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Over at Violent Metaphors Jennifer Raff has another review of A Troublesome Inheritance, this time focusing Nicholas Wades’ interpretation of population genomics. I don’t want to be cliche, but if there’s one thing to like about Wade’s book it’s that lots of people are talking about human population genetics. Then again, if there’s one thing to not like about Wade’s book it’s that lots of people are talking about things that they don’t grasp in much detail, and confusing the issues. Jennifer obviously knows quite a bit about the population genomics, but I’ll be frank in suspecting that some of her fans who are praising her to the heavens find her conclusions congenial, and can’t really follow the technical details she’s fleshing out. They trust her, and that’s an acceptable position. More concretely she implies that model-based clustering (e.g., Structure, Admixture, and Frappe) will naturally produce a set of individuals composed as a combination of K ancestral populations. There’s nothing privileged about a particular K. But there are ways to more formally establish which K is the best “fit” to the data. Rather than talking I’ve set Admixture to run some HapMap data and will check the cross-validation results to get a sense of which K values are most reasonable.

I could say much more, but I’m getting bored with this interminable debate. I’ll focus on one aspect of Jennifer’s exposition: that human genetic variation is clinal. This is a defensible position, and may even be a majority position among population geneticists. But I no longer believe one can take this at face value as the null model that can be used to dismiss ideas such as discrete racial categories. The clinal expectation is predicated on an isolation by distance dynamic. As a rough stylized model you can see the schematic above, which shows three lineages separated by geography and exchanging genes continuously over time. This certainly applies across broad swaths of the world, but there are in fact sharp discontinuities in regions just where traditional racial boundaries are often asserted. For example genetic variation across distance increases sharply at the Himalaya mountain range. Obviously there is admixture across East and South Asia (10-15% of my own genome is East Asian, and I’m South Asian), but the people of South Asia on the whole exhibit greater affinities to Europeans than they do to East Asians. This does not mean isolation by distance is useless; in fact it shows the importance of geography and how it can force isolation by distance to modulate.



clusterBut I have a bigger qualm with the clinal model: it leads people to assume that the extant human populations descend from a diversification of lineages out of Africa,which have been somewhat isolated since the initial settlements. The genetic distance is then simply a function of time since divergence, as well as the magnitude of gene flow (which is inversely proportional to geographic distance). But this model is probably wrong. Going back to South Asians, putting them on a genetic-geographic map and attempting to adduce deep demographic history is total folly, because evidence is building that they are a compound synthetic population, whose origins in time are relatively recent. The position of South Asians on a PCA plot conveniently between West and East Asians is not due to an ancient divergence stabilized by equidistant geographic position. It is due to the fact that South Asians are admixed between (a) West Eurasian population(s), and an ancient indigenous group which has somewhat closer affinities to East Asians. ~10,000 years ago the correspondence between genes and geography would have been very different.

A great deal of Jennifer’s post about Wade’s book is rooted in interpretations of Noah Rosenberg’s work. I’m sure Rosenberg appreciates being dragged into this argument, but I couldn’t help but notice one section of his 2005 paper, Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure:

For population pairs from the same cluster, as geographic distance increases, genetic distance increases in a linear manner, consistent with a clinal population structure. However, for pairs from different clusters, genetic distance is generally larger than that between intracluster pairs that have the same geographic distance. For example, genetic distances for population pairs with one population in Eurasia and the other in East Asia are greater than those for pairs at equivalent geographic distance within Eurasia or within East Asia. Loosely speaking, it is these small discontinuous jumps in genetic distance—across oceans, the Himalayas, and the Sahara—that provide the basis for the ability of STRUCTURE to identify clusters that correspond to geographic regions.

Two exceptions to the pattern include the Hazara and Uygur populations, from Pakistan and western China, respectively, whose genetic distances scale continuously with geographic distance both for populations in Eurasia and for those in East Asia. These populations were evenly split across the clusters corresponding to Eurasia and East Asia, and thus, unlike most other populations, they do not reflect a discontinuous jump in genetic distance with geographic distance….

As can be inferred from the title he is attempting to resolve the clusters/clines debate, and explaining why geographic clusters emerge from model-based clustering (and PCA as well). But his two examples of ethnic groups which are positioned exactly where their geography would predict are also instances of very recent admixture events between West and East Eurasian populations. They don’t reflect the deep time history of the human race, but are products of recent folk wanderings. In the case of the Uygurs: the likely migration of West Eurasians into the Tarim Basin three to four thousand years ago, and then a subsequent influx of East Eurasians within the last two thousand years. The Hazara a compound of Mongol refugees from medieval Persia and the local Dari speaking substrate of the Afghan highlands.

And the Uygurs and Hazara may actually be far more typical in terms of their genetic ethnogenesis than we previously had thought. It seems likely that Native Americans, South Asians, Southeast Asians, and Europeans are all the products of just this sort of fusion between very distinct branches of humans. Detecting many of these admixture events is not trivial for various technical reasons, and it seems to me that these new facts should update our prior expectations of other groups. East Asians may not seem admixed only because of a lack of reference populations.

