The silent majority: liberals who support free speech

onlibertyAt this point you have heard about the controversies at Yale and Missouri. If you haven’t, just Google it. Among liberals there has been some debate and soul searching about the value of free speech, and its diminishing status as inviolate among youth. Jon Chait has a pretty thorough take over at New York Magazine. You can follow links to the arguments of those who contextualize and apologize for the more Maoist of the protesters to “get the other side.”

Since I support free speech, offensive speech, and engage in a fair amount of offensive speech, obviously I have a reflex to side with Chait on principle. Additionally, I’m a conservative who finds intra-Left/liberal conflicts pretty interesting and delicious. Finally, I don’t think that America is horribly racist, nor do I think institutionalized racism is a huge problem on campus (and perhaps not so much outside of campus, at least insofar as policy can and should address it), and, I don’t think that much consideration should be given to “marginalized populations” in terms of being particularly sensitive or apologizing for them (there is a whole lexicon which has cropped upon the Left which has a lot of meaning within-group, but is useless when attempting to communicate out-group; I reject the legitimacy of the terms of the debate as it is presented by many on the Left and liberals).

711zuJb66HLIn my more cynical moments I’ve stated that we need to stick a fork in John Stuart Mill, and the idea of a free exchange of ideas. The Left has started to go full Marcuse, to the point where even the language used by conservatives is deemed illegitimate. Yes, there are liberals who attempt to enforce the old rules of tolerance of vigorous dissent, but at the end of the day there’s not much broader policy daylight between the two campus, so will they stand up for unpopular views when push comes to shove? The best bet then would be to join in the animal-battle for the authoritarian state of yore as it comes back to life. Kill or be killed, while the libertarians keep shouting “can’t we just get along?!?!?!”

But my old standby is what do the data say? Back when “trigger warnings” were in the news I noticed that there was a question in the general social survey about the removal of library books. There is a variable LIBMSLM which asks about an “anti-American Muslim clergymen’s book”:

If some people in your community suggested that a book he wrote which preaches hatred of the United States should be taken out of your public library, would you favor removing this book, or not.

There are also similar questions about anti-religious books, militarist books, a book promoting homosexuality, and a book promoting racism. My question is simple: what demographic groups support the removal of these books? The detailed methods are at the end of this post (you should be able to replicate), but what I basically did is used a logistic regression to compare the effects of several variables at once in terms of predicting attitude toward book removal. The samples were limited to the year 2000 and later.

What did I find?

* Liberals support free speech more than conservatives. Even in cases, such as racist books, where ideologically you would suppose they would oppose it (and there is a modest trend if you look at the period between 1990 to 2014 for liberals to be more supportive of removing the racist book).

* The more educated and more intelligent support free speech more than the less educated and less intelligent (the effects hold independently of each other).

* Whites are more supportive of free speech than non-whites, except in the case of a book promoting homosexuality, where there is no difference.

* Atheists and agnostics are moderately more in favor of free speech than the very religious. They are not very differentiated when it comes to the anti-American Muslim clergymen, confirming secular discomfort with fundamentalist Islam.

If one follows Twitter of the elite media one might be surprised that liberals are more supportive of free speech than conservatives. A different set of similar variables support the same conclusion. So what’s going on here?

First, I do think that the hot-house of the campus environment results in distortion and extremism which has minimal support more broadly. My Twitter following is very diverse, and many liberals have been direct messaging me expressing worry and anger at the anti-free speech antics of the protesters. But please observe: the have been direct messaging, rather than putting up their objections in my public timeline. Though the majority of liberals still support free speech, the loudest and most organized element seem to be much more “nuanced” on the issue of freedom of thought.

