare); such dynamics can also affect patterns of identity-by-descent (IBD) among admixed and non-admixed individuals. To shed insight into historical mating and migration, we study genome-wide genotype data of over 800,000 AncestryDNA customers, as well as a subset of over 400,000 born in the US. First, we use a supervised algorithm to estimate individuals’ genetic admixture proportions across 26 global regions. We measure correlations between the estimated ancestries, and find certain sets of ancestries to frequently co-occur in individuals’ estimates. Such relationships may reflect historical events; e.g., the association between ancestry from the Americas and the Iberian Peninsula could reflect Colonial Era admixture. In addition to historical mating patterns, however, the admixture inference procedure and the delineation of global regions could also impact such correlations. To disentangle whether these trends could reflect mating patterns and preferences, we examine associations between the estimated ancestries of the parents of over 10,000 trios. Observed correlations agree with many of those identified within individuals, and potentially reflect more recent historical trends. Thirdly, we extend our study to IBD patterns in an inferred IBD network among genotyped individuals. Sub-clusters of the IBD network, which can often be annotated by ethnicity or historical US migration, are often inter-connected by bridging IBD connections; we highlight several connected sub-clusters in light of findings from genetic ancestry. Finally, we corroborate findings from these three analyses, as well as their potential timescales, by examining over 500,000 AncestryDNA customer pedigrees. Associations of country-level birth locations between pairs of couples support many of the non-random associations of ethnicities and IBD connections identified using genetic data. Many of the associations we observe reflect historical phenomena, and while not conclusive about their cause, suggest that many individuals with admixed ancestry, including those in the US, have present-day genetic signatures reflecting the migration and subsequent non-random mating of their ancestors.

Ancient genomes from Iberia

Both papers are freely accessible.

A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures (pdf; supplementary material)

The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: an initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK tradition, which followed the Danube River into Central Europe. While genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400 year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter-gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques (pdf; supplementary material)

The consequences of the Neolithic transition in Europe—one of the most important cultural changes in human prehistory—is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter–gatherers. The proportion of hunter–gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

Group Size and Social Interaction: a Canada-US Comparison of Interracial Marriage

Group Size and Social Interaction: a Canada-US Comparison of Interracial Marriage (pdf)

Abstract: While black-white intermarriage is uncommon in the United States, blacks in Canada are just as likely to marry whites as to marry blacks. Asians, in contrast, are more likely to marry whites in the US than in Canada. We test the claim that high rates of interracial marriage are indicative of high levels of social integration against Peter Blau's "macrostructural" thesis that relative group size is the key to explaining differences in intermarriage rates across marriage markets. Using micro-data drawn from the American Community Survey and the Canadian Census, we demonstrate that the relative size of racial groups accounts for over two-thirds of the US-Canada difference in black-white unions and largely explains the cross-country difference in Asian-white unions. Under broadly similar social and economic conditions, a large enough difference in relative group size can become the predominant determinant of group differences in the prevalence of interracial unions.

The fine-scale genetic structure of the French population

The fine-scale genetic structure of the French population (preprint):

The existence of population stratification is a major problem in case-control association studies and there is a need for a better assessment of allele frequency variation within populations at all geographic scales. Such efforts have been conducted in different European countries where strong patterns of geographic variations were found. The genome-wide extent of variations in allele frequencies of common variants has however never been documented at the scale of France. In this study, we describe these patterns of variation using genome-wide SNP chip data from 4,433 individuals, recruited as part of the Three-City study and whose places of birth in France were available. We show that there is a strong correlation between the top three principal components extracted from the genetic data and the latitude and longitude of birth places. Using multiple linear regression models, we were able to determine the birth places within less than 197 km of the reported origin for 50% of the individuals. Using model-based clustering with seven main geographic regions, we found that individuals were assigned in majority to their true region of origin. However, we found that information on ancestry could not be retrieved by using a small panel of Ancestry-Informative Markers (AIMs).

Ethnic origins of the Washington Post's top 28 American Communists of all time

In 2013, the Washington Post decided to come up with a list of "America’s top communists of all time". Unsatisfied, Washington Post blogger Dylan Matthews came up with his own list of America's "top Communists" (which he then promoted on twitter, spawning the comment thread that featured Ross Douthat's exaggeration of Maoism at Harvard). I've combined (and somewhat arbitrarily sorted) the lists below (the italicized text comes from the original lists; most of the quoted, bracketed text comes from wikipedia).