An alternative to isolation by distance and the clinal model would be that in the Pleistocene human populations were sparse and highly differentiated because of low gene flow due to low population densities. There were occasional admixture events, as occurred with the ancestors of the Native Americans. But it was during the Holocene that a revolution occurred, as a few populations picked up cultural characteristics which allowed them to blossom demographically. These explosions swamped out much of the previous variation, and also admixed across one another. What we see today is a palimpsest accumulated from these discrete pulse events.

I’d bet reality is probably somewhere between these two models, with variations from region to region. But they need to be kept in mind.

 
• Category: Race/Ethnicity, Science 
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  1. Other than for purposes of possibly illustrating human history, I still don’t understand why the discrete versus clinal thing matters to, say, the place of”race” in the social world. After all, populations which are classified by criteria with social significance (religious groups, ethnolinguistic groups, regional subpopulations, etc.) do have objectively measurable differences whether genetically, physically or socially…

  2. absolutely fantastic post. maybe all we can do for people like her is to ask if she thinks different species exist. Your “races/species aren’t isomorphic” quote is probably the best you can do though you’ll probably get no response. Endangered Species Act is grossly misinformed according to her, then, right??

  3. Mostly, I agree with pseudoerasmus here, though I would expand on his point.

    I would turn the “race is a social construct” argument on its head. I would grant that we pick out groups in no small part because of the way they figure into our broad social context. But I would point out that the way they figure into our broad social context may have everything to do with their distribution of genes.

    Even if it had turned out that there were no barriers like the Sahara or the Himalayas or the oceans over which there was a discontinuous jump in genetic variation, mostly it wouldn’t matter for the things we actually care about.

    What we actually care about in groups of human beings most importantly is precisely how they fare on socially important traits. If two groups, such as subSaharan Africans and Europeans, differ significantly in on a socially important trait — say, IQ — and do so largely in virtue of genetic differences, then that is a very good reason for us to see them as importantly different from the standpoint of the things of significance to us as social beings ourselves. That becomes a good reason to consider these groups as more or less unified, even if there were a continuous gradation in genes — even genes related to IQ — in the regions that serve as buffers between Europe and subSaharan Africa. These differences certainly matter to us far more than differences in height or speed or color of skin or shape of body. We don’t care much whether there is a continuous gradation between these groups – we care instead about how much the two large groups of Europeans and SubSaharan Africans differ on socially important traits. We care more about a large such difference even if there’s gradation in genes than a small difference if there’s discontinuity.

    Why should we, as social beings, pretend to be caring about something else?

    So, yes, race is in no small part a social construct — for it is the social traits that matter to us. But, again, there’s little serious doubt that genetic differences figure into differences on these traits.

  4. Josh says:

    Razib, I am a layman, so excuse me if I sound like an idiot.

    It seems to me that the biggest point of contention in the race debate at Raff’s blog is the arbitrariness of K. I think that the arbitrariness of K is irrelevant, and here is why:

    Let’s say that one did a cluster analysis on a sample of humans and chimpanzees, and that one arbitrarily set K=2. The clusters that would form from this would obviously be a chimpanzee cluster and a human cluster, just as one would expect.

    But according to Raff, this result is (a) wrong and (b) meaningless because K was arbitrarily set to 2. However, I am certain that even Raff would admit that humans and chimps really are distinct clusters, so clearly the arbitrariness of K does not render the clusters that form meaningless or incorrect in this instance.

  5. Josh says:

    Razib, just one more thing. Could you tell me if there is anything wrong with this argument.

    “K is arbitrary, but all values of K are correct.

    Everybody inside of cluster A has more similarity than a random member of A has with a random member of cluster B.

    BUT– and please grasp this — it’s possible for members inside of cluster A , call these individuals A.1, to have more similarity than a random member of A.1 has with a random member of A*(A* is A – A.1).

    If one wanted A.1 to form its own cluster, then one would simply increase K.

    Let me give you an example:

    1. Two random Amerindians have more similarity than a random Amerindian has with a random Mongolian.
    2. A random Amerindian and a random Mongolian have more similarity than a random Amerindian has with a a random African.

    Both statements are correct, but they arise under different values of K.”

  6. With due respect, I think you’re giving far too much weight to a literal interpretation of the phrase “isolation by distance.” I don’t think anyone would seriously claim that “distance” means geographic distance as the crow flies. Humans are not crows. “Distance” is rather taken to mean isolation by geography and its effect on the ease of movement for human populations.

    Here’s a quote from the Rosenberg paper you mentioned:

    “Examination of the relationship between genetic and geographic distance supports a view in which the clusters arise not as an artifact of the sampling scheme, but from small discontinuous jumps in genetic distance for most population pairs on opposite sides of geographic barriers, in comparison with genetic distance for pairs on the same side.”

    As technology has progressed, so has our mobility. Of course there is genetic structure in human populations. Of course the tendency has been for our genetics to become more homogeneous. Of course that homogenization is a stochastic process, with all kinds of interesting discrete events to discover and study. I don’t think any of that the idea of discrete “races” a very helpful or useful concept. For one, it’s specific to only a very high level of that structure, and exactly how high a level is not very well defined. Can anyone give me an precise number for how many races there are? Is that number commonly accepted, or is it just one of those terms that means different things to different people?

    I think everyone debating this one way or another could use a refresher on fuzzy logic and