Second, the modern Left is a coalition of very different groups. The majority of the non-white sample above was black, and it is clear that in regards to speech non-whites are less supportive of tolerance of taboo or unpopular ideas than whites. White liberals may be very strong supporters of free speech, but their political allies may not be. And, the reality is that in terms of intra-coalition dynamics white liberals have to be very careful in how they talk to non-whites, lest they be accused of racism (I’ve been told by my wife to curtail my trolling on Twitter, but pretending to be an SJW of color is pretty fun when engaging with white liberals, since they let you slice off their balls at will, and don’t even object when you’re totally incoherent in your argumentation). This probably explains some of the private expression of support for free speech, but the subdued public sentiments. Liberals who support free speech also still want to eliminate institutional racism and oppression toward marginalized groups, so they have to balance their values when they seem at tension, and don’t want to be supporting those who oppose their policies even if they support the right of those people to disagree.

Finally, the robust support for free speech by the intellectual and social elites is heartening, and suggests that the courts are going to consistently serve as a legal bulwark against attempts to curtail dangerous ideas and sentiments. But obviously that’s not going to always translate into social norms.

Ultimately the question comes down to will. The broad sentiment of liberals does remain in the corner of liberty of thought, right or wrong. But will they stand up for unpopular views, as they have in the past, because in this country you can? That’s an open question I guess.
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A golden age of quantitative genomics here

512px-Bellcurve.svgThis year at ASHG one of the most fascinating talks was Po-Ru Loh’s, where he reviewed the BOLT-REML method. It’s introduced in the paper, Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis. As you likely know many diseases such as schizophrenia manifest as complex trait; that is, they’re basically quantitative in their genetic architecture. Lots of alleles in the population, at varied frequencies (e.g., it might be low frequency and large effect, or higher frequency and smaller effect). In the abstract they state that “We also observe significant enrichment of heritability in GC-rich regions and in higher-frequency SNPs for both schizophrenia and GERA diseases.” In other words, they’re getting toward the holy grail of these sorts of studies, actually fixing upon likely loci which explain the variation.

But the genesis of these methods goes back to the late 2000s, when some statistical geneticists began to synthesis the power of genomics with classical quantitative genetic frameworks and insights. Another paper which sums up this tradition is Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index. That is, the authors have confirmed the classical heritability estimates for height, using inferences such as twin studies, with genomic methods. Many geneticists operating just outside this field are totally unaware of the power, precision, and rapidity in advance of this set of techniques. If so, I suggest you read A Commentary on ‘Common SNPs Explain
a Large Proportion of the Heritability for Human Height’ by Yang et al. (2010)
(ungated). Here is the final paragraph:

Why have we encountered so much apparent misunderstanding of the methods and results in the human
genetics community? The core of our method is heavily steeped in the tradition of prediction of random effects and the estimation of variance due to random (latent) effects. While estimation and partitioning of variance has a long history in human genetics, in particular in twin research, the prediction of random effects is alien to many human geneticists and, surprisingly, also to statisticians (Robinson, 1991). Another reason could be the simultaneous use of population genetics and quantitative genetics concepts and theory in our paper, since these are usually applied in different applications, e.g., gene mapping or estimation of heritability. All concepts and methods that we used are extensively described in the textbooks by Falconer and Mackay (1996; chapters 1, 3, 4, 7–10) and Lynch and Walsh (1998; chapters 4, 7, 26, 27).

Please, if you read anything on this blog, read this.

Size (population) matters for inbreeding

440px-Daphnia_pulexYesterday I read a paper which utilized Daphnia as a model to explore a very important theoretical question, which relates the role of effective population size to the genetic load (they’re inversely correlated). The theoretical aspect I am aware of, but I don’t know much about Daphnia. The paper is titled Genetic load, inbreeding depression and hybrid vigor covary with population size: an empirical evaluation of theoretical predictions, and it’s in Evolution. It’s not open access, and I can’t find a preprint around, for which I apologize (you could pester the first author on ResearchGate or something). But one reason I’m interested is that they assert this:

Our results are in clear support of theoretical models based on recurrent mutation to unconditionally deleterious alleles on the effects of population size on inbreeding depression, hybrid vigor, and genetic load. This study is the first to find such clear and unequivocal evidence for all of the predicted effects.