Summary: 9/28 who made the list are Jewish (including two who are half-Jewish); 5/28 are black; 4/28 potentially have half or more New England ancestry (and no one else on the list appears to have 1/4 or more New England ancestry); 3/28 have half or more Irish ancestry (and 6/28 are at least a quarter Irish); 3/28 are at least half Southern (and 4/28 likely a quarter or more Southern); 2/28 are half-Scandinavian; 1/28 is Finnish.

This fairly arbitrary list of prominent Communists is of course not representative of CPUSA membership as a whole, which was even more heavily Jewish and foreign (and even lighter on New England-descended children of rich families, notwithstanding moldbug's attempts to hold up John Reed -- the only person on this list who falls into that category -- as in any way representative of US Communists.)

At least 4/9 Jews on the list (White, the Rosenbergs, and Dohrn) are known to have spied for the Soviets or been involved in terrorist activity, along with 2/3 Southerners (Browder and Hiss). As far as I know this can be said of only 1/4 of those of early New England-stock on the list (Bentley, who also happens to be the one who ended up turning on her handlers and exposing Soviet intelligence operations in the US). More representative samples are even more extreme:

Jews were also vastly overrepresented in high-profile cases among those invoking the Fifth Amendment right not to incriminate oneself, so that public hearings like McCarthy's inevitably highlighted the Jewish role in communism. For example, in 1952, of 124 people questioned by the Senate Committee on Homeland Security and Government Affairs, Weingarten identifies 79 Jews, 32 non-Jews and 13 with unknown ethnicity. All invoked the Fifth.

Even more remarkably, of the 42 people who were dismissed from their positions at the Fort Monmouth Laboratories in New Jersey on suspicion of constituting a spy ring (the same one that Julius Rosenberg belonged to), 39 were Jews and one other was married to a Jewish woman.

Also see:

• "The 25 Most Influential Liberals In The U.S. Media" (2009) by ancestry
• Ethnic origins of The Nation's "Fifty Most Influential Progressives of the Twentieth Century"

Party leaders / labor leaders

Earl Browder

Leader of the U.S. Communist Party from the early 1930s until his expulsion in 1945. Under his guidance, the party reached its peak membership of nearly 100,000 and developed influence in key sectors of American life. Collaborated with Soviet intelligence agencies; expelled after Soviet criticism for minimizing the role of the party.

["Earl Browder was born in Wichita, Kansas on May 20, 1891, the eighth child of an American-born father sympathetic to populism.[1] He joined the Socialist Party of America in Wichita in 1907 at the age of 16 and remained in that organization until the party split of 1912". Southern (Tennessee and Virginia) ancestry.]

William Foster

Foster, a trade union militant, secretly joined the party in the early 1920s and ran for U.S. president in 1928 and 1932. He died in Moscow.

[From Beyond the American Pale: The Irish in the West, 1845-1910:

William Z. Foster was one of America's most militant Communists. That much is well known. Less so is that Foster's working-class parents were born in Ireland and that his christening as William Edward took place in a Catholic church in New Jersey. He grew up in one of Philadelphia's toughest Irish neighborhoods, the aptly named Skittereen. By any accounting, William Z. Foster (the "Z." was given to him by the Communist Party) was a part of the Irish strain in American labor.

But Foster was also part of labor's western heartland. He spent most of his working life in the West and learned his hardest lessons there.

]

Jay Lovestone

Lovestone was the party's leader in the 1920s but was expelled by Stalin in 1929. He became a key figure in the American Federation of Labor and worked with the CIA to combat communism in unions overseas.

["Lovestone was born Jacob Liebstein into a Litvak [Jewish] family in a shtetl called Moǔchadz in Grodno Governorate (then part of the Russian Empire, now in Grodno Region, Belarus)."]

Eugene Dennis

Two longtime party leaders. Dennis fled to Moscow in the 1920s to escape criminal prosecution for communist organizing, later became U.S. party leader. Dennis was the lead defendant in the trial of party leadership in 1949 on charges of conspiring to teach and organize the overthrow of the U.S. government. Jailed in the early 1950s, he resumed leadership role after leaving prison, swung support to hard-liners and died of cancer in 1961.

