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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.

pydata_cover 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.

103296Admixture 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.”

Reproducible Research Practices and Transparency across the Biomedical Literature:

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.

Related: What this scathing exchange between top scientists reveals about what nutritionists actually know.

• Category: Miscellaneous • Tags: Open Thread

Twitter workforce breakdown

diversity_brief_fig2 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….

• Category: Race/Ethnicity • Tags: Race


41d3NIUbD8L._SY344_BO1,204,203,200_ 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.

Adam Kok III, last of the Griqua captains

Adam Kok III, last of the Griqua captains

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….

• Category: Science • Tags: Genetics, South Africa


51pgrGlsM4L._SX327_BO1,204,203,200_ 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).

u5 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.

• Category: Science • Tags: Genomics

51Y1vJLRcLL._SX362_BO1,204,203,200_ 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….

debt 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.

• Category: Miscellaneous • Tags: Open Thread

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.

nihms137159f3 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. Malala_and_Freida_Pinto_meet_the_Youth_For_Change_panel_cropped_frida 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.

nihms137159f4 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!

Screenshot from 2016-01-26 23:29:21 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.

• Category: Science • Tags: South Asian Genetics

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.

• Category: Science • Tags: Ancient DNA, Genomics

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations:

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.

• Category: Science • Tags: Genetics, Human Genetics

Youngronaldfisher2In New Creationists a philosopher at Duke recounts his experience when he attempted to explore the implications of group differences in ethics. He stated:

After reading some recent work on the biology of group differences last summer, it occurred to me that as an ethics professor, I should write something about the moral upshot: if there are such differences, what are the consequences for how we should treat one another? Should we support policies that attempt to equalize opportunities only if they produce equal outcomes?

My conclusion was modest: if there are biological differences between groups, and if, as Lee Jussim has argued, some stereotypes turn out to be accurate in part because of correct generalizations about biological differences, these facts should not undermine our commitment to treating one another as moral equals, or to increasing opportunity for all, regardless of group membership.

But I had committed a sin in the eyes of the two referees who read and commented on my paper. I simply acknowledged the possibility of group differences while arguing that whether or not they exist, they should not matter. For having done that, the two journal referees used expletives and exclamation points to give the most venomous and dismissive feedback I have ever encountered. (Needless to say, the paper was not accepted for publication after such hostile comments.)


This is obviously a touchy subject to many reasons. But, the extremely vehement reactions on this topic reveal an aspect of how ideas are policed in our society. Because I have a particular reputation I am privy to viewpoints from many people that they would be terrified to share with others. For example, many young geneticists seem to view the idea that “race is a myth” to be a noble lie.

There are legitimate issues in regards to phylogenetic classification systems. But, the key that many geneticists have noticed is that the lay public makes incorrect inferences from the assertion that “race is a myth.” For example, many people are confused as to why human populations exhibit structure, and one can generate phylogenetic trees. That’s because people translate the idea that race does not exist to one where human population structure is arbitrary and trivial. The conclusion obviously does not follow, depending on your definition of race. But I think one can see how the educated public is coming to these conclusions.

Here’s an article from the year 2000 in Do Races Differ? Not Really, Genes Show:

Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level. But the more closely that researchers examine the human genome — the complement of genetic material encased in the heart of almost every cell of the body — the more most of them are convinced that the standard labels used to distinguish people by “race” have little or no biological meaning.

They say that while it may seem easy to tell at a glance whether a person is Caucasian, African or Asian, the ease dissolves when one probes beneath surface characteristics and scans the genome for DNA hallmarks of “race.”

On the one hand there is an aspect of this article which is almost quaint. Note the references to 80,000 genes and such. But the general spirit captures the modern Zeitgeist well, and it is not dated at all. The idea of race implicit in this piece, and commonly held by the general public, is typological. That is, races are like Platonic ideal forms, and genes and traits are used to explore these ideal forms.

This is false. Races are not like ideal forms. That’s in part because modern human populations are by and large the consequence of massive admixture events between deeply diverged lineages. But, that does not negate the reality that population structure is a robust phenomenon, and, that its consequences are not trivial. My hunch is that some of the eye rolling that I’ve seen when younger geneticists refer to the idea that race is a myth has to do with the fact that population structure is such a big deal for genome-wide associations.

One of the implications of the above passage is that visual inspection allows for a clearer differentiation between individuals from different populations than genetics. This is false. As it happens the groups referred to above are among the most differentiated, as they don’t share common ancestors for ~40,000 years (South Asians on the other hand share ancestry with both “Caucasians” and “Asians” over the last 40,000 years), and are positioned at the extremities of the Afro-Eurasian world island. Genomics actually gives a clearer and more precise picture of population genetic differences.

The problem, if there is one, is that these population genetic differences are not necessarily good fits if one assumes a Platonic model of racial categorization. I think this explains the irritation and frustration with people who are confused as to the ancestral quantification results from firms like 23andMe. The results are true, and robust, reflections of genetic variation. But population groups are reifications, attempting to squeeze human digestible insight from systematic variation at hundreds of thousands of markers whose pattern of differences are a consequence of tens of thousands of years of population history.

Which brings me to the UNESCO statement on the Race Concept. Published around 1950 in a few versions these statements were signals that there was a change in the winds after World War II. Much of today’s conventional wisdom is prefigured in these statements. But if you read the 1952 version much of it is pretty moderate and I think it would be seen as “problematic” by many thinkers today. There are many familiar names (and some not familiar to me) in terms of scientists consulted. E.g., H. J. Muller, Theodosius Dobzhanksy and Ernst Mayr. But for me R. A. Fisher’s comments stood out. I knew he was a dissenter from the statement, but I’m going to cut and paste the whole section from him because I think it’s pretty interesting (and many might agree with him):

In so far as the Statement condemns any defamation of races and emphasizes the appalling nature of the recent abuse of racial theory, it has my full and unqualified approval. I wholeheartedly agree, also, with its explicit and implicit finding that anthropology and racial studies afford no justification for the assumption that members of any particular race are not entitled the enjoyment of all fundamental rights, or for any form of racial discrimination. And I am very glad that, after all the horrors that have been perpetrated, these principles should have been enunciated clearly and publicized widely by an organization of such standing and by distinguished men as the authors of this Statement.

But the Statement also purports to be an authoritative body of scientific doctrines, and this is quite a different matter. Without touching upon the content of these doctrines, and quite apart from whether or not they meet with my approval, I must register my fundamental opposition to the advancing of scientific theses as such, and protest against it.

I recall the National Socialists’ notorious attempts to establish certain doctrines as the only correct conclusions to be drawn from research on race, and their suppression of any contrary opinion; as well as the Soviet Government’s similar claim on behalf of Lysenko’s theory of heredity, and its condemnation of Mendel’s teaching. The present Statement likewise puts forward certain scientific doctrines as the only correct ones, and quite obviously expects them to receive general endorsement as such. I repeat that, without assuming any attitude towards the substance of the doctrines in the Statement, I am opposed to the principle of advancing them as doctrines. The experience of the past have strengthened my conviction that freedom of scientific enquiry is imperiled when any scientific findings or opinions are elevated, by an authoritative body, into the position of doctrines.

A different section of statement relays Fisher’s view of the empirical realities, which would make him extremely unpopular today:

Sir Ronald Fisher has one fundamental objection to the Statement, which, as he himself says, destroys the very spirit of the whole document. He believes that human groups differ profoundly “in their innate capacity for intellectual and emotional development” and concludes from this that the “practical international problem is that of learning to share the resources of this planet amicably with persons of materially different nature, and that this problem is being obscured by entirely well intentioned efforts to minimize the real differences that exist”.

This sort of comment from Fisher makes sense in light of his personality. I’m tempted to think that today he would be diagnosed as being “on the spectrum.” Arguably the most eminent evolutionary geneticist of the 20th century, he also made many original contributions to statistics. But as documented in his daughter’s biography of her father, he was a monomaniacal and selfish person, who lacked many social graces. There is a section in R.A. Fisher: The Life of a Scientist which documents his tendency to engage in arguments with people who shared his general conclusions on a given topic, but where he believed they engaged in fallacious reasoning (in this he seems to resemble Karl Popper). This tendency is clear above. Though he agrees with a broad liberal humanitarianism which looks darkly upon considerations of race, he disagrees with the presumption that these values are rooted in empirical facts.