This makes me think of Richard Lewontin’s assertion back in the 1970s that theoretical population genetics was basically a machine designed to operating upon inputs which weren’t available (data). I don’t know this literature well, but it’s shocking that these ideas have only been robustly tested now! Or, perhaps these results are false positives of some sort, as it does note it’s the first to find clear and unequivocal evidence for a prediction.

The basic issue is that in small populations genetic drift has the potential to overwhelm the power of selection in purging deleterious alleles. How deleterious an allele is varies. Some alleles have very strong negative selection coefficients. For example, those with dominant lethal effects are going to be purged immediately for obvious reasons (if it’s dominant, it’s always expressed, and if it’s lethal, it isn’t passed on). The situation differs for those with recessive expression patterns. Even if it is lethal in homozygous form, an allele can persist at low frequency if the population is random mating, as the vast majority of copies will be in heterozygotes whose fitness is not impinged. But if the selection coefficient is low enough than even dominantly expressed alleles may not be purged. The variance in allele frequencies due to sampling is inversely proportional to the population size, so as that converges upon the selection coefficient in terms of magnitude, the efficacy of natural selection diminishes. This is at the heart of the nearly neutral theory, which suggests that a lot of variation is due to the input of very weakly deleterious alleles which can’t be purged in population sizes where drift is above a particular threshold.

originsgenomearchitecturePresumably, in large populations there will be many low frequency variants of weak deleterious effect and recessive expression. In contrast, in small populations the power of drift is such that even rather deleterious alleles can be fixed against the gradient of selection. At cross-purposes with this is the idea that because inbreeding populations tend to “expose” alleles which express recessively to selection they can “purge” the genetic load which drags on fitness. For example, with dog breeds there is some evidence that inbreeding needs to be conditional upon breed level variation, as some of the load may have been purged.

Apparently Daphnia are a species which exhibit a wide gradient of variation in genetic diversity (heterozygosity in this case), allowing one to test various hypotheses by crossing lineages sampled from wild populations in the laboratory. Their molecular assay of diversity were ~30 microsatellite loci. What they found is that in line with theoretical prediction those sampled from large populations had lots of segregating deleterious alleles, which manifested in strong inbreeding effect when individuals were purposely crossed with those genetically similar. In contrast, those from small populations did not exhibit so much inbreeding effect, indicating that a lot of the deleterious alleles were already fixed and so exposed. These individuals from small populations also exhibited lower fitness than those from large populations, reflecting in all likelihood their genetic load. Crossing individuals from different small populations resulted in immediately hybrid vigor, as the fixed variants differed across lineages.

There are a lot more details in the paper. If you have academic access, read the whole thing. If not, there’s always #icanhazpdf. I’m more interested in general conclusions. Two preprints just came out which addressed the reality that Neanderthals seem to have had a small effective population size. Meanwhile, the issue is very real and live in conservation genetics, and even in the understanding of mammalian lineages more broadly, many of which have gone through bottlenecks even human intervention aside. But how much can we generalize from the Daphnia, which has a small genome (<10% of the size of the human genome, which is around average for mammals), but ~1/3 more genes? I’d wager a lot. But I’m really going to be interested when there are whole-genome analyses of this sort of study done in Daphnia, and we can look at the site frequency spectrum, instead of just inferring from the fitness.

Finally, I do want to emphasize here a lot of the problems relating to inbreeding seem to be due to segregation load of partially recessive low frequency variants. This is an important foundational insight that allows us to properly conceptualize what’s happening in small populations, or in lineages that have gone through a bottleneck, and why that’s a problem.

Open Thread, 11/08/2015

41L69h9XdRL._SX331_BO1,204,203,200_At ASHG this year a friend and I were talking, and we noted in passing how much R. A. Fisher anticipated in The Genetical Theory of Natural Selection. In some ways it resembles Charles Darwin’s The Origin of Species. But while The Origin is an illustrious book, widely read, and even more widely owned, The Genetical Theory of Natural Selection remains somewhat obscure to the broader public, who are often under the illusion that Stephen Jay Gould is a grand evolutionary theorist, as opposed to a competent paleontologist who also became a master of self-aggrandizement. Any reader of this weblog interested in the science should think about getting a copy of The Genetical Theory and reading it, especially the more technical and abstruse first half.

