A young friend of mine was asking for recommendations on an introduction to Chinese philosophy. Xunzi: The Complete Text would be hard going for him I suspect, as he has minimal background. My inclination is to suggest A Short History of Chinese Philosophy. My personal experience (yes, I’m still slogging through the medieval section of A New History of Western Philosophy) is that a narrative historical framework makes the abstruse nature of philosophical reflection go down a bit easier.
If you want to get primary sources (translated obviously), Sources of Chinese Tradition would be a good bet, but it’s probably too much without having any reference points. Any thoughts from readers? T. Greer can probably help here….
Cultural appropriation must be one of the stupidest concepts to come out of the critical race theory milieu. Back in the day you could just admit that a particular juxtaposition of motifs was dissonant (e.g., I think mixing Arctic and Indian ones might be) or disrespectful (e.g., putting a picture of Jesus on a toilet). Now it requires an NPR think-piece. Despite its jargon, it does strike me that a lot of the long-form discussion veers into the sort of kvetching over intellectual property rights which I find quite annoying and overdone.
A friend of mine was freaking out about Pandas recently. As most of you may know I’m going to be transitioning from Perl to Python, so I was really curious when he mentioned that moving to Pandas also obviated the need for R. So I just got a copy of Python for Data Analysis: Data Wrangling with Pandas, NumPy, and IPython. Figured it would be a good complement to Data Science from Scratch: First Principles with Python.
Since I don’t like to spend time on useless things, I’ve been following the primary race very superficially (sometimes to the extent of asking my labmate every few days what’s going on). But I’d say go long on Rubio. Those following closely freak out too much over debates.
Was talking with a friend recently about the lack of emphasis in biological journals on methods, even though in the long run methods are often more impactful than singular empirical results. Would recommend all readers peruse Ancient Admixture in Human History, with a focus on methods. The paper is now open access.
Admixture into and within sub-Saharan Africa, a pre-print worth reading. That being said, I always have a hard time digesting fineSTRUCTURE work. It seems that a lot of stuff is coming out on Africa right now. If so, then it is important to actually know something about the history and geography of the continent. John Reader’s Africa: A Biography of the Continent is the best I’ve run into in that vein. Though The Fortunes of Africa looks interesting, I haven’t read it.
The 13th Bay Area Population Genomics Meeting is going to be held at UC Berkeley on February 13th, next Saturday. As usual, thanks to Dmitri Petrov for starting this, and Fernando Racimo for taking the lead this time around, and the CCB and AncestryDNA for hosting and sponsoring. I plan to be there….
If you live in California, the The California Weather Blog is a must bookmark/subscribe. When I was a wee lad I used to be a weather nerd. I can’t imagine what it would be like growing up today….
Sick and Tired of ‘God Bless America’: ‘The population of nonreligious Americans — including atheists, agnostics and those who call themselves “nothing in particular” — stands at an all-time high this election year.’ This is arguably wrong. During the early American republic with restricted suffrage a large proportion of the eligible electorate may have been freethinkers, at least judging by the fact that the first six presidents would not be considered orthodox Christians by modern evangelical Protestants. The first president who was probably an orthodox Christian while in office, Andrew Jackson, was an ardent church-state separationist:
“I could not do otherwise without transcending the limits prescribed by the Constitution for the President and without feeling that I might in some degree disturb the security which religion nowadays enjoys in this country in its complete separation from the political concerns of the General Government.” — letter to the Synod of the Reformed Church of North America, 12 June 1832, explaining his refusal of their request that he proclaim a “day of fasting, humiliation, and prayer.”