Finally, I want to quote page 238 of my edition of The Genetical Theory of Natural Selection:

The general consequences of race mixture can be predicted with confidence…Their general character will therefore be intermediate, but their variability will be greater than that of the original races. Morever, new combinations of virtue and ability, and of their opposites, will appear in the mixed race, combinations which are not necessarily heterozygous, but may be fixed as permanent racial characters. There are thus in the mixed race great possibilities for the action of selection. If selection is beneficient, and the better types leave the greater number of descendants, the ultimate effect of mixture will be the production of a race, not inferior to either those from which it sprang, but rather superior to both, in so far as the advantages of both can be combined. Unfavorable selection, on the other hand, will be more rapidly disastrous to a mixed race than to its progenitors. It should of course be remembered that all existing races show very great variability in respect of hereditary factors, so that selections of the intensity to which mankind is exposed would be capable of producing rapid changes, even in the purest existing race.

41PHSZN6AEL Fisher was writing this in the 1920s. This was near the tail end of the peak of white supremacy across the world. Charles Davenport, the director of Cold Spring Harbor Laboratory, published Race Crossing in Jamaica in 1929. It presented a view where mixed-race children suffered due to crossing between diverged lineages. This was not an atypical view at the time. The man whom Fisher succeeded to a great extent as Britain’s most eminent statistician, Karl Pearson, was a socialist and feminist (Fisher was a political conservative whose views on women were more regressive than Pearson) who also believed that inter-group competition with “inferior races” was a major driver of the evolutionary progress of Europeans. The above passage shows that Fisher’s logical mind internalized Mendelianism and its necessary implications to such a great extent that as early as the 1920s he was already dismissive of the racialism ascendant at the time. But by the 1950s the dominant viewpoint differed, and here Fisher again stood his ground, not changing the things he had written in the later eugenic sections of tGToNS.

R. A. Fisher had some unfortunate views on smoking. See When Genius Errs: R. A. Fisher and the Lung Cancer Controversy.

• Category: Race/Ethnicity, Science • Tags: R. A. Fisher, Race

silicon-valley I watched a few episodes of Silicon Valley at a friend’s house this Friday when I was in the Bay area. I though it was pretty funny. I was at the Googleplex during the day, so it was interesting to see how it influenced the show. But in general I thought the Peter Thiel influenced character Peter Gregory was probably the best thing about the show. Unfortunately the actor who played Peter Gregory died during the first season. (A friend believes that I somewhat resemble the character Erlich Bachman.)

I think Steve mentioned that one unrealistic aspect of Silicon Valley is that the day-to-day action seems relatively detached from the ubiquitous nature of the internet, and the fixation that modern Americans have on their phones. But the reality is that having scenes dominated by characters staring at their phones would probably be quite boring.

You have probably heard about the Free Harvard/Fair Harvard campaign. Here are the detail of how to help:

Thus, anyone holding a Harvard degree who is interested in signing our petitions and perhaps changing the world should email us at, and include your mailing address to obtain a petition for signing. If you can commit to quickly gathering an additional signature or two and also include your phone number, we will FedEx you a petition. The more Harvard alumni signatures all of you can quickly gather, the more likely Harvard will soon become both free and fair.

Alumni here includes both undergraduate and graduate levels. Steve Hsu has part of this too. The deadline is February 1st.

41n4rA-gvoL._SY344_BO1,204,203,200_ As many of you know, I have a passing interest in psychometrics. What for me defines a passing interest? Unlike Roman history, for example, psychometrics is not a topic I follow in depth, or closely in any way. I know the basic outlines, and use that make judgments about the nature of the world. The question of where the general intelligence factor comes from in a biophysical sense is not a major concern of mine. Rather, I’m interested in what intelligence can tell us about life outcomes and such. That is, I’m an instrumentalist.

But I’m starting to become a little worried at how much ignorance there is among the intellectual elite on the topic. It is not uncommon for people to be entirely unaware of basic facts, in which case their inferences are derived from false premises. So how to remedy the situation? Arthur Jensen’s The g factor is dense and expensive, so I can’t recommend it casually. Hive Mind has a good introduction, but the topic is ultimately not intelligence as such. So I think I’d recommend Stuart Richie’s Intelligence: All That Matters. Any other suggestions? What is intelligence? by James Flynn is OK, but that’s an older book.

A response to Limitations of GCTA as a solution to the missing heritability problem is now up, Commentary on “Limitations of GCTA as a solution to the missing heritability problem”.

Some refugees are going back to Syria. I suspect there’s an economic angle here. The genuinely poor are probably not going to go back to these countries because being on welfare benefits of some sort in a wealthy country beats being on the margins in a less wealthy country. But many of the middle-class migrants seem to be realizing that they miss their social status when in countries where they are guaranteed to be marginalized for at least a generation, or longer.

51sdHZvYfTL._SX334_BO1,204,203,200_ Then there is the issue of cultural differences. I have written a few posts recently about the nature of these sorts of things. Over the medium-term culture is quite malleable and protean. But in a very general sense it does not change very fast in the short term (though specific aspects of culture can change fast). Here is a passage from The Secret of Our Success:

In Iraq, in the aftermath of the American military victory in 2003, many assumed that once freed from the dictatorial oppression of Saddam Hussein and presented with new state-of-the-art political and economic institutions imported from the United States and Europe, Iraqis would rapidly take to these institutions and start acting like people in Ohio. That did not happen, probably in part because new formal institutions and organizations have to fit with people’s social norms, informal institutions, and cultural psychology

One of the major sources of migration to Europe today is Afghanistan. Afghans have very different values from Europeans. To illustrate, here is a story from The New York Times, Flawed Justice After a Mob Killed an Afghan Woman. From the explanation of the video’s context: “Farkhunda Malikzada, a 27-year-old Muslim woman falsely accused of burning a Quran, was killed by a mob in central Kabul as hundreds watched and filmed.”

Let’s unpack the issue here.

1) A woman was killed in broad daylight
2) In the largest most cosmopolitan city in Afghanistan
3) The killing was a matter of mob justice, and by the end young boys are encouraged to throw stones at the dead body in an almost initiatory manner
4) She was killed because she was accused (falsely it turns out) of burning a Koran

Initially prominent political leaders praised the mob justice because they believed the account of her blasphemy. Later there was anger when it came out that she was falsely accused due to a petty squabble.

My point is that hundreds of thousands of men from this particular culture are now living in Europe. It seems implausible that just by drinking European water they would magically become democratic liberals. Though the social context is such that this sort of mob justice is not going to occur in Berlin or Stockholm, it is also almost certainly true that many of the informal and tacit views of these Afghan migrants aligns with the men and boys of Kabul who killed Farkhunda Malikzada.

I was talking recently about how I go about deciding on my “intellectual diet” (similar to the “media diet”) with my friend Carl Schulman. Over the years (I’d probably date the genesis of my habits to when I was eight years old or so) the domains which I explore have varied. I try to balance being focused on issues of particular and personal interest, with an occasional sampling of the parameter space of ideas and topics which are novel to me. There are books I read for really practical reasons. E.g., my friend Joel Grus’ Data Science from Scratch: First Principles with Python (I’m in transition from Perl to Python). There are others I read for professional reasons. An Introduction to Population Genetics Theory. Though I read few genetics books in my field aside from theoretical texts, since the papers are where the latest research is in any case. On the other hand there are topics which have been long-running interests of mine. As is obvious from my Good Reads, I read a lot of history. In particular, Roman and Chinese history. I’ve been doing so since I was about 12 years old. There are other topics, like religion, which I’ve focused on for a while, before moving on when I thought I knew what I needed to know. But occasionally I’ll read something random, such as Alexei Panshin’s The World Beyond the Hill: Science Fiction and the Quest for Transcendence. Most of the time these forays are one-offs, but occasionally I discover a new interest.