41oVg-wh-1L._SX333_BO1,204,203,200_Speaking of Gould, he again makes an appearance in Robert Trivers’ autobiography, Wild Life: Adventures of an Evolutionary Biologist. One chapter is basically the same as Vignettes of Famous Evolutionary Biologists, Large and Small, published on this website a few months back. But most of the book, which I’ve skimmed through, is more explicitly autobiographical. In response to a comment on an earlier thread, Trivers does get into detailed aspects of the mental illness that he has experienced. One of the stranger, but plausible, elements of the narrative to me is that during one episode he became convinced only he understood Wittgenstein. I think that’s rather funny, because from what I’ve read Wittgenstein himself went through phase when he thought he was crazy due to the nature of his own conclusions about the world (he apparently approached Bertrand Russell to inquire where he was insane or not).

885753For me though, if you want an introduction to the classical Robert Trivers, Natural Selection and Social Theory: Selected Papers of Robert Trivers, is a definitely “must have.” I’ve read this book a few times cover to cover, and it’s very rewarding. It takes the same format as W. D. Hamilton’s Narrow Roads of Gene Land. Key scientific papers are presented, but interleaved with these are commentaries and introductions, rich with autobiographical context. I wish there were more books in this format.

I’ve been reading Frank McLynn’s Genghis Khan: His Conquests, His Empire, His Legacy, and switching back to his Marcus Aurelius: A Life. Two rulers who could not have been more different! Genghis Khan is a good book, but I’m not sure I’d recommend it for someone who hasn’t read other work on this topic, as McLynn’s scholarly judgement on what is, and isn’t, plausible from The Secret History of the Mongols isn’t something you want to rely too much on. In fact it has crossed my mind that people might be well served by reading Pamela Sargent’s historical novel, Ruler of the Sky: A Novel of Genghis Khan, as it presents the biography pretty faithfully, and more entertainingly than non-fiction (from what I recall Ruler of the Sky sugar-coats Temujin’s relationship to his brother Khasr a bit though).

In National Review Jonah Goldberg has a piece up, Fusionism, 60 Years Later. Recent events have made me convinced that really there’s no way American libertarianism can have an influence outside of the Right and the broad tent of conservatism. That means there will always be the sort of culture clash on a personal level, as the cultural preferences and mores of libertarians are more like that of liberals. But the Obama years seems to show that the Left really has no ability to put a stop to the warfare state (though I grant McCain really might have done some crazy things if he’d been elected!). Liberal internationalism is really the only game left in the Democratic party, just as a flavor of foreign policy neoconservatism is the only option in the Republican party. Additionally, I don’t really think of modern liberalism as “socially liberal.” With the rise of affirmative consent and a near maximalist idea of gender fluidity becoming normative, it sure doesn’t seem as if the cutting edge social movements on the Left want to “stay out of your bedroom,” and the events at Yale are a signal that freedom of thought in practice is something that isn’t even given the fig-leaf of protection from critique. There’s a specter haunting the American Left, and it’s Marcuse.

51VLZmyVmRL._SY344_BO1,204,203,200_But I want to highlight one aspect of Goldberg’s piece which I want to dissent from somewhat: “The Founding Fathers were all classical liberals, but unlike many of their opposite numbers in the French Revolution, they were largely conservative in manners, morals, and faith. Their conservatism was not labeled as such because it suffused the culture and was simply taken for granted.” One needs to be careful about transposing modern categories back into the past. After all, to some extent modern Left-Right concepts come out of the maelstrom of the French Revolution itself, which post-dates the American Founding. But one of the most influential books in my own thought in attempting to understand the nature of the American Founding has been Jay Winik’s The Great Upheaval. It’s a broad work, but one thing it emphasizes is that the idea of a secular republic was rather strange when the United States was assembled out of the thirteen colonies. There were a range of arrangements. The medieval Christian model was one where one particular religious institution has a monopoly on the public life of the polity. The ancient Roman one was more pluralistic, though in practice state subsidies tended to flow toward established and favored cults. In the Chinese imperial system religious sects were controlled and managed by the state, so that they were much more explicitly subordinate to the powers that be than in the medieval Christian context. But, the imperial order was still rooted in a metaphysical understanding of the social and political structure as being reflective of something deep in the natural and spiritual world.