There is a growing movement to encourage reproducibility and transparency practices in the scientific community, including public access to raw data and protocols, the conduct of replication studies, systematic integration of evidence in systematic reviews, and the documentation of funding and potential conflicts of interest. In this survey, we assessed the current status of reproducibility and transparency addressing these indicators in a random sample of 441 biomedical journal articles published in 2000–2014. Only one study provided a full protocol and none made all raw data directly available. Replication studies were rare (n = 4), and only 16 studies had their data included in a subsequent systematic review or meta-analysis. The majority of studies did not mention anything about funding or conflicts of interest. The percentage of articles with no statement of conflict decreased substantially between 2000 and 2014 (94.4% in 2000 to 34.6% in 2014); the percentage of articles reporting statements of conflicts (0% in 2000, 15.4% in 2014) or no conflicts (5.6% in 2000, 50.0% in 2014) increased. Articles published in journals in the clinical medicine category versus other fields were almost twice as likely to not include any information on funding and to have private funding. This study provides baseline data to compare future progress in improving these indicators in the scientific literature.
The above statistics on the labor force at Twitter compared to the overall labor force indicate that non-Hispanic whites are underrepresented in tech firms in Silicon Valley. This is true overall in prominent tech firms. 51% of Facebook’s employees are non-Hispanic whites.
So how to make sense of these sorts of articles: Twitter’s White-People Problem? And what about passages such as this which seem to totally defy statistical/demographic reality:
But while Twitter the platform is bustling with all types of racial diversity, Twitter the company is alarmingly white.
Twitter isn’t alone. Most of the biggest tech companies in Silicon Valley are overwhelmingly white and male. While blacks and Latinos comprise 28 percent of the US workforce, they make up just 6 percent of Twitter’s total US workforce and six percent of Facebook employees.
Of course this is just a lie. Very few people would say a workforce that is 50 to 60 percent white, true of both Google and Microsoft, is “overwhelmingly white.” In fact, it’s less non-Hispanic white than the US labor force as a whole. I’ve linked to statistics in this very piece. They take about 10 seconds of browsing search queries to understand this.
But you don’t need to know statistics. Eat at a Google cafeteria. Or walk around the streets of Cupertino. There is no way that one can characterize Silicon Valley as overwhelmingly white with a straight face. Silicon Valley is quite diverse. The diversity just happens to represent the half of the human race with origins in the swath of territory between India and then east and north up to Korea.
The diversity problem isn’t about lack of diversity. It is about the right kind of diversity for a particular socio-political narrative. That’s fine, but I really wish there wasn’t this tendency to lie about the major obstacle here: people of Asian origin are 5% of the American work force, but north of 30% in much of the Valley. If you want more underrepresented minorities hiring fewer of these people would certainly help. In particular the inflow of numerous international talent coming from India and China could be staunched by changes to immigration law.
But these are international companies. Though they genuflect to diversity in the American sense (blacks and Latinos), ultimately they’ll engage in nominal symbolic tokenism while they continue on with business, with an increasingly ethnically Asian workforce and and increasingly Asian economic focus. Meanwhile, the press will continue to present a false caricature of a white workforce because that’s a lot more of a palatable bogeyman than Asian Americans and international tech migrants, and the liberal reading public seems to prefer the false narrative to engaging with reality.
Addendum: The first article was in The Nation. Take a look at their masthead. Most of the names I recognize are mighty, perhaps even alarmingly, white….
Southern Africa is kind of a big deal. Not because it is the seat of human origins; I am beginning to think that question is “not even wrong.” Nor because it contains the “oldest human population” in the world; we are all the oldest human population in the world. Rather, the genetic variation one can find across a small region in southern Africa is incredible, and, it is one of the few regions of the world where hunter-gatherers have persisted in a culturally pristine fashion. By this, I mean that there is no evidence that the hunter-gatherers of southern Africa practiced another way of life (i.e., that they are marginalized agriculturalists or nomads), or, that their language was adopted from agriculturalists (as is the case with the Pygmies of central Africa). In other words, the continuity of the peoples of southern Africa is more notable not for their genetics, but their culture. That being said, the cultural conditions under which the KhoeSan peoples existed are of genetic interest, because their high degree of variation may reflect aspects of population dynamics common to hunter-gatherers as a whole.