Of course the reality is that these sorts of methods and strategies change over time. Between my work and personal life I don’t see much room for reading fiction at this point. But perhaps there will be a time when I’ll go back to that habit.

Some of you now I experiment with things like Soylent. One thing I would like to add though: I think the focus on perfectly optimizing nutritional intake is pretty short-sighted. The reality is almost no one is going to move wholly to meals-ready-to-eat, and variation in the population in nutritional needs does exist. I bring this up because I’m going to try MealSquares soon.

Speaking of food, China Village in Albany, CA, has pretty good Szechuan.

Brian Boutwell and Amir Sariaslan are two accounts on Twitter you should follow. They do a really good job reintroducing the wisdom of behavior genetics into the public discussion.

I find this interesting, because Muslims have never told me that I should change my name. It seems that this is because though my name is operationally Muslim, neither Razib nor Khan are Arabic and explicitly tied to Islamic history. Razib is simply a Bangladeshi variant of the common Bengali name Rajib, which is a variant on the more well known name Rajiv, whose ultimate origin is Sanskrit. And Khan is a Turco-Mongol title, which for various reasons became associated with Muslims in South Asia.

The Day the Mesozoic Died.

• Category: Miscellaneous • Tags: Open Thread

513C5X3UhAL._AC_UL320_SR220,320_ As one might expect, the piece that I co-authored with Brian Boutwell, Heritability and why Parents (but not Parenting) Matter, has stirred up some irritation and even anger. Part of this is simply due to the mildly hyperbolic nature of the title. Obviously on some level parents matter a great deal. What we were attempting to get at though is that most parents have far less precise control of the outcomes of their children than they think they do (you do have great control if you beat or starve your children though!). The lack of control is one reason siblings vary so much.

To make it concrete, imagine across the population variation of personality is 30% heritable, 15% accounted for by shared environment, and 55% explained by non-shared environment. The parental effect is captured in the shared environment. When behavior geneticists downplay the role of parents in affecting outcomes, they are doing so because of this value. In this example the proportion explained by the parents’ genetic variation is twice as large as the conscious environmental choices. But, note that most of the variation is not necessarily due to genetic factors!

What is this variation? The short answer is that we don’t know. One hypothesis, promoted by Judith Rich Harris in The Nurture Assumption, is that it is one’s social milieu. That is, peer groups. To my knowledge in the past 15 years there has not been much support for this thesis, suggesting to me that we’re still at a loss to explain non-shared environment. In fact it may just be an intractable stochastic aspect of life outcomes (or if you want to reduce it to biology, developmental stochasticity).

People become uncomfortable with these statistics because they suggest that the most immediate personal control you can have on the character of your offspring is through the spouse you select. Your spouse (or you) may change values over time, but you are not going to change your genes. This is not very congenial with the modern American conservative orthodoxy that crystallized after World War 2 which placed the nuclear family at the center of the culture (basically, fusionism). The rise of “family values” as inoculation against liberal permissiveness is to a great extent predicated on the idea that shared environment is very powerful over the long term. The data just don’t support this proposition.

We can see this when you look through recent history. Some of the response to the Quillette piece emphasized and reiterated that we missed something when we ignore and dismiss the importance of values that parents’ instill in their children. But values are malleable. A whole generation of Southerners grew up in the 1950s and 1960s with racial values taught to them by their parents, and they also grew out of those values as a generational cohort. Or, look what’s happening with gay marriage: …Evangelicals Are Changing Their Minds on Gay Marriage:

The shift is especially visible among young evangelicals under age 35, a near majority of whom now support same-sex marriage. And gay student organizations have recently formed at Christian colleges across the country, including flagship evangelical campuses such as Wheaton College in Illinois and Baylor in Texas.

Obviously this goes back to Judith Rich Harris’ general insight: social consensus and cultural cognition are real phenomena which are enormously impactful. But please remember that this doesn’t necessarily explain non-shared environment, as these sorts of dynamics are forces for conformity and homogenization. When we are thinking about control of outcomes, usually you need to focus on:

- Culture
- Genes
- Parents

In that order. The non-shared environmental variance will still be substantial, but we don’t have a good sense of what’s causing it yet. And we may never. But we can choose a lot of life outcomes by selecting the nation we migrate to, or, by the community with which we identify. For example, if I migrated back to Bangladesh and raised my daughter to be a staunch atheist with a generally liberal-individualist ethos, those values might stick. There’s probably some heritable aspect to my character which makes atheism and liberal-individualism “a good fit.” But, there is a strong chance that my daughter will conform to the milieu in which she grows up, and with which she may identify. The exception to this would be if she found a subculture which insulated her from broader social conformity pressures, and allowed her to develop her worth and identity differently.

I’m not totally sure of the political implications of this perspective in the United States. My own position is that the rhetoric of “family values” on the American Right today has been strongly suffused with an individualist ethos that is common in Anglo-American evanglical Protestantism, and can find its roots in the somewhat atomized nature of Scots-Irish and lowland South culture in the United States. A contrast with this model is that of Mormons, who share values with evangelical Protestants, but whose folkways reflect the more communitarian ethos of New England Yankees and German or Scandinavian peoples. I suspect that the lower divorce rate (and social pathology more generally) among Mormon Americans in comparison to white evangelical Protestants has more to do with the nature of their collective institutions than the individual dispositional nature of believers.

50thversion On the other hand, this viewpoint does not necessarily support the instincts of modern technocratic liberalism. In general technocratic liberals seem to think that many social ills have a small number of causes, and so are tractable through public policy. Often these causes are pinned down on single institutions (e.g., schools), or, a lack of funds. Recently universal pre-school has been all the rage because of its near magical ameliorative properties. But the social science on that is decidedly mixed. I suspect that universal pre-school as a simple institutional fix is far inferior to the rich civic and social matrix which Jane Jacobs described in The Death and Life of Great American Cities. Not only because organically developed social and civic institutions provide services which pre-school can not replace, but also because a society which gives rise to such institutions is by its nature more healthy and exhibits less anomie. In some ways Mao was right that a true solution toward fixing social ills is a “cultural revolution.”

• Category: Science • Tags: Behavior Genetics

smith-devilI’m not sure I believe the methods, but the paper is open access, Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales:

Ancient population expansions and dispersals often leave enduring signatures in the cultural traditions of their descendants, as well as in their genes and languages. The international folktale record has long been regarded as a rich context in which to explore these legacies. To date, investigations in this area have been complicated by a lack of historical data and the impact of more recent waves of diffusion. In this study, we introduce new methods for tackling these problems by applying comparative phylogenetic methods and autologistic modelling to analyse the relationships between folktales, population histories and geographical distances in Indo-European-speaking societies. We find strong correlations between the distributions of a number of folktales and phylogenetic, but not spatial, associations among populations that are consistent with vertical processes of cultural inheritance. Moreover, we show that these oral traditions probably originated long before the emergence of the literary record, and find evidence that one tale (‘The Smith and the Devil’) can be traced back to the Bronze Age. On a broader level, the kinds of stories told in ancestral societies can provide important insights into their culture, furnishing new perspectives on linguistic, genetic and archaeological reconstructions of human prehistory.

• Category: History • Tags: Folklore

ncomms10326-f351IQSePVDRL._SY344_BO1,204,203,200_ It has been an open question for historians of the fall of the Roman Empire the extent to which ethno-tribal migrant caused the transformation toward the post-Roman order. In Britain, for example, there has long been debate as to whether the shift from a predominantly Celtic population with a cosmopolitan Latin-speaking patina (at least demographically in terms of origins; I understand there are those who argue that late-Roman Britain was predominantly Latin-speaking), was due to a mass migration of Germans, or more a matter of institutional and cultural defection and conversion. In the early 20th century the model in vogue was predicated on migration. The Welsh and English were perceived by many to be distinct races, with the latter having affinities with the Germanic peoples in blood as well as speech. In the late 20th century the pendulum swung in the other direction. I recall reading Norman Davies’ The Isles in 2000, and he relayed the conventional view of historians of the period that the post-Roman world of Britain saw the conversion through elite emulation of Britons into Saxons (and Angles and Jutes) based on documentary evidence of co-existence and subordination of a Celtic population in early Anglo-Saxon England.