The American federal republic was revolutionary, and not conservative, in that it marginalized the role of specific sectarian commitments in the public sphere. Today we take it for granted, but at the time it was very strange and peculiar. Though the Founders were not atheists, a disproportionate number seem to have had sympathies toward a liberal religious world-view, with some veering toward private heterodoxy. This was not rare among the elite of the period, Frederick the Great being an exemplar of a ruler who was well known to be privately irreligious. But though his Prussia moved a bit toward relative liberality in matters of religion, it remained fundamentally a Protestant domain, where Catholics suffered discrimination, and Jews were marginally tolerated. The American republic did something radically different, a rupture with the norms not just of European civilization at the time, but the standard mode of operation of complex polities since the rise of civilization itself, privatizing the gods!

Of course the Founders would never have countenanced anything like the sectarian and anti-clerical atrocities that occurred in the War in the Vendee. In this way the period of the American Founding is going to always be difficult to interpret in a modern framework because everything changed after the French Revolution. The possibilities for social upheaval, for good or bad, were qualitatively different after emergence of a French republic, and Napoleon’s wars against the older aristocratic order.

What $45,000 in tuition buys you at Yale

At Reason, Watch Students Tell Yale to Fire a Staffer Who Upset Their Safe Space. The ‘staffer’ in question is Nicholas Christakis, a scientist whose work I’m mildly familiar with actually. The whole affair was kicked off by Christakis’ wife sending this email, where she said perhaps it was not the university’s job to patrol costume choices (for Halloween).

All this emerged in the context of the rumored white girls allowed only frat party at Yale. I say rumored because I don’t believe that it happened (which is pretty obvious from the link if you read it, despite trying to give accusations of racism the benefit of the doubt). The issue is that the sort of people who get accepted into Yale know exactly what to say in regards to issues relating to diversity to maintain appropriate optics. They would never be so crudely racist, even if the reality is that most men in that particular frat would prefer white girls attend their parties. As I noted on Twitter, all the of the men Taylor Swift dates are white (unless you count part-Native Americans Taylor Lautner and Joe Jonas as not), and that’s not a big deal. But if she said in public that she only dates white men, like her ex John Mayer admitted about women, she would become public enemy #1.

It strikes me that in our American culture right now what matters is less what you do, but what you say and signal. Erika Christakis dissented ever so slightly from the regnant norms in her elite university milieu, and now she’s paying for it. But the reality is that people like Erika Christakis live lives of cosseted privilege and insulation from the difficulties of the world, but that’s not worth comment. Rather, what matters is that she follow the appropriate norms and symbolic gesturing which we take for granted in our society.

This is not entirely unreasonable. Manners and decorum, even ritual that might not be heartfelt, tie societies together. By the public performance of words and actions, even if they are belied by revealed day to day preferences, we outline the moral fabric which we aspire to. But at some point it becomes a farce. By the end of the Communist period in the Soviet Union everyone was going through the motions, with no sincere belief. That explains partly why the system collapsed and reconfigured itself so rapidly; it was not robust, but brittle. Some level of hypocrisy is inevitable in any society which aspires to virtue, but when the chasm between words and deeds, between external signalling and internal sentiment, become too large then the system is ripe for overturning.

Though your guess is as good as mine about what might come next.