In light of all this a new preprint on bioarxiv is quite interesting, Fine-scale human population structure in southern Africa reflects ecological boundaries. The title rather says it all, but I’ll admit that it’s hard to keep track of all the populations. It certainly strikes me as plausible, as the genetics suggests that there’s a lot of structure that built up over the years. Of note: “To contrast this with Europeans, the ≠Khomani and the Ju/’hoansi may have diverged over 30,000 ya but live only 1,000 km apart, roughly the equivalent distance between Switzerland and Denmark whose populations have little genetic divergence.” They report trans-Kalahari F st values on the order of 0.05, which is quite high, on an order of magnitude or so greater than what can be found in Northern Europe. But the latter is more comprehensible when you consider the genetic character of the North European plain only arrived at its current state ~4,000 years ago.Since the above is a preprint, some critiques are in order. The authors use ancestry tract lengths to assess admixture of Bantu, Asian, and European, elements into the KhoeSan. The implication is that these were separate admixture events. Some of them certainly were. But I’m a little skeptical of the power of these methods to distinguish admixture between the last two non-African components (also, I think it is probably advised for a population genetics paper to dispense with the cultural construct of Asian and make the clear distinction between South and East Asians, since the former are often genetically closer to Europeans, and this previously inflated the European proportion among Cape Coloureds). It’s been many years since I read A History of South Africa, but one of the more interesting aspects that I recall from this book was the cultural distinctiveness of what has now come to be called the Cape Coloured people, and their role as mediators along a fluid cultural frontier with the KhoeSan people. The history of the Griqua in particular shed light on how one might imagine European and Asian (South and East) ancestry arrived into the KhoeSan. Though racially mixed, the Griqua resembled the Dutch in formal and institutional aspects of their culture by the 19th century. But, as a semi-nomadic and pastoralist group they also had affinities with their African neighbors (and often, they played the role of predators with the Africans and their herds), with whom they clearly shared ancestry. It was not an unknown phenomenon to have Griqua scouts “go home to their mother’s people.” Even if their literal mother was also a Griqua, they seem to have had a sense that their maternal ancestors were invariably non-European, and often derived from the KhoeSan (many Griqua still spoke the now extinct Cape Khoi language, though they were shifting toward a Dutch Creole). The probability of assimilation of unadmixed Europeans, South Asians, and East Asians, into KhoeSan groups is not zero, but it strikes me as quite low. On the other hand, Griqua, who were mixed between all the populations of southern Africa, and culturally quite at home in the semi-desert wilderness, seem ideal candidates for the population which could serve as the vectors for transmission of these ancestral elements into the KhoeSan.
A second issue with this preprint is that I’d like to see more methods. E.g., three and four-population tests and TreeMix in particular, since with 320,000 SNPs these should be totally feasible with genotype data. These are not groups that most people have much familiar with, so PCA and ADMIXTURE tend to overwhelm. To develop a decent intuition about what’s going on trees and tables are often helpful (I don’t like tables usually, but often when you are focusing on a finite number of populations per row they can allow for greater focus). Also, there are now interesting ways to analyze spatial genetics beyond Mantel tests.
Ultimately these results confirm what I already held as a prior. It strikes me that the relationship we see between language and genes today is largely a function of the reality that much of the population genetic structure we see around us is a recent phenomenon. That is, massive migrations due to cultural changes (e.g., agriculture) were accompanied by both language and genes, and only a few thousand years are simply not enough time to allow for linguistic differentiation to obscure common origins. In contrast, if, as seems plausible, many of the KhoeSan people were resident in southern Africa for tens of thousands of years, then correlations between language and genes should slowly decouple (in part because deep linguistic affinities may not be discernible). That being said, I would not be surprised if ancient DNA from southern Africa at some point overturns conventional wisdom that these peoples are truly primal….