Ten years later Peter Heather wrote Empires and Barbarians to resurrect a moderate migrationism for the post-Roman world. What he was rebutting was the perception that the idea of German folk migrations, which included the movement of women and children along with men, was a post hoc myth. Though even the most extreme cultural constructionist would assent to the proposition that some Germans did migrate into the late Roman world and capture the post-Roman successor states, they usually emphasized that tribal identities were ad hoc, novel and newly constructed, and German identity was highly malleable easily co-opted by aspirant non-Germans. In other words, the Goths, Vandals, and Anglo-Saxons were motley coalitions of opportunists, whose ethnic self-identity was a matter of recent myth.

Some of this is certainly true. Going back to Anglo-Saxon England, Alfred the Great’s early genealogy is littered with names that seem to exhibit a British, not German, provenance. It is not unreasonable that British warlords would on occasion switch sides to maintain their position at the top of the status hierarchy, just as some Visigothic nobles in Spain after the Muslim conquest converted to the new religion and became progenitors of the local Islamic aristocracy.

But we shouldn’t go too far. Last year PoBI finally published their paper, The fine-scale genetic structure of the British population, and confirmed the suggestions of earlier genetic work that a substantial proportion of the ancestry of the contemporary English population derives from Germans. Not the majority, but a substantial minority. In other words, Peter Heather was correct in England. Cultural change was catalyzed by substantial demographic change. There is more and more evidence that in two areas of the post-Roman world where Romanitas faded, with the local decline or extinction of Christianity and Roman speech (whether Latin or Greek), Britain and the Balkans, there was substantial demographic change induced by a migration into Roman territory of Germans and Slavs respectively.

51sdHZvYfTL._SX334_BO1,204,203,200_ With that, I submit two open access papers on ancient genomes from Britain: Genomic signals of migration and continuity in Britain before the Anglo-Saxons and Iron Age and Anglo-Saxon genomes from East England reveal British migration history. The plot at the top of this posts shows a striking result: most of the Roman era individuals are genetically least differentiated from the Welsh, and modern East Anglians are the most shifted toward the Dutch. This is exactly the pattern we would expect from archaeology, as the pale of German settlement was along the Saxon Shore.

So genetics tells us that extreme positions of total replacement or (near) total continuity are both false. Rather, the genetic landscape of modern England is a synthesis, with structure contingent upon geography. But, it also shows us that substantial demographic change which produces a genetic synthesis can result in a total cultural shift. Though we may think of elements of culture as entirely modular, with human ability to mix and match components as one might see fit, the reality is that often cultural identities and markers are given and taken as package deals. But, it probably took the transplantation of a total German culture through a mass folk movement to give the Saxons enough insulation from the local British substrate to allow them to expand so aggressively and become genetically assimilative and culturally transformative.

• Category: History, Race/Ethnicity • Tags: Anglo-Saxons, Genetics

tnapb4 The “nurture assumption” is basically the idea that parents really, really, matter in affecting variation in individual outcomes in their children. Judith Rich Harris famously wrote a book length critique, The Nurture Assumption: Why Children Turn Out the Way They Do, which was published in 1999. I’ve argued that the Steven Pinker’s The Blank Slate is important in large part because it introduced a broader audience to Harris’ conclusions. Though the pattern that she observes, that most variation in outcomes for individuals does not seem to be accounted for by shared environment, that component that is under parental control, is a robust behavior genetic finding it runs against deep human intuitions. This is one domain where political Left and Right share the same sympathies, though the details differ. Many cultural conservatives in the United States impute to parents an almost alchemical power to shape the nature of their children through inculcation. Similarly, cultural liberals attribute the same sort of power to society broadly construed.

If you’ve been reading me for 13+ years you know all this. As a parent these last four years I’ve had to struggle with the nurture assumption myself. For psychological and social reasons the impulse is strong within us. Recently Brian Boutwell has been doing the Lord’s work, so to speak, in Quillette, reintroducing these ideas to a general audience. Now he and I have co-authored the latest installment, Heritability and why Parents (but not Parenting) Matter. I invite you to check it out!

• Category: Science • Tags: Behavior Genetics

41Ryk7GgnlL._SX331_BO1,204,203,200_ I’ve been very busy the past week or so. There’s a lot I could blog, but I just don’t have the time. I should mention that I’m now reading my friend Garett Jones’ book Hive Mind: How Your Nation’s IQ Matters So Much More Than Your Own. It’s a good complement to Joe Henrich’s The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. Reading them in sequence reminds me of how One Explanation to Rule Them All is usually not a good fit with reality broken down into its more complex bits. I’m about ~2/3 of the way through Garett’s book, and it’s a pretty quick read. I feel a bit bad for Garett though because he has to spend so much time justifying the utility of intelligence testing (much of it reads like Intelligent: All That Matters). Like The Secret of Our Success I’d really recommend Hive Mind if you have a background that’s outside of its core area of economics and psychometrics; there’s a lot you’ll learn, and it’s not a heavy lift.

k10181 One the issues that Garett mentions in Hive Mind is that IQ is only a modest (though robust) predictor of income. This explains why there are so many stupid people who happen to be well off, and vice versa. Much of where you end up in life is stochastic, in addition to other factors like personal background (i.e., “connections”), appearance, and personality. That being said when looking at groups of people as a unit IQ is much more predictive. It strikes me that this is just a lot of the random/stochastic effects being cancelled out, as they’re not systematically biased. I think there’s a relationship here to the dynamics that Greg Clark explored in The Son Also Rises: Surnames and the History of Social Mobility. While Garett surveys spatial patterns, Greg was highlighting temporal (inter-generational) patterns.

What else is going on?

• Category: Miscellaneous

41uhvVKVH+L._SX331_BO1,204,203,200_ Over the past several years ancient DNA has opened a startling window onto the settlement of the European continent during the Holocene. The story is one of migration, replacement, and repeated pulsing of populations from the fringe toward the North Sea. In short, the model that farming spread to Europe predominantly through cultural diffusion is dead. Though the genetic legacy of the indigenous hunter-gatherers persists in modern Europeans, it is through their amalgamation into the populations of farmers with roots in the Near East, as well as later peoples who arrived from the Eurasian steppe. Not because they adopted the culture of the newcomers.

But while the cultural diffusionist model has been falsified, the customary alternative, demic diffusion, has not been entirely validated either. This model posits the expansion of farming as a mechanistic, mindless, process analogous to thermodynamics and the expansion and diffusion of heat. It is in many ways a “culture-free” model, as farmsteads expand in an ad hoc and uncoordinated fashion across an empty landscape. And, as L. L. Cavalli-Sforza pointed out it was actually compatible with a predominant Pleistocene period ancestry for modern Europeans, because as the wave of demographic advance proceeded it would mix with the indigenous peoples on the frontier, diluting the distinctive original genetic signal.

I won’t repeat what’s been stated a thousand times in this space. Basically, rather than a gradual movement, the DNA is suggesting that there were starts and fits, and later equilibrations. For a thousand years or so it looks as if in the region of modern Germany during the early Neolithic the farmers and hunter-gatherers remained apart, with genetic distances comparable to that between modern Northern Europeans and Han Chinese. To account for this I have presented a rough model which I termed “leapfrogging,” as farmers migrated to ecologically favored terrain, leaving much of the hinterland in the hands of Mesolithic hunter-gatherers.

It turns out that none of my ideas were original, down to the terminology! A book chapter in The Colonization of Unfamiliar Landscapes: The Archaeology of Adaptation, prefigures almost all of my thoughts. Additionally, though published in 2003 I would argue it was relatively prescient. Here is one section:

The Neolithic colonization of Europe was a complicated process that took more than 2,500 years to unfold. Analysis of calibrated radiocarbon dates reveals a series of punctuated, rapid expansions, interrupted by periods – 500 to 1,000 years long – of stasis and in-filling. The earliest colonists in Southeastern Europe sought out floodplains and lake basins that were close analogues to familiar ancestral habitats in Anatolia and optimal for their farming practices. The two-stage structure of the Early Neolithic expansion and the selectivity of initial settlement locations imply carefully planned colonizing ventures, based on detailed prior knowledge of the landscape. The second-stage farmers may have derived this vital geographic information from fishing groups that initially created settlement facilities on the Greek coast to support long distance fishing trips. These frontiersmen probably shifted opportunistically from hunting and fishing, to herding, to trading.