["He began life as Francis Xavier Waldron Jr. on August 10, 1905, in Seattle, Washington. His father was Irish American, and his mother, Nora Vieg, of Norwegian descent."]

Gus Hall

Hall became the leader of the declining party in the early 1960s. Opposed Gorbachev's policies of glasnost and perestroika, later promoted North Korea as a communist model. Died in 2000.

["Hall was born Arvo Kustaa Halberg in 1910 to Matt (Matti) and Susan (Susanna) Halberg in Cherry, a rural community on Northern Minnesota's Mesabi Iron Range.[2] Hall's parents were Finnish immigrants from the Lapua region, and were politically radical: they were involved in the Industrial Workers of the World (IWW) and were early members of the Communist Party USA (CPUSA) in 1919.[3] The Mesabi Range was one of the most important immigration settlements for Finns, who were often active in labor militancy and political activism.[4][5] Hall's home language was Finnish, and he conversed with his nine siblings in that language for the rest of his life.[2] He did not know political terminology in Finnish and used mostly English when meeting with visiting Finnish Communists.[2]"]

James P. Cannon

I mean, c'mon, dudes. You can't do a list of American Communists and just include folks who sided with Stalin against Trotsky. Cannon was converted to the cause on a trip to Russia in 1928, during which he read one of Trotsky's critiques of the Third International (better known as Comintern), the Soviet Union's international coalition of Communist Parties, and was persuaded. [. . .] The move got him and his co-conspirators expelled. No matter; they formed the Communist League of America (Opposition), which in 1934 merged with the trade unionist American Workers Party, run by the noted Marxist Christian pacifist A.J. Muste, to form the Workers Party.

[From James P. Cannon and the Origins of the American Revolutionary Left, 1890-1928:

A Midwestern, native-born Bolshevik whose parents were Irish immigrants, Cannon shared much with other centrally important individuals in the communist milieu of the 1920s and beyond, among them William Z. Foster, Earl Browder, and Jay Lovestone.

Cannon's benefactors were not his Rosedale chums, the old-style Irish patriots. "I was sick and fed up with the Irish by then. . . . [W]hen I looked around and saw all the god-damned Irishmen were either cops or politicians or grafters and contractors and prosecuting attorneys, I said to hell with it. I disaffiliated." Rescuing him from jail were Kansas City's "radical socialistic Jews," one component of the mass base of the foreign-language federation's left wing.

Released from his cell, Cannon surveyed the revolutionary Left and saw the carnage of the state's campaign of terror and suppression. Alexander Bittelman later characterized 1920 as "the worst year in the history of our movement." As he brooded in the office one day, his clothes a seedy match for his mood, Cannon was suddenly and unexpectedly confronted by three determined Jewish comrades. They hustled him down to a Jewish merchant's clothing store, where he was introduced as a distinguished revolutionary. "The Irish community had thought that I was a damn ne'er-do-well," Cannon recalled, "[b]ut there it was a great honor--editor of the paper and a speaker for socialism." Outfitted with a new suit of clothes, the socialists demanded that the merchant cut the price down to wholesale, and kick in an extra five-dollar reduction as his own contribution. It was all for "Comrade Cannon," and it slashed $30 worth of apparel to a mere $15, which the hard-bargaining radicals handed over to the haberdasher. "I walked out of the store with a brand new suit of clothes and an uplifted spirit that kept me going for a long time," Cannon remembered with fondness. "Now, how could I quit on people like that?" A revolutionary native son thus sealed a pact with immigrant left-wingers.

]