Smite the Unbelievers

Sharia should be law of land Muslims who believe sharia should be law who accept death penalty for apostasy % of Muslims who accept death penalty for apostasy
Afghanistan 99% 79% 78%
Pakistan 84% 76% 64%
Egypt 74% 86% 64%
Palestinian territories 89% 66% “59%
Jordan 71% 82% 58%
Malaysia 86% 62% 53%
Iraq 91% 42% 38%
Bangladesh 82% 44% 36%
Tunisia 56% 29% 16%
Lebanon 29% 46% 13%
Indonesia 72% 18% 13%
Tajikstan 27% 22% 6%
Kyrgyzstan 35% 14% 5%
Bosnia 15% 15% 2%
Kosovo 20% 11% 2%
Turkey 12% 17% 2%
Albania 12% 8% 1%
Kazakhstan 10% 4% 0%

41nsHqj5QIL._SY344_BO1,204,203,200_The above data is from Pew. Questions were asked only of Muslims. In some nations, such as Turkey, “Muslims” include basically the whole population, at least nominally. In others, such as Malaysia it is somewhat over half the population. The first response column is the proportion of Muslims who wish to enact sharia as the law of the land in a given nation. The second set of responses are those Muslims who agree with the first question, and also agree with the traditional death penalty for apostates in Islam. Multiplying the two out, and you get the total proportion of Muslims in a given country who assent to the traditional death penalty for apostates in Islam. This is probably a floor, in that a minority of those Muslims who don’t want sharia enacted may agree with the death penalty for leaving Islam for a variety of reasons (Muhammad Ali Jinnah, who was neither personally religious or observant, nevertheless defended the killer of a “blasphemer” during the British period on the grounds of communal honor).

What you see above are a range of attitudes, and interesting conflicts with public practice. In Indonesia it is not illegal to convert from Islam to another religion, and this is done. But about ten percent of the population still accepts the death penalty for apostasy, at least nominally. In Malaysia it is very difficult for an ethnic Malay to convert to another religion, as the connection between that identity and Islam is quite close, though there is often more latitude for non-Malays. About half of Muslims accept the death penalty for leaving Islam. The difference between Indonesia and Malaysia probably is a reflection of divergent social norms which arose in different historical contexts (in Indonesia, the conflicts were as much between Muslim groups of various sects and ethnicities, while in Malaysia the cleavage was more between the non-Muslim Chinese and the Muslim Malay). Just because a given percentage agree with the death penalty for apostasy does not entail that they’d automatically kill an apostate personally, but it probably indicates a level of tolerance and acceptance of intimidation and violence directed toward the act of apostasy.

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Sequencing costs begin crashing again


Nathan Taylor points out that sequencing costs are crashing again. Not very surprising from what I’ve been hearing about the direction that firms like Illumina are moving. The cost of sequencing isn’t going to be the rate limiting step in the near future. Here’s some raw data for the past year:

Cost per genome
Jul-14 $4,905
Oct-14 $5,731
Jan-15 $3,970
Apr-15 $4,211
Jul-15 $1,363

Fires in the forest: the revolution in human evolution

He under whose supreme control are horses, all chariots, and the villages, and cattle; he who gave being to the Sun and Morning, who leads the waters: He, O men, is Indra.

To whom two armies cry in close encounter, both enemies, the stronger and the weaker; whom two invoke upon one chariot mounted, each for himself: He, O ye men, is Indra.

Rig Veda

Sons of Indra
Sons of Indra

Five years ago I found out that my friend Daniel MacArthur and I are members of the same Y chromosomal haplogroup, R1a. Both of us thought it was rather cool, that ~5,000 years ago there lived a man who was ancestral to us both on the direct paternal line. Five years on, and both Dan and I have sons who continue this lineage. True, surely Dan and I share more than one lineage of connection over the past ~5,000 years, the Y chromosomal one is simply the one that is genetically irrefutable since recombination does not break apart the sequence of variants, the haplotype, allowing the inference to be as simple as taking candy from a baby. The common ancestral information is transmitted as a whole block, excepting the mutations which separate us from our common forefather. Additionally, since he has attested South Asian ancestry (< 200 years), we probably share many lines of descent over the past ~3,000 years (one of Dan’s ancestors was stationed in Bengal in the 19th century, so I think our genealogies intersect a decent amount for non-related individuals).