You can read the whole chapter, Deerslayers, pathfinders, and Icemen: origins of the European Neolithic as seen from the frontier, at

• Category: Science • Tags: Neolithic

So Taylor Swift looks scary to Koreans? A couple of the guys seem to have been unaware that Beyonce Knowles is black (one of them commented on being ambivalent about her dark tan, only to be surprised when told that that wasn’t a tan, that she’s black).

51sdHZvYfTL._SX334_BO1,204,203,200_ I’m done with Joe Henrich’s The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. I would recommend it to anyone who wants to know more about the field of cultural evolution (the author is one of the major people behind the idea of WEIRD psychology). For myself, one of the main upsides was that the book had a lot of empirical illustrations I wasn’t familiar with. Unfortunately some of the references to genomics are out of date, because he was writing the book in 2014. Also, I found the chapter on language somewhat unsatisfying.

The best passages so far that I recall. Page 234:

…Even ultra-verbal academics frequently use air quotes, an iconic gesture derived from the use of scare quotes in writing, to imply some disagreement with their terminology or its implications. I’ve seen many a humanities scholar, with a latte in one hand and a book in the other, struggle to communicate, unable to deploy air quotes to shield themselves from any undesirable implications of their words.

And from page 95:

…What we need is a more evolution-grounded science on genes, culture, ethnicity, and race, not less.

These insights will continue to fuel the spread of a new social construct: the view that all people, perhaps some other species as well, are endowed with certain inalienable rights-we call these human rights. No new facts about genes, biology, or culture can alienate a person from these rights.

Though Henrich is skeptical about the utility of the race construct, his thinking is in line with A.W.F. Edwards’ in his essay Human Genetic Diversity: Lewontin’s Fallacy. Grounding human rights in empirical facts which are subject to change is…problematic!

41Ryk7GgnlL._SX331_BO1,204,203,200_ The emphasis on collective intelligence in The Secret of Our Success is an interesting complement to Hive Mind: How Your Nation’s IQ Matters So Much More Than Your Own. Though I was familiar with the model of technology loss because of drift, I was surprised how much return to population size there is in relation to the rate of innovation.

Glenn Reynolds often links to Amazon Kindle “Daily Deals”. I mostly ignore these though I’m a bit of a Kindle-holic. It’s for the same reason I canceled Kindle Unlimited, so many of the books on offer are just crappy (albeit, from my own subjective perspective). But on a lark, I clicked, and found some good stuff by drilling down to the subject categories.

61XC3xuXP2L._SY344_BO1,204,203,200_ I purchased John Darwin’s The Empire Project: The Rise and Fall of the British World-System, 1830-1970. Since I enjoyed After Tamerlane I’m expecting to not regret ponying up $2.99 or whatever it cost (“for the price of a Starbucks coffee….”). I also got a biography, Elizabeth Cady Stanton: An American Life. I’ve always been sympathetic to her, but my knowledge of her views and life are rather superficial (sometimes you get unfortunately surprised, R. A. Fisher: Life of a Scientist seems to confirm that he was a major league asshole). Speaking of biography, some reviewers were irritated that Constantine The Emperor read less like a narrative about his life, and more like a monograph of the culture of the Roman Empire of the time.51YhNdG3q3L._SY344_BO1,204,203,200_ Of course all that did was induce me to purchase it! Finally, I got two science(ish) books. Longitude by Dava Sobel, and To Explain the World, a history of science by by Steven Weinberg. In general I find Weinberg’s quasi-scientistic social and historical analyses rather uninteresting, but it was cheap, and the summary indicates that he begins in Miletus, a city whose role as the midwife for proto-science has always been near to my heart.

PAG is going on. If you are interested in genomes not human, I recommend the you check out the #PAGXXIV hash-tag on Twitter. There is lots of good science being done, but if you are interested, check out my friend Dave’s poster, Genetic Characterization of Indicators for Diazotrophic Recruitment in Zea mays.

Speaking of posters, I’m trying to get my data analyzed well enough to have a poster for BAPG XIII in Berkeley on February 13th. #Excited

New dietary guidelines. Frankly, the US government doesn’t have a good track record on this. My main qualm is that Average is Over.

41f8rXshBRL._SX331_BO1,204,203,200_ Rounding out my personal population genetics library, I purchased An Introduction to Population Genetics Theory, by James F. Crow and Motoo Kimura. This book was published in 1970, so 45 years ago, but pretty much everyone on Twitter who would be in a position to know stated that it was a worthy purchase for more than historical reasons. It goes to show the value of old theoretical books in the field. I also purchased a copy of Male, Female: The Evolution of Human Sex Differences, because the topic isn’t something that I take for granted anymore in the sort of society we live in, where “cis-heteronormative binaries” or whatever considered “problematic.” 51UUhrJMhpL._SY344_BO1,204,203,200_ For more purely historical interest I also got a copy of The Monk in the Garden: The Lost and Found Genius of Gregor Mendel, the Father of Genetics About 15 years ago I read the first 1/3 of this book, but I never finished before I had to return it to the library. At this point I’m much more invested in genetics, so I figure I should give it a second go.

I watched Idiocracy. It was OK. My wife was disappointed by the lack of world-building. One thing to observe: no one is looking at their phone in the future, and there are still payphones around. The film was made in 2005, before that particular revolution.

CYQeUxuUwAAoelX Someone on Twitter asked me to take the Political Compass test. I’m not a big fan of it, as I think it lacks subtly, and its libertarian-centric orientation is pretty obvious. But you can see my results. Probably not a big surprise. I’m moderately skeptical of democratic populism, so I’m not sure if many of these quizzes capture my own orientation correctly. But then again, everyone thinks they’re a special snowflake.

Screenshot from 2015-12-31 13:56:34 There’s a new book, The South African Gandhi: Stretcher-Bearer of Empire, which got an interesting review in The Wall Street Journal. The subhead: “Gandhi fought for Indian rights in South Africa, but his concern for the black majority was minimal.” This has been known for a while, so why is this portion of Gandhi’s life so eternally controversial? I think it’s because Mohandas Karamchand Gandhi has gone through the apotheosis, and the reality that he was a man of his time is uncomfortable for many. The past today is populated by gods and devils, not men. But Gandhi was a man.

Like Slate I’m skeptical of Twitter’s latest moves. I’ll be pretty sad if Twitter turns into a form of Tumblr, and I might have to move on to something else. Which would be lame as I’ve invested a lot in my Twitter presence. As I’ve noted before at this point when I go to a scientific conference people know me more for my Twitter than my blog. Turning Twitter into a more full-fledged blogging platform is totally useless and counter-purpose for me, since I already have a blog….

Opinions on the best Szechuan in San Francisco?

The pull-up tower I purchased last week? It’s been awesome. My motivation remains pathetic, but the activation energy of just walking up to it and doing pull-ups and chin-ups is so minimal that I work-out every day now as a matter of course. Though as the New Year’s crowd clears out I’ll probably venture back to the normal gym, the tower is a great supplement and keeps me at a good baseline.

• Category: Miscellaneous • Tags: Open Thread

korean I am wont to say that the genomics of human pigmentation are solved. Arguably this has been one of the major successes of the early GWAS era. In 2005 the postscript to Mutants: On Genetic Variety and the Human Body alluded to the fact that the genetic architecture of pigmentation in humans was relatively mysterious. A year and a half later reviews such as A golden age of human pigmentation genetics where being published. What happened?

First, and foremost, the genetic architecture of human pigmentation variation is characterized by the reality that most of the variation is due to a handful of loci. In other words, skin color is not monogenic Mendelian, but neither is it highly polygenic in the same fashion as height or IQ, where variation is distributed across so many loci that alleles have nearly an infinitesimal effect size. The small sample sizes and simple methodologies of aught era genomics were sufficient to capture the relatively large effect variants segregating in many populations. A second major aspect to pigmentation genomics is that the pathways seem strikingly conserved across vertebrates. That means that pelage color research could inform human genetics, and vice versa.Some of the most interesting confirmations of the power of loss of function mutations in humans occurred by inducing a similar change in zebrafish! One inference that I think one might take away from this is that ancient human populations likely exhibited variation due to polymorphism around the same set of loci as modern humans.