Max Shachtman

While Cannon stayed true to the Marxist flame, his ally Max Shachtman had a more interesting trajectory. While he followed Cannon to the Communist League of America, and then to the Workers Party, and then to the Socialist Workers Party, in 1940 he clashed with Cannon and Trotsky over World War II. The latter wanted to maintain a position of unconditional defense of the Soviet Union, which would entail honoring the Molotov-Ribentropp Agreement between the Soviets and Nazi Germany, supporting the Soviet "Winter War" against Finland, and backing of the Soviet/Nazi divvying up of Poland. [. . .] Where Shachtman went next was pretty surprising. He started a new party, the Workers Party (a call-back to the Trotskyist party he and Cannon had formed in 1936), which advocated for a so-called "Third Camp" that rejected the two imperialist camps of a) the then-allied Soviets and Nazis and b) the U.S. and British opposing them. [. . .] By the time of his death in 1972, Shachtman was arguing against unilateral withdrawal from Vietnam and refused to endorse George McGovern because of his support for it. [. . .] By that point, he had totally broken with the Trotskyist movement and had become a godfather of sorts to the neoconservative one. As Jeet Heer has noted, Shachtman's follower Albert Wohlstetter was a mentor to Paul Wolfowitz and Richard Perle, and Shachtman was close to Senator Henry "Scoop" Jackson (D-Wash.), who was infamously hawkish on defense and whose office employed Perle, Wolfowitz, Elliott Abrams, and Douglas Feith at various points. After the 1972 split in the Socialist Party, Shachtman's followers started the Social Democrats USA, whose members, including Abrams and UN ambassador Jeane Kirkpatrick, featured prominently in the Reagan administration.

["Shachtman was born to a Jewish family in Warsaw, Poland, which was then part of the Russian Empire. He emigrated with his family to New York City in 1905."]

Harry Haywood

Harry Haywood is probably the most important theoretician the Communist Party in the U.S. produced. He served on the Central Committee of the party from 1927-1938, including a 1931-1938 stint on the Politburo. he also lived for four and a half years in the Soviet Union, where he was an active member of the Soviet Communist Party. His chief idea was that African-Americans living in the "black belt" in the South have a right to national self-determination, same as any other national group under Stalin's theories of nationalism. They should secede and form a Marxist workers' state, he argued. The area in question looks like this: In the 1950s, he judged that the Communist Party had fallen down on its commitment to black Americans, and realigned himself with Mao Zedong, who at the time was feuding with Soviet leadership. Eventually he and other Maoists started the "New Communist Movement" of the 1970s and 1980s, which sought to capitalize on revolutionary energy generated by opposition to the war in Vietnam and had some success in organizing black auto workers in Detroit.

[Black.]

"Activists"

John Reed

Harvard grad, prominent journalist, Greenwich Village bohemian and radical enthusiast, who was portrayed by Warren Beatty in his 1981 film “Reds.’’ In Moscow during the Russian Revolution, he wrote the widely praised book “Ten Days That Shook the World.” After helping found the U.S. party, returned to Moscow to fight for recognition from the Comintern against rival American sects. He died of cholera in 1920 at age 32 and was buried in the Kremlin Wall. File photo

["John Reed was born on October 22, 1887, in his maternal grandmother's mansion in Portland, Oregon, with Chinese servants[1] in today's Goose Hollow neighborhood. He wrote of paying a nickel to a "Goose Hollowite" (young toughs in a gang in the working-class neighborhood below King's Hill) to keep from being beaten up. A memorial bench overlooks the site of Reed's birthplace in Washington Park [2] His mother, Margaret Green Reed, was the daughter of a leading Portland citizen who had made a fortune through three enterprises: as owner of the first gas works in Oregon, owner of the first pig iron smelter on the west coast, and as second owner of the Portland water works.[3] John's father, Charles Jerome Reed, was the representative of an agricultural machinery manufacturer who had come to town from the East. With his ready wit, he quickly won acceptance in Portland’s business community.[4] The family's wealth came from the Green side, not the Eastern-transplanted Reed side." No doubt had significant New England ancestry via upstate New York, but also had some Welsh and German Pennsylvania and New York ancestry.]

Bayard Rustin

In his youth, he was a member of the Young Communist League — the youth branch of the Communist Party USA — owing to the fact that the Communists were just about the only political party in the 1930s to be fully opposed to segregation. "Living in Harlem, he saw that whenever blacks got into trouble, it was invariably the Communists who were willing to defend them," his biographer, John D'Emilio, writes. "Other radical groups, like the Socialist Party or assorted Trotskyist organizations, promised gains only after the revolution." His ties to the party would get him investigated by the FBI once he became a well-known leader of the civil rights movement.

[Black.]

Hilary Putnam

He also used to be a Maoist. In the late 1960s, he was a member of the Progressive Labor Party, a still in existence group that rejected the Soviet Union of the time as a perversion of true Marxism-Leninism and embraced developing world regimes like those in China and Vietnam instead. Putnam was targeted by the Harvard administration in the late 1960s for his views, despite being a tenured professor, and in turn was intensely critical of more conservative faculty who he thought were collaborating with the Vietnam war or promoted scientific racism.