About ten years ago a standard model of the understanding of the peopling of the world by modern humans was that ~50,000 years ago a massive demographic swell out of eastern Africa overwhelmed, to elimination, all other human populations. With a few exceptions, such as the New World, these modern Africans quickly settled down, and the extant distributions of genes, generally mtDNA and Y lineages, reflected the long equilibration between then and now (the recent changes in the New World being an exception to that). Human genetic variation then could be understood as having been shaped by a rapid pulse expansion, and then a subsequent stabilization where genetic variation was maintained by geographic barriers across founding populations, and diminished by gene flow governed by isolation-by-distance. To a great extent this is the story you’ll find in Stephen Oppenheimer’s Out of Eden: The Peopling of the World.
To a large extent that story was wrong. Ancient DNA in particular, though not exclusively, has reshaped our understanding of the past (see Toward a new history and geography of human genes informed by ancient DNA). The ubiquity of population discontinuity and admixture suggest that it was naive to assume that modern genetic variation in any way reflects the founding stock which initially arrived in the first wave in many regions of the world. Additionally, the existence of archaic admixture in most modern lineages attests to the fact that the chasm between “them” and “us” was not perhaps quite as great as some might have claimed.
The ubiquity of population replacement is the reason I recent predicted that the first Aurignacian genome would show no relation to modern Europeans. (I was correct for what it’s worth) That is, modern humans in Europe have no special relationship to the first modern humans that settled Europe 45,000 years ago. The work on ancient DNA does suggest that modern Europeans have hunter-gatherer ancestry…but how deep does this go? I hazarded that perhaps the Gravettians are the earliest candidates for being the direct ancestors of the “Western Hunter-Gatherers” (WHG), who contribute a substantial portion of their genes to modern Europeans through Mesolithic hunter-gatherer populations. But, I wouldn’t be surprised if the genomic character of European Mesolithic hunter-gatherers was determined after the Last Glacial Maximum, ~20,000 years ago.
A new paper in Current Biology, seems to tip toward the latter conclusion. Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe. In particular, using a confluence of “best of breed” phylogenoomic methods and archaeological dating the authors contend that there was a major turnover in the mtDNA heritage of Europeans ~14,500 years ago, during the Bølling-Allerød interstadial, a relatively mild and warm period of the Pleistocene before the sharp and harsh regression of the Younger Dryas. The big result is that some very old (pre-LGM, Gravettian) belong to mtDNA haplogroup M. This is one of the two major groups common outside Africa, but it is absent in Europe today (the Roma harbor M because of their South Asian heritage).
The lineage that to a great extent has been canonical as that of European hunter-gatherers, U5, seems to have increased in frequency only late in the Pleistocene, during the above warm period. Because of the nature of random genetic drift we do expect lineage to go extinct over time. These are mtDNA, direct maternal lineages, so only one locus in the genome (though mtDNA is copious, so tends to be low hanging fruit for any new extraction technique). The combination of low long term effective population sizes and meta-population dynamics on the Eurasian fringe might mean that these are not unexpected results. But as suggested in the paper there is also a great possibility that the disruption of the interstadial resulted in some advantage to a particular subset of Pleistocene Europeans, who expanded rapidly, replacing their competitors. Many of the hunter-gatherers of the Mesolithic have relatively low genetic diversity in comparison to modern populations, suggestive of the small population sizes on the European frontier.
The expansion of U5 at the expense of other lineages though around ~14,500 years ago does seem to not be attributable purely to chance according to the models tested within the paper. Then what? One hypothesis is that the climate change resulted in extinction of many populations ill equipped to adapt to climate change, and these were later replaced by newcomers. Another, not exclusive, model is that there was conflict between different groups, and the climate change opened up opportunities for one subculture. There is an allusion to megafaunal extinction in the paper around this period…perhaps we should think of humans as just another megafauna for the super-predator cultures?