Screenshot - 10272015 - 03:41:22 PMBut there’s something special about R1a beyond the fact that it binds me paternally with a host of people who I know from all around the world. The figure to the right is from the supplements of a Genome Research paper, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. You see that R1a1 diverges by very few mutational steps, and a rake-like pattern defines the phylogeny. That is in keeping with a history of relatively recent diversification, and rapid population expansion. The Genome Research paper found that R1a, along with a host of other Y chromosomal lineages, have undergone very rapid demographic expansion over the past when put through the sieve of phylogenomic inference. This is similar to what you see with the Genghis Khan haplotype. Remember, this is a very specific signature of direct male descent. It does not necessarily extrapolate well to the rest of the human genome. So, though Daniel MacArthur and I share a common Y chromosomal lineage, he is Northern European and I am South Asian, with all that implies for the set of genealogies which come together to contribute to the patterns of variation we see in our whole genomes.

Screenshot - 11012015 - 11:20:26 AMBut recently we’ve been gaining even more understanding at the phylogeography of R1a, and its likely history. To the left is a figure from the supplements of Reconstructing Genetic History of Siberian and Northeastern European Populations. You see in this chart a few important things. First, the sister to the haplogroup R, which includes R1b and R1a, and therefore huge numbers of European, West, and South Asian men, is Q, an Amerindian one. The Mal’ta boy, who lived ~24,000 years ago, seems likely to have carried a basal R1 lineage. This is reasonable because most people peg the divergence of R1a and R1b ~20,000 years ago (or somewhat more recently). A major takeaway here is that the dominant lineages across much of western Eurasia today on the male side seem to derive from a group with central Eurasian affinities. The two R1 lineages are very rare in Europe before ~4,000 years ago, according to ancient DNA. This is also concomitant with the arrival of “Ancient North Eurasian” (ANE) ancestry, which is closer to that of Mesolithic European hunter-gatherers than East Eurasians, but still rather anciently diverged, on the order of ~30-40,000 years before the present. Amerindians also have substantial admixture from this group, as do many groups in the Caucasus, and South Asia.


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Open Thread, 11/1/2015

k10543Been too busy to read much, but Joe Henrich’s The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter, is out. I have read a little bit of Genghis Khan: His Conquests, His Empire, His Legacy. A touch too over-dramatic and credulous in regards to colorful legends for my taste so far to be frank.

Two Neandertal preprints you might want to check out, The Strength of Selection Against Neanderthal Introgression and The Genetic Cost of Neanderthal Introgression. If you haven’t checked out, you should. Though not totally clear how it’s much different from openSNP.

Nathan Taylor has a post up, Homo naledi and the braided stream of humanity. It’s miscegenation all the way down. I can agree with it in its broadest strokes. On Facebook I posted a link to some stuff about selection for height in Europe, and a reader asked “what does this mean for white people?” My simple response was nothing, because for much of this period people who we would recognize as white didn’t really exist. The ancestral genetic elements which combine to produce most of the population of Europe did not cohere together into one population until ~4,000 years ago, give or take. And, the most recent data suggest that the pigmentation loci which result in the typical light complexion of Northern Europeans did not arrive at their current allele frequencies until sometime after this period.

This isn’t to make Europeans special. I think this sort of reality probably holds for most of the major world populations. A recent paper on the Ainu seem to confirm that they’re relatively basal in relation to other East Asian populations. My own suspicion though is that this is simply because a lot of groups were absorbed or demographically marginalized by expanding groups of farmers from the region between the Yellow and Yangzi rivers.

Halloween was fun. But boy is it way more regimented than when I was a kid. Trick-or-treating at stores in the afternoon and very early evening downtown seems to be edging out the old traversing blocks at night.