In 1973, Putnam quit the party and has said he regrets his membership.

[1/2 Jewish and 1/2 Southern/mid-Atlantic.]

Bernardine Dohrn and Bill Ayers

The Progressive Labor Party, of which Putnam was a member, was the chief rival of the Revolutionary Youth Movement (RYM), a group, also Maoist in orientation, within the anti-war Students for a Democratic Society group. RYM later renamed itself the Weathermen, and then the Weather Underground, and began a campaign of bombings meant to defeat the U.S. government, end the war in Vietnam, and create a socialist workers' state in America.

Among its most prominent leaders were the married couple of Bernardine Dohrn and Bill Ayers. The latter came from a prominent Chicago family, and his father ran the biggest electrical utility in Illinois. That connection got Dohrn hired by the Chicago firm Sidley Austin, despite her inability to join the Illinois bar. She's currently a clinical associate professor of law at Northwestern.

[Dohrn: half-Jewish, half-Swedish. "While in high school, Dohrn's father changed the family name from Ohrnstein to Dohrn because he wanted to avoid being accused by his customers of "Jewing" them out of their money. Dohrn attended Miami University of Ohio, where she tried to get into one of the most exclusive sororities but was rejected because of her father's Jewish background. She then transferred to the University of Chicago in her junior year. This change of academic location sharpened her social awareness of inequality and racial discrimination." [Klaus P. Fischer. America in White, Black, and Gray: A History of the Stormy 1960s]

Ayers: "Ayers grew up in Glen Ellyn, a suburb of Chicago, Illinois. His parents are Mary (née Andrew) and Thomas G. Ayers, who was later chairman and chief executive officer of Commonwealth Edison (1973 to 1980),[4] and for whom Northwestern's Thomas G. Ayers College of Commerce and Industry was named.[5][6] He attended public schools until his second year in high school, when he transferred to Lake Forest Academy, a small prep school.[7] Ayers earned a Bachelor of Arts in American Studies from the University of Michigan in 1968. (His father, mother and older brother had preceded him there.)[7]"

Ayers's father is 1/2 Scottish, 1/4 post-1790 German, and 1/4 Southern and Mid-Atlantic via the Midwest. His mother is 1/2 (Scottish-surnamed) Canadian and at least 1/4 (probably 1/2) post-1790 German.]

Angela Davis

Davis, a philosopher and protege of the critical theorist Herbert Marcuse, was a longtime member of CPUSA. That membership, indeed, got her fired from UCLA's philosophy faculty, at the direction of then-California governor Ronald Reagan. Shortly thereafter, she was tried for her alleged involvement in a hostage-taking incident at a courthouse in Marin County, California. She owned the guns used in the event but was found not guilty.

[Black.]

Entertainers / "intellectuals"

Woody Guthrie

Oklahoma-born singer and songwriter joined the party in California. Major figure in evolving folk-song movement, singer for party benefits and, eventually, famous for "This Land Is Your Land" and other songs. Inspired several generations of folk singers, including Pete Seeger and Bob Dylan. Hear Woody Guthrie.

["Guthrie was born in Okemah, a small town in Okfuskee County, Oklahoma, the son of Nora Belle (née Sherman) and Charles Edward Guthrie.[4] His parents named him after Woodrow Wilson, then Governor of New Jersey and the Democratic candidate soon to be elected President of the United States." 3/4 Southern, 1/8 Irish, 1/8 New England.]

W.E.B. DuBois

African American intellectual, author of “The Souls of Black Folks,” founder of the NAACP. Moved close to the party in 1930s and 1940s, moved to Ghana in 1961 and joined the U.S. party that year.

[Black.]

Paul Robeson

Talented African American athlete, actor and singer who secretly joined the party. Robeson was identified with communist causes for years. Despite knowledge of Soviet persecution of Jews, he refused to publicly criticize the Soviet Union. He charged the United States with committing genocide against blacks and praised Stalin. Blacklisted and in declining health, his career never recovered.

[Black.]