One way to look at geological process is that it is uniformitarian, not catastrophic. But it strikes me that with human demography catastrophic pulses are quite common on a geological scale. Why? Likely because cultural evolution is not quite so gradual and continuous, but that innovative revolutions and rapid sweeps of inter-group competition “thin the field,” so to speak.
The main caution I would add is that though we know a lot more than we did, we still no little. What was the ancient population structure in prehistoric Europe? Really we don’t know much, as the sampling is thin at best. That is changing.
When I was younger I used to follow politics somewhat closely. Every year I would read The Almanac of American Politics. With sites like Politico and Wikipedia there’s really no point. Additionally, I gave up my interest in closely following politics at around the same time (or a little later) I stopped closely following professional sports. To a great extent it was a matter of the opportunity cost, and the fact that I find most of the major camps rather uncongenial to me (e.g., I dislike the multiculturalism which seems embedded within the Democratic party today, and, the militarism which is reflexive for modern Republicans). But I do have one observation to make: the intensity of support for Bernie Sanders and Donald Trump are things I’ve noticed. I’d still bet that neither will win their parties’ nominations, but it definitely makes you wonder.
I’ve been very busy, so no time to really read many books. But I did do some preliminary analysis of 1000 Genomes’ data. Judging from the samples I wouldn’t be surprised if there is more evidence of inbreeding from genetics in the British Bangladeshi community than in the samples from Dhaka. The Gujarati Patel community exhibits somewhat more elevated rates of runs of homozygosity in comparison to Europeans or Bengalis, but the range and median in Pakistani populations is pretty extreme (while South Indian groups do evidence of consanguinity as you’d expect). Also, the ethno-linguistic identity of Pakistani populations is pretty obviously fluid. More on that later….
Daniel Falush is going to draft up a write-up on how to/not to use ADMIXTURE analyses….
— daniel falush (@DanielFalush) January 27, 2016
I’m pretty skeptical of reparations on prior grounds, and have long been so. I read The Debt: What America Owes to Blacks, 15 years ago, and recall it being more substantive that what’s on offer in our day. But, it has crossed my mind recently that cash has been shown to be very effective in development aid contexts. So why not in this situation? Yes, there are plenty of reasons to object, but it strikes me many of the same reasons apply in developed economies as well. It seems that the key for reparations to work and have some “buy-in” is it to be linked to a rollback of positive discrimination in public life. So it’s probably a nonstarter.
The schizophrenia paper. People have asked. Yes, this is a very big deal.
The above plot I generated using the 1000 Genomes data set. BEB = Bangladeshis from Dhaka, STU are Sri Lankan Tamils, ITU are Telegus, while PJL are Punjabis from Lahore, and GIH are Gujaratis (collected in Houston). These are big categories. The South Indian population sets exhibit some structure in terms of caste; there are a few Brahmins, as well as some Dalits. The Bengalis are strangely coherent for a South Asian population, shifted toward Cambodians. The Gujarati are differentiated between a large number of Patels, and other various groups. To my surprise the Punjabi samples are very diverse.
To a great extent it recapitulates the results of the 2009 paper Reconstructing Indian Population History. What you see to the left is the “ANI-ASI cline.” Basically South Asians, from Pashtuns all the way to Paniyas fall along a spectrum of genetic distance from West Asian and European populations. A secondary element is that some groups, such as Bengalis and many Austro-Asiatic tribes, are shifted toward East Asians. An old hypothesis of the ethnogenesis of South Asian peoples is that they are a variegated mix of “Caucasoid” populations intrusive to the subcontinent, which was originally inhabited by an “Australoid” element. Though these terms are somewhat archaic, the general point seems to get at something visually clear: some South Asians look nearly Mediterranean in appearance, while others are hard to distinguish from Australian Aboriginals (at least superficially). And of course, most of us are somewhere in the middle.