But, and there’s a big but, is that though the set of loci which are responsible for pigmentation variation across human populations are familiar, finite, and well characterized, the particular mutations responsible within a given locus varies quite a bit. Because derived mutations which result in reduced pigmentation are mostly loss of function all you need to do is “break” the functionality in some manner. Therefore, you might target a regulatory element, or, the exonic sequence itself, but the possibilities are rather numerous. Heather Norton’s publication from 2007, Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians, is still rather relevant. For various reasons the pigmentation of Europeans has been well elucidated. That means that to a great extent the variation in West and South Eurasians more generally (and North Africans) is well understand because most of the same variants seem to be at play. The big lacunae, as pointed out by Norton et al., concerns East Asians. This is a population which is light-skinned, but lacking in the typical set of European “light” alleles.

Unlabeled_Renatto_Luschan_Skin_color_map.svgThe title of the post is “white-skinned”, and not “white”, because the conventional understanding is that East Asians are not white. That term is reserved in world-wide usage for people of European descent (or to a lesser extent related peoples, such as Turks) for historical and cultural reasons.

But this is a recent development. From what I am to understand historically the peoples of Northeast Asia did refer to themselves as white in contrast to the browner people of Southeast Asia (in an analogous fashion, the people of West Asia as far east as Afghanistan consider themselves white, in contrast to the black people of South Asia). Additionally, when Europeans first encountered Northeast Asians in large numbers in the 16th century they observed that physically the people of nations such as Japan and Korea were white in color. Only with total domination of the globe by Europeans in the 19th century did the identification of white and European become such as that Northeast Asians were classed among the “colored” peoples (the appellation “yellow” was taken up by early 20th century East Asian intellectuals). But both quantitative empirical evidence and simple visual inspection can remind us that many Northeast Asians are as light in complexion as many Europeans, albeit never as pale as many Northern Europeans.

A new paper in Molecular Biology and Evolution, A genetic mechanism for convergent skin lightening during recent human evolution, goes a major step toward pinpointing what is going on in a functional sense in relation to East Asians. In fact they’re doing what occurred ten years ago for Europeans. First, they’re finding the variant through GWAS, and second, they are confirming through molecular methods and animal models that the variant of interest is actually the causal mechanism. And, they are also attempting to establish a temporal narrative by adducing signatures of selection.

rs180014 The major finding is that variation on a particular SNP in OCA2 is responsible for differences in pigmentation across many groups in eastern Eurasia. You should remember OCA2, since the region that spans it and HERC2 accounts for the pattern of blue and brown eye variation in Europeans. The SNP, rs1800414, is in the ancestral state in Europe and Africa, but derived in Northeast Asia. The results from the left are from the HGDP browser. The only thing is that I can’t find the SNP on the browser. So I looked for that particular SNP on my own HGDP data sets, and couldn’t find it. The SNP is in ALFRED, and you can see that the results are somewhat different. OCA2_labels_S The HGDP results (which for whatever reason I can’t replicate) show that the derived allele is modal in Northeast Asia, and, that it is present in the New World. In contrast, the ALFRED map shows that the derived allele is modal among more southerly groups (including indigenous non-Han groups in South China), and absent in the New World. The 1000 Genomes has fewer populations, but large sample sizes. The allele frequency in Japan in the 1000 Genomes matches Alfred more than the HGDP results.

All that being said, the general stylized facts are in alignment. The derived allele is common on the eastern coastal region of Eurasia, and nearly absent in Africa, Europe, and West and South Asia. But a curious aspect to me is that in the 1000 Genomes data the allele is nearly as absent in the Bangladeshi samples as it is in other South Asians. In contrast, the derived variant of EDAR, which is diagnostic of East Asian or Amerindian ancestry, is present at 5% frequency in Bangladeshis, about what you would expect assuming the attested levels of gene flow from an East Asian population. While the authors in the above study found that the effect of the allele is additive, it is curious that in the 1000 Genomes there is no variation across Japanese, North and South Chinese, and Vietnamese. The implication is that the average between group differences across these populations has to be due to variation on other loci. The indigenous Dai people in fact had the highest frequency of the derived allele in the 1000 Genomes.

Austroasiatic-en.svg A final issue that is important to note is that the phylogenetic framework the authors are using is probably wrong. The major value-add of this paper is that they include several Austro-Asiatic populations to the data set, and compared individuals phenotypically between the Austro-Asiatic group and among the Han Chinese. Because the supplemental information isn’t online I don’t know which Austro-Asiatic groups they included in China, but there aren’t too many, so one can guess. The main problem though is that they presume these Austro-Asiatic are basal to the Han. This probably isn’t true. Rather, there was probably a migration of early rice farmers from what is today China proper southward, that resulted in the spread of the Austro-Asiatic languages to Southeast Asia and further west toward India. Vietnamese and Cambodian are two numerous languages which are Austro-Asiatic. Bringing together all the genomic evidence, it seems that a substantial minority of the ancestry of these Austro-Asiatic people are from the descendants of hunter-gatherers who were resident in Southeast Asian during the Pleistocene, but the majority of their ancestry derives from farmers who pushed south.

These details matter because the authors estimated how deep the selection sweeps around this locus must be in terms of time. Using two methods they arrive at a figure between 10 and 15 thousand years (one method is closer to 10, another to 15). That implies that selection began before the Holocene. The interpretation the authors put on these results is that the northern East Asian groups experienced selection as they migrated up from Southeast Asia during the Pleistocene, with the Austro-Asiatic groups being basal and reflecting the ancestral state. The problem, as I suggest above, is that the Austro-Asiatic populations are a compound of genuinely basal groups (their minority ancestry) to the Northeast Asians, and a population to which other Northeast Asians further north may be basal!

One thing Eight thousand years of natural selection in Europe tells us using ancient DNA that a history of admixture is important to understanding the specific dynamics of selection. Though the haplotype based methods were roughly correct, they did not exhibit the granularity necessary to make fine-grained inferences, and did not totally predict what the empirical ancient DNA is telling us about allele frequencies across time. For example, earlier attempts to infer the selection sweep which resulted in high frequencies of SLC45A2 in Europe arrived at a figure a bit north of ~10,000 years. But it seems that a great deal of selection on this locus has been occurring more recently than 5,000 years.

And on a final note, I would point out that the intermediate frequencies of the derived allele in much of East Asia are suggestive to me that the genuine target of selection here is not skin color, but a dominant trait. The fact that the derived allele is nearly absent in Bangladeshis indicates that either the sweep up in frequency is very recent, so that not all East Asian populations experienced it, or, more likely to my mind, there is constraining selection on the trait which is the genuine target of interest in other genetic backgrounds. To decrypt what I’m saying, the derived allele is probably useful in East Asia, but entails some cost. South Asians may already have another allele which gains the same function, and so the cost resulted in purification of the derived allele in Bangladeshis (who are ~10% derived from a group very similar to the Dai).

As should be clear, this paper has some confusions. But it’s a taste of things to come. There are many Chinese who are interested in the genomics of their region, and ancient DNA should begin to unveil the past in the next few years.

• Category: Science • Tags: Genomics, Pigmentation

plant-introductions-evolution-hybrid-speciation-and-gene-transfer-18-728nature09103-f3.2Is there a difference between admixture and introgression? I think there is. Or have always assumed there is. But of late I’m wondering if a distinction is widely accepted, and what sort of distinctions people make. That is, in some cases it seems clear that admixture and introgression are used interchangeably as meaning the same thing. I’ve seen this in scientific papers, and often just do a mental substitution. But in other cases I’m wondering if people are using the terms in a different sense than I am. Probably the latter is more worrisome.