Howard Fast

Best-selling novelist, author of books such as "Spartacus" and "Freedom Road." Fast was a prominent communist activist in 1940s and 1950s, left the party in 1956 and published a scathing attack on it called "The Naked God." Worked as Hollywood screenwriter and published a popular book series, "The Immigrants." Before his death in 2003, he repudiated his anti-communism, writing another autobiography that praised the party.

[Jewish.]

James Burnham

Burnham, an ally of Shachtman's in the Socialist Workers Party, resigned in 1940 after the latter was purged. However, unlike Shachtman, he combined his resignation with a wholesale rejection of Marxism, which became clear in his 1941 book, The Managerial Revolution. He argued that Nazism, Italian fascism, Bolshevik Communism, and New Deal liberalism all moved in the direction of societies governed by a special class of "managers" that controlled the means of production. He was clear that the New Deal was the mildest form of this, but argued it undermined support for capitalism all the same. He predicted that this sort of managerial system would eventually replace capitalism altogether.

Burnham moved even further to the right in the 1940s and 1950s, becoming an ardent Cold War hawk and helping William F. Buckley found the National Review. In 1983, Ronald Reagan gave him a Presidential Medal of Freedom, as seen in the above photo.

[Zero grandparents born in America. Father born in England. Maternal grandmother born in Ireland. Of Highland Scottish ancestry via Prince Edward Island on maternal grandfather's side. Raised Catholic.]

Max Eastman

Eastman, like Burnham and, to a lesser extent, Shachtman, was a Trotskyist who became a true right-winger by the end of his life. He was the one who raised the funds so that John Reed (the Warren Beatty character in Reds; Eastman was played by Edward Herrmann) could go observe the October Revolution in Russia. He performed a true service to Trotsky by making Lenin's Testament — a document that, while also critical of Trotsky, made it clear the Soviet leader did not want Joseph Stalin to succeed him — widely known in the West, and was friends with Trotsky until his assassination in 1940.

But by then Eastman was distancing himself from Marxism and becoming enamored of free market economists like Ludwig von Mises and Friedrich Hayek. In his role as an editor at Reader's Digest, Eastman serialized the latter's The Road to Serfdom, which includes an account of Eastman's alienation from socialism. Eastman joined the free market Mount Pelerin Society, as well as the anti-Communist American Committee for Cultural Freedom, and was briefly a fan of Joseph McCarthy's (though he later labeled him a "reactionary"). He was one of the initial editors of National Review, whose board he left when he felt it had become too explicitly Christian.

He's also responsible for one of my all-time favorite quotes about Marxist philosophy: "Hegelism is like a mental disease; you can't know what it is until you get it, and then you can't know because you have got it."

[Eastman's father was a Congregational minister, likely of predominantly New England stock. However, his mother was of Pennsylvania ancestry, including German, and evidently Eastman and his sister "attributed their progressive ideas to their mother’s influence."]

Pete Seeger

The original Post list had Woody Guthrie, but his friend and fellow folk singer Seeger was a card-carrying CPUSA member for many decades. He joined the Young Communist League in 1936 and the actual party in 1932, and, along with Guthrie and the Almanac Singers, wrote anti-war songs in 1941 until the Soviet Union was invaded, at which point he switched to supporting intervention.

[Roughly 3/4 New England, 1/8 mid-Atlantic, 1/8 French]

Miscellaneous communists

J. Robert Oppenheimer

Prominent physicist and secret U.S. party member in the late 1930s. Dropped out of party activities after being selected to head the Manhattan Project. Despite numerous efforts by Soviet intelligence to contact him, steadily moved away from the party as he played major role in postwar U.S. atomic policy. Lost his security clearance in 1954 amid charges of communism and lying to U.S. security. Directed the Institute for Advanced Study in Princeton, N.J., from 1947 to 1966, a year before his death.

["Oppenheimer was born in New York City on April 22, 1904,[7] the son of Julius Oppenheimer, a wealthy Jewish textile importer who had immigrated to the United States from Germany in 1888, and Ella Friedman, a painter."]

Alger Hiss

Hiss and Whittaker Chambers were protagonists in a spy case that helped establish anti-communism as major factor in American political life and that boosted the career of Richard M. Nixon.

[One grandparent born in Ireland, other three in Maryland.]