The insight of the Reich group was to use Andaman Islanders as a proxy for a primal indigenous population, and infer that the admixture alluded to above consisted of a very West Eurasian-like population, the Ancestral North Indians (ANI), and an indigenous group closer to East Eurasians, though very diverged, the Ancestral South Indians (ASI). Ergo, the ANI-ASI cline. Using the most closely related population to infer the “ghost population,” they were able to infer admixture proportions even though no “pure” ASI group was available as a reference against which they could judge. Clever strategies like this are important, because the reference populations you use to adduce admixture events (or lack thereof) strongly impact the nature of your results. Using simple PCA or model-based clustering, as with ADMIXTURE, one would fix South Indian Dalits and tribal populations as the “purest” aboriginal people. ~100% “Australoid.” And other groups could be modeled as a “Caucasoid/Australoid” mix. But this model was not satisfactory because even low caste South Indian groups were more shifted toward West Eurasians than you’d expect.
Using a statistic called the F4 ratio the they estimated that ANI ranges from 65-75% in the Northwest Indian populations, down to 15-30% in the lower caste South Indian ones. A 2013 paper, Genetic Evidence for Recent Population Mixture in India, attempted to infer an admixture period (two to four thousand years before the present), as well as a possible secondary pulse in some Indo-European groups. This stands to reason today when you note that most Indian groups share the most unique drift trajectory with the ancient Caucasian hunter-gatherer found in Kotias, but a minority, mostly upper caste, are closer to Sintashta steppe culture.
I’m putting this post up because people are asking me about a paper profiled in ArsTechnica, The caste system has left its mark on Indians’ genomes. Actually the 2009 Reich lab paper already concluded this. So what’s the major finding of this paper that makes it unique? We’ll start with the abstract, Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure:
India, harboring more than one-sixth of the world population, has been underrepresented in genome-wide studies of variation. Our analysis reveals that there are four dominant ancestries in mainland populations of India, contrary to two ancestries inferred earlier. We also show that (i) there is a distinctive ancestry of the Andaman and Nicobar Islands populations that is likely ancestral also to Oceanic populations, and (ii) the extant mainland populations admixed widely irrespective of ancestry, which was rapidly replaced by endogamy, particularly among Indo-European–speaking upper castes, about 70 generations ago. This coincides with the historical period of formulation and adoption of some relevant sociocultural norms.
So the two major results which warrant this paper being published are that instead of two ancestral populations, they posit four, and, the admixture between some of these is considerably more recent than in the 2013 paper. I think the first conclusion is wrong, and the second is too strong.
The authors make much of the fact that they have new samples. And their SNP-chip has a high density. But I’m confused why they didn’t integrate the 1000 Genomes data. The paper was received in early July 2015, and I know there was 1000 Genomes data from all the above groups by then. They didn’t even bother to use the HapMap GIH sample, which was definitely there!
The figure to the right shows the crux of their results. They used ADMIXTURE to break apart the ancestries of their Indian data set into four clusters. Through cross-validation they established that a K = 4 was optimal parameter fit for their data. Two of the populations are previously known: ANI and ASI. But they also find that there is an “Ancestral Austro-Asiatic,” and “Ancestral Tibeto-Burman,” cluster, AAA and ATB repectively. Because they did not use full labels, it can be hard to decipher, but they use this plot to assert that people of the Khatri caste are nearly 100% ANI, while Paniyas are nearly 100% ASI. Additionally, they found several groups which were nearly 100% AAA and 100% ATB.
Long-time readers will see the immediate problem: you can’t use ADMIXTURE like this! There is no guarantee that a group that is 100% x actually is in a situation where x corresponds to a genuine discrete ancestral population that existed in reality. That is, these sorts of models push a certain number of ancestral populations, and force individuals into being combinations of those. The model is constrained by the data you are putting into it to generate the results. For example, if I took Uygurs and Europeans, and did a K = 2, the Uygurs may form one cluster, and the Europeans another, at 100% levels. But we know from history and other methodologies that the Uygurs are a recently mixed group (within the last 2,000 years). Nevertheless if you tell the package to assume K = 2 with Uygurs and Northern Europeans, then it will place these into two distinct groups. And in fact, the result tells you something real and significant about the relatedness of the individuals in the data…but it doesn’t tell you necessarily anything about the real population history.