The figure to the left was generated by Admixture, a software package which takes population genetics assumptions (models) and data, and shows you the best fit of the data to a particular model. In this case the bar plot shows you the admixture of a given individual when you posit them to be a combination of K ancestral populations. The individuals are clustered by population, so you see population-wide profiles. The details of the model, and whether the model accurately captures reality (i.e., were there actually K populations at any time in the past?), is less important for this post than the fact that Admixture is reflecting admixture on a genome-wide scale between two or more populations. The input data are represented by hundreds of thousands of single nucleotide polymorphisms distributed across the whole genome. The question of interest is whether a population can be represented as a pulse mixing even between two hypothetical groups, which were at some point phylogenetically distinct.

Introgression in contrast focuses on the question of genetic variants which are penetrating one population from another, and becoming common in the target population. A classical method of generating introgression in plant genetics was to engage in extensive backcrosses of mixed lineages with a trait of interest against a parental population. If one continued to select for a particular trait among the progeny one could introgress the trait and allele in a daughter population which was almost identical to one of the parent populations on a genome-wide scale, but identical to the other at one gene of interest. The practical reason for this is obvious. Imagine you have a variety of cold adapted rice which is susceptible to a particular type of fungal infection. Then, you have a heat adapted rice which is resistant to the fungal infection. All you want is fungal infection resistance, maintaining all the other characteristics that keep the cold adapted rice optimal for its climate. So you cross the two, and continue to cross progeny against cold adapted rice while selecting for the resistance phenotype. Eventually you’ll get the allele you want introgressed while maintaining the genetic background you want. In contrast, if you just allowed for admixture between the two lineages, you might get a population which was in between on a whole host of phenotypes which make them suboptimal for any climatic regime.

An example from human population genomics can be found in the paper Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. What occurred here is that a very common variant in Tibetans implicated altitude tolerance and adaptation seems to be phylogenetically closer to those you find in the Denisovan hominins than in other human populations. This, despite the fact that Denisovan ancestry is nearly nonexistent in Tibetans (the latest work suggests admixture in East and Southeast Asia on the order of 0.1 to 0.5%, with the highest fractions being among certain Southeast Asian and South Asian groups).

nature13408-f3 The network plot to the right illustrates the issue. On a genome-wide admixture plot Tibetans look like any East Asian population. They seem to be a mix of farmers related to the Han to the east and indigenous groups long resident at these high altitudes. But on the region around EPAS1 their genetic variation matches not modern humans, but the Denisovan hominin, which diverged ~500,000 years ago from the population gave rise to 90 to 99% of the ancestry of our own lineage.

So what happened? We know that there were low levels of hybridization between very diverged human lineages in the past. Because of genetic incompabilities it seems that in fact there was some selection against distinctive alleles from archaic lineages in our own genome. That is, the percentage of Neanderthal ancestry on the genomic level is probably lower than you’d get from doing a genealogical analysis of all lines of ancestry back to 100,000 years ago, because there has been selection against Neanderthal variants in the dominant human genetic background. But not in 51r8Ph-vcaL._SY344_BO1,204,203,200_ all cases. In a minority of instances the Neanderthal and Denisovan variants were not less fit, nor were they neutral, but rather, they were favored!

So, imagine a scenario where in the initial generation admixture between a large human population and a small Neanderthal population leads to admixture on the order of ~5% in the descendants. Over the generations due to selection against Neanderthal alleles the genomic ancestry from this group converges upon ~2.5%. But, on a subset of loci the Neanderthal alleles will have increased in frequency, and in some cases introgressed to high levels. This could be due to randomness; in a genome with billions of base pairs and tens of millions of nucleotide polymorphisms some alleles will drift up to higher frequencies randomly. But it is in the set of high frequency alleles from Neanderthals that you might find variants that have become common due to adaptive introgression. See this paper in AJHG, Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors. Immunological variation is always an excellent candidate because genetic diversity at these loci are highly favored, and long resident populations often have local adaptations.

Because my focus is generally in microevolutionary process, the sort of thing population geneticists are interested in, I’ve really not been talking about species-level dynamics (though the hominins are arguably distinct species). Much of the work on admixture and introgression is done by biologists focused on inter-specific differences, but the general framework holds I believe (in fact, questions of admixture and introgression and more clear and distinct across diverged lineages). In plants in particular hybridization and introgression are common in wild and domestic lineages.

I’m not putting this post up as definitive. When I read papers where there is talk about “introgression of ancestry” it is clear that today people are merging and bleeding the definitions. I actually checked for definitions of introgression and admixture in . Principles of Population Genetics and Elements of Evolutionary Genetics. There wasn’t anything, because debate on this issue isn’t/wasn’t very live in these fields. At this point I’m really curious what other biologists think. I still find the distinction important, and more critically, useful. If one doesn’t, I’d like to hear opinions. If one has different definitions, I’d like to hear opinions.

• Category: Science • Tags: Adaptation, Genetics, Introgression

The Goat?

A friend of mine, a man-in-tech of eminently WASP background of moderately liberal orientation in case you care, has been bemoaning the downstream consequences of the floundering of Marissa Mayer of Yahoo!, the confused direction of 23andMe under Anne Wojcicki, and finally, there is Elizabeth Holmes and Theranos. These are three separate cases. I don’t believe that Mayer ever had a high probability of success at Yahoo!; it was a legacy of the late 1990s that had never managed to pivot and find a new direction. Even a company with as many resources as Microsoft has been having difficulties finding domains where it can both be dominant and produce growth. Yahoo! never had the success of Microsoft, and so doesn’t have as much margin.

Of course long odds does not mean that a turnaround was impossible. I’m old enough to remember when Steve Jobs came back to Apple and many people shrugged, as it looked inevitable that the firm’s future was in diminishing returns on the margins of the consumer and educational PC market in the shadow of Microsoft and PCs (at one point Microsoft was making more profits on sales of Apple computers than Apple because of the Office productivity suite from what I recall). Obviously it didn’t play out like that. If Marissa Mayer had turned around Yahoo! she’d be a genius. If she failed, as she seems likely to at this point, there will be some sort of exit strategy where she will save face, and there will be no threat to her solid position among the firmament of American oligarchs. The likes of Mayer are seeking glory like the Roman Senators of yore. Only a few will go down in history as men or women of renown, but all will die rich and comfortable.

As Marissa Mayer is a beautiful and intelligent woman who will reproduce above replacement, of course I was always rooting for her. Beauty and intelligence are good. In some measure ambition is as well. And when was being coldly analytic an insult? I couldn’t care less about Yahoo!, as it’s irrelevant to the American economy as a whole. But I cared a bit about Mayer’s success, though I was always pessimistic. Probably some of the same dynamic applied to my attitudes toward Elizabeth Holmes, who seemed smart and attractive, though I didn’t pay attention closely to her claims or business. The issue which many, including Steve Sailer, have suggested, and which my friend agrees with, is that because of the cultural expectation that the tech sector promote “diversity”, Holmes went somewhat under the radar due to dampened due diligence. An extreme case of this sort of thing occurred with Jayson Blair at The New York Times, where Howell Raines admitted that as a liberal white Southerner he was inclined to treating Blair “gently”. Ballooning of reputations and media hagiographies of tech visionaries are not without precedent (it’s a substantial proportion of the copy of glossy business magazines), but some have wondered if Elizabeth Holmes’ story was just too good to inquire too closely. Not only did she fit the stereotypical motif of Silicon Valley entrepreneurs (e.g., Stanford dropout attempting to “disrupt” a sector with innovation), but she also served as an exemplar of a young woman who falsified the idea that the sector was doomed to remain a man’s game.

With 23andMe and Anne Wojcicki, I have no idea what’s going on, but it is, and always has been, confused. I found out from inside sources what happened with the initial FDA letter, and what I can say is that it wasn’t part of the plan in any way but a total f**k up. 23andMe has a high valuation, and an incredible database, and seems totally pivoting to the health market, shaking off its past in recreational genetics (read: genealogy, etc.). But from what I’ve heard Ancestry has surpassed, or is close to surpassing, 23andMe’s database (speaking of, as of this writing Ancestry has a 20% of sale, on checkout at Amazon). I wonder if 23andMe isn’t getting a bit overconfident, as Ancestry is going to shift into the health space too.