Whitaker Chambers

Chambers was the star government witness in the spy case. Hiss, a high-ranking State Department official, was convicted of perjury for lying about Chambers's charge that Hiss had provided him with secret government documents in the 1930s. The case riveted the nation and remains controversial today, despite overwhelming evidence that Chambers told the truth.

["Whittaker Chambers was born in Philadelphia, Pennsylvania,[. . .] His family moved to Lynbrook, Long Island, New York, in 1904, where he grew up and attended school. His parents were Jay Chambers and Laha (Whittaker). Chambers described his childhood as troubled because of his parents separation and caring for their mentally ill grandmother. Chambers' brother committed suicide shortly after withdrawing from his first year of college. Chambers would cite his brother's troubled life and eventual suicide as one of many reasons that he was drawn to communism as a young man.[4]

After graduating from South Side High School in neighboring Rockville Centre in 1919, Chambers worked at a variety of jobs before attending Williams College in 1920. He later enrolled as a day student at Columbia University.[4] At Columbia his fellow students included Meyer Schapiro, Louis Zukofsky, Clifton Fadiman, John Gassner, Lionel Trilling [. . .]

In 1930 or 1931,[8] Chambers married the young artist Esther Shemitz (1900–1986).[4] [9] Shemitz, who had studied at the Art Students League and integrated herself into New York City's intellectual circles, met Chambers at the 1926 textile strike at Passaic, New Jersey."

Appears to be 9/16 (post-1790) Irish and Scottish; on the predominantly colonial American half of his ancestry, it looks like three great-grandparents were born in Pennsylvania, and one in New Hampshire (but with a father who was born in England).]

Elizabeth Bentley

A Vassar grad dubbed ''the blond spy queen,'' Bentley joined the party, worked for and eventually became the lover of Jacob Golos, the U.S. party's contact with Soviet intelligence. After Golos's death in 1943, she took over supervision of his espionage rings, most of them composed of government employees in Washington. Unstable and depressed by Soviet efforts to push her aside, Bentley went to the FBI in 1945, setting off a major investigation of Soviet espionage. Although unable to prosecute anyone because of a lack of hard evidence, the government confirmed her charges through decrypting of Soviet messages. Bentley helped stoke the anti-communist fervor of the 1940s and 1950s.

["Elizabeth Terrill[4] Bentley was born in New Milford, Connecticut to Charles Prentiss Bentley, a dry-goods merchant, and May Charlotte Turrill, a schoolteacher.[5] In 1915 her parents had moved to Ithaca, New York, and by 1920 the family had moved to McKeesport, Pennsylvania and then to Rochester, New York.[6] Her parents were described as strait-laced old family Episcopalian New Englanders." She does appear to be predominantly of early New England ancestry. Golos was Jewish.]

Julius and Ethel Rosenberg

The Rosenbergs were low-level communists. Julius, an engineer, volunteered to assist Soviet espionage and developed a highly effective ring of former college classmates working in the defense industry during World War II. Turned over vital information on jet propulsion, radar, sonar and the proximity fuse, as well as atomic bomb information provided by Ethel's brother, David Greenglass, a machinist at Los Alamos, N.M. Convicted of conspiracy to commit espionage, the Rosenbergs went to the electric chair rather than reveal members of their ring, becoming martyrs to the pro-Soviet left. A campaign to clear their names continues today, despite abundant evidence that they were guilty.

["Julius Rosenberg was born to a family of Jewish immigrants in New York City on May 12, 1918. . . . Ethel Greenglass was born on September 28, 1915, to a Jewish family in New York City."]

Harry Dexter White

As Neil's interview with Benn Steil explains, Harry Dexter White was a senior FDR-era Treasury department official, who eventually was tasked with negotiating the Bretton Woods agreement, which would establish the World Bank, IMF, and General Agreements on Tariffs and Trade (GATT, now the WTO). White was not an official member of the Communist Party, but he did pass state secrets to the Soviet Union during World War II. Steil notes in his book that White's actual economic views didn't appear all too Marxist, but it seems clear that at least at some moments in time, White sympathized with the Soviet economic model. "Russia is the first instance of a socialist economy in action," he wrote in a 1944 manuscript. "And it works!"

["Harry Dexter White was born in Boston, Massachusetts, the seventh and youngest child of Jewish Lithuanian[3] immigrants, Joseph Weit and Sarah Magilewski, who had settled in America in 1885."]