There’s a fair amount of evidence that Austro-Asiatic populations in India are not indigenous, nor are they pure. A major hole in this paper is the total lack of acknowledgement that Austro-Asiatic languages are much more common in Southeast Asia, and it seems likely that they were intrusive to India. If so, modern Austro-Asiatic peoples can be thought of us a compound of migrants with the local substrate.
The ATB element is found only in Austro-Asiatic tribes and Bengali Brahmins. That’s reasonable, because both populations exhibit a relationship to East Asian groups. While the Brahmins of South India absorbed a minor element of local Dravidian ancestry, those of Bengal absorbed Tibeto-Burman and Austro-Asiatic, which is found in higher concentrations among Bengalis proper.
To repeat, ADMIXTURE does not necessarily give you real population combinations!!! In fact, populations are to some extent a social construct, insofar as they’re just really collapsing the genetic variation which is the result of a particular demographic and pedigree history. The “ANI” group proffered here is an artifact. The Khatri are not a representative of a pure population which is similar to the ancestral ANI. The Paniya are not 100% ASI, they are just the most ASI. The Birhor are not 100% Ancestral Austro-Asiatic, they are just the most distinctively Austro-Asiatic. The Jamatia are not pure Ancestral Tibeto-Burman; most of these Northeastern tribes have some ANI/ASI admixture. They’re just the most Tibeto-Burman.
Instead of relying on ADMIXTURE so much, they should have also utilized D-stats and f-stats (not as sensitive to drift), as well as TreeMix. I think that would have quickly shown that some of these “pure” groups were mixed.
Second, there is the issue of time-since-admixture. They obtained lower values than the 2013 paper. Why? Because they use source populations (and probably the methodology) which are somewhat different from that earlier work. Honestly if some of these populations are compounds, then it doesn’t make sense to necessarily use them as idealized donors in an admixture event. The AAA tracts are most definitely artifacts in my opinion, since the tracts are the outcome of a previous admixture event.
Finally, the authors allude to a “Southern Route” out of Africa, and, imply that the Austro-Asiatic arrived with this. The best work today suggests that Austro-Asiatic peoples expanded with an agricultural wave ~4,000 years ago, with a locus of origin in the uplands of South China. Therefore, they are not primal. A simple inspection of the map of Austro-Asiatic languages forces one to ask the question of direction of migration.
I offer this critique in the spirit of post-publication review. Perhaps the authors will clarify, as I’m genuinely puzzled by the interpretations they offered.
Last fall while at ASHG this paper came out, Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent:
Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.
Turns out that there was a bioinformatics error which negates the magnitude of these results. Erratum to Gallego Llorente et al. 2015:
The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few Sub-Saharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.
We thank Pontus Skoglund and David Reich for letting us know about this problem.
First, scientists are humans and mistakes happen. So respect that the authors owned up to it. On the other hand, the conclusion never smelled right to many people. I was confused by it. I asked Iosif Lazaridis at ASHG. He was confused by it. I asked Pontus Skoglund. He was confused by it.
Unfortunately the result from the bioinformatics error was emphasized on the abstract, and in the press. In The New York Times:
“The most astonishing thing is there’s quite a lot of backflow in all modern African populations,” Dr. Pinhasi said. He and his colleagues estimate that 7 percent of the genomes of the Yoruba people of Nigeria are of Eurasian origin. In the genomes of Mbuti pygmies who live in the rain forest in the Democratic Republic of Congo, 6 percent of the DNA comes from Eurasians.
Ryan L. Raaum, an anthropological geneticist at Lehman College, part of the City University of New York, called the new study “fantastic” but questioned its conclusions. If people from the Near East moved into Africa, he argued, a drastic shift in the archaeology of the region would logically follow. But no such shift occurred. It is also possible that Eurasian DNA moved into Africa earlier than 3,000 years ago, Dr. Raaum argued. Mota might have simply lived in an isolated community that never encountered people with those genes.