Obviously biases are real. CEOs tend to look a certain way. They’re far taller than average. And in Silicon Valley they’re disproportionately white males, as in the rest of corporate America (though less so). The die is probably loaded in favor of white males in relation to getting to the top of management. I’ve had enough experience in “industry” (i.e., the real world), as they would say in academia, to know that “corporate culture” often does have connotations which exclude particular groups naturally. If, for example, you are a business person in South Korea, the marathon drinking sessions are going to disadvantage many women and teetotalers. I think one of the reasons that Asian Americans, and in particular East Asians, are under-represented in management roles in Silicon Valley in relation to their representation in engineering positions has to do with personality, cultural norms (e.g., Asian parents not emphasizing sports and the sort of comradeship that it engenders and translates into the business world), and just the “look” (too many Asian American engineers are short and not fit).*

But I think the example of Elizabeth Holmes suggests that shifting the playing field a bit in business journalism does no one a service. The next time a young blonde attractive woman makes a pitch to investors no doubt one prior that is going to rattle in their brains is going to be “is she going to be another Elizabeth Holmes?” That’s just a cognitive bias. Though privately people will likely state this openly.

51sdHZvYfTL._SX334_BO1,204,203,200_ Speaking of cognitive biases, I’m about halfway through The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. Yes, it’s as good as readers have told me. But, I’ll be honest and state that I knew most of it already in the generality, though not the ethnographic details (for example, I did not know that Inuit ate deer feces like “berries”; thanks for that Joe!). Part of this has to do with the fact that I’ve kept up on the author’s research since 2004, when I encountered his models of skill decay in Tasmanian Aboriginals. And, I’m familiar with the fields of cultural evolution more broadly. Additionally, I’ll bring it up in my review, but I think that he wrote at an unfortunate time when it comes to drawing lessons from human genomics, because some of his assertions have been falsified! (he wrote the preface in January of 2015, a year ago).

Reading The Secret of Our Success after I finished Consciousness and the Brain was also pretty lucky, as some of the assertions made in the former book seem much stronger and robust after the background provided by the latter. In the near future I plan to re-read both Origin of Mind: Evolution of Brain, Cognition, and General Intelligence and The g Factor: The Science of Mental Ability. Sometimes re-reading is about refreshing, but I don’t feel that in this case I understood human evolution well at all when I read these previously.

Steve Pinker has something out in The Wall Street Journal, Steven Pinker on New Advances in Behavioral Genetics:

But new studies looking for small effects of thousands of genes in large samples have pinpointed a few genetic loci that each accounts for a fraction of an IQ point. More studies are in the pipeline and will link those genes to brain development, showing that they are not statistical curiosities. The emerging picture is that most behavioral traits are affected by many, many genes, each accounting for a tiny percentage of the variance.

51Y4n2TIgiL._SY344_BO1,204,203,200_ When Pinker says that studies are in the pipeline, he’s thinking of concrete studies which are in review, and which will blow your minds (though the usual suspects will obfuscate and ignore).

In relation to Steven Pinker, he gets a lot of hate and dismissal. Even Joe Henrich in The Secret of Our Success uses him as somewhat of a foil, though in a good-natured manner (Henrich and Pinker are now colleagues at Harvard, so collegiality is probably for the best). I still think that for writing The Blank Slate alone Steven Pinker will go down in history as an important thinker (though The Language Instinct was the most revelatory book of Pinker’s for me).

When I run TreeMix I often get gene flow edges from Africans or to Africans from a region of the graph basal in eastern Eurasians. I ignore these because they don’t make sense. But they don’t make sense because I’m missing something in the bigger picture. I’m sure a year or two years or three years from now it will all make sense. Just filing this away as results which I can’t make heads or tails of, but which are telling us something with Delphic clarity.

On to genetic data sets. I’ll post on this soon. But the 1000 Genomes are a disparate bunch when it comes to South Asians. The Tamils and Telegu speakers have three Brahmins each in them. Also, both groups have rather endogamous low caste populations as a small subset, distinct from the broader mass. The Gujaratis are highly structured, with a large cluster of Patels, but also various other groups in the mix in a cline out toward Northwest Indians (so I assume middle castes and Guju Brahmins). The Punjabis, sampled from Lahore, are also strange, because they exhibit a very extreme cline, from near the Gujaratis all the way toward West Asian/European populations as far as Pathans. Does this have something to do with people of Muhajir background or mix identifying as Punjabi? Finally, the Bengalis are curious, because they are different from the other South Asian groups in exhibiting minimal structure. These were people sampled in Dhaka, but the cluster is very tight, except five individuals who are closer to the South Indian groups. Two of these five have sample numbers adjacent, so I wondered if they were collected together. Unlike the other Bengalis these individuals don’t seem to have substantial East Asian admixture. I have no idea what group this might be, but I have a hunch that they’re derived from an endogamous caste (probably Hindus) who migrated to the area of Bangladesh in the last few hundred years from another region of South Asia. Finally, I have to note that the Bengali populations exhibit far fewer individuals with long runs of homozygosity than the other South Asian groups. Less than the Punjabis or South Indians, which stands to reason since these groups engage in high levels of consanguinity. But also lower than Gujaratis. The implications of this later….

Xinjiang Seethes Under Chinese Crackdown. I wish the media would explore the relationship of Uighurs, and Hui Muslims, in Xinjiang (the latter are called Dungans in Central Asia). That would get at the ethnic vs. religion tensions. Though in China proper the Hui are often proud of their Islamic identity, in Turkestan their affinities to the Han group, both physically and linguistically, become salient. Because of their Muslim religion and martial character the Hui/Dungans were often used as enforcers of Chinese hegemony by the Manchus. A somewhat greater number of Muslims in China are Hui than Uighur.

10403266_10153388206137984_3744690303848345018_n I stole my kids’ candy-canes. It was for their own good! Am I a bad person? Christmas was fun. My wife read Selfish Reasons to Have More Kids, but I did not (aside from a chapter Bryan Caplan asked me to read to check for any issues). I don’t need selfish reasons to have more kids. I like kids. Christmas was fun when I was a kid. But it’s more fun by far when you have kids. sequencedOne Watching my ~1.5 year old son sit down with his new board book is pretty awesome. The world is his oyster. Or at least toy truck.

I haven’t read the GCTA isn’t all that paper in PNAS. Yes, it’s not titled that, and also, am I a bad person? Yaniv Erlich is a good person, as he has read and responded. The Twitter reaction seems to be skeptical, but cautious. The reality is when the great Alkes Price or Michael Goddard weighs in we’ll know if this is simply a pretender to the throne.

A big deal at some point: phenopredict21.

Uncovering the genetic architectures of quantitative traits. On my “to-read” after the GCTA-sucks papers. (if you don’t know what GCTA is, shame on you! Read this: GCTA: A Tool for Genome-wide Complex Trait Analysis).

Edge, 2016 : WHAT DO YOU CONSIDER THE MOST INTERESTING RECENT [SCIENTIFIC] NEWS? WHAT MAKES IT IMPORTANT? To some extent if it doesn’t match =~ /CRISPR/ somewhere I’m underwhelmed. Did you see In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy?

Michael Shermer: Murdering the facts about Homo naledi? Shermer also parrots those who criticize the H. naledi team for not publishing in Nature or Science. I happen to have been in Washington, D.C., when Lee Berger gave a private presentation on the findings over two years ago. And he already told me that the key was getting this research out quickly, and, dumping the data out there so that others could have access to it. It’s not just about H. naledi, it’s about changing how palaeoanthropology is done.

For those of you in Houston, I know that Cooking Girl has better Yelp reviews than Mala. Doesn’t deserve it in my opinion, though I’ll have to sample Cooking Girl more than once….

Also, I’ve spent some time in Austin, TX, recently. I lived in Portland, OR, years ago. Those who say that Austin is like the Texas version of Portland seem to totally capture it.

* I say Asian Americans, because internationals have obvious cultural handicaps in an American corporation.

• Category: Miscellaneous • Tags: Open Thread
Razib Khan
About Razib Khan

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