The best way to test the conclusions of Dr. Pinhasi and his colleagues, Dr. Raaum said, would be to gather more DNA from African fossils of the same age. If the researchers are right, they would also lack Eurasian DNA. “Then the argument starts to seem a lot more plausible,” Dr. Raaum said.
A rule of thumb in science is when you get a shocking and astonishing result, check to make sure you didn’t make some error along the sequence of analysis. That clearly did not happen here. The blame has to be distributed. Authors work with mentors and collaborators, and peer reviewers check to make sure things make sense. The idea of massive admixture across the whole of Africa just did not make sense.
If something like this happened to me I’d probably literally throw up. This is horrible. But then again, this paper made it into Science, and Nature wrote articles like this: First ancient African genome reveals vast Eurasian migration. The error has to be corrected.
An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out-of-Africa migrations that occurred between 125,000 and 60,000 yr ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups, and these genomes showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out-of-Africa bottleneck but before the major Neanderthal admixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, although the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out-of-Africa migrations.
This is a good paper. They’ve taken a stab at it, and are very circumspect. But in the end they state that “these two conclusions therefore point to the Bedouins being direct descendants of the earliest split after the out-of-Africa migration events that established a basal Eurasian population.”
To catch everyone up, Lazaridis et al. suggested based on results from ancient DNA that many West Eurasian populations have an ancestry which derives from a lineage basal to all other non-Africans unmixed with this population. That means that the genetic distance of this group to Pleistocene European hunter-gatherers and Pleistocene Australians is the same, while the genetic distance between these two groups is smaller than between them and this population. Therefore they are termed “basal Eurasians,” or bEu.
But it is also important to note that they are a construct. The ancient DNA has not found any unmixed basal Eurasians. This is in contrast to other groups which are used as donor populations: European hunter-gatherers and Siberian hunter-gatherers. About ~50% or so of the ancestry of the Anatolian farmers who were the precursor of the first agriculturalists in Europe derive from bEu ancestry, with the balance consisting of a heritage similar to to European hunter-gatherers. The hunter-gatherers recently discovered in the Caucasus also have this bEu ancestry. Ergo, almost all West Eurasian and South Asian populations have bEu ancestry.
In the paper above, which is open access, the authors found a group of Qatari Bedouin, who seem to have low admixture from Africans or other Middle Eastern groups. Though some preliminary analysis was done with SNP-chips, they went whole genome for most of the work (allowing them to look for rare variants, etc.). I would have been convinced to a great extent if they put a TreeMix graph out which showed that their indigenous Arab population was a good donor to ancient Anatolians along with European hunter-gatherers. But I did not see that. Or they could have done an F4 ratio test showing that the Bedouin were more basal Eurasian than any other modern population. I did not see that.
I did see an F4 ratio test for Neanderthal admixture. I am not confident that their assertions hold. Take a look at the pattern of Neanderthal admixture in the supplements; it’s all over the place. It isn’t in line with the broad patterns found in the latest work out of David Reich’s lab.
There are also some assumptions within the paper which I think are untenable. They seem to be positing a continuity of these Qatari Bedouin within the Arabian peninsula for tens of thousands of years. The divergence of the bEu population, putatively ancestral to these Bedouin, occurred from other non-Africans even before the settlement of Australia, over 50,000 years ago! I don’t think it is likely that the Bedouin were resident in or around the Arabian peninsula for that long.
Finally, there’s some reference to effective population sizes vs. X and autosome. This isn’t a major part of the paper, but I would be skeptical of these sorts of claims. There is a lot of work in this area, and it turns out everything is way more clouded than you might think on first blush.
Overall, good paper. But there’s still a mystery here. The only solution is clearly more ancient DNA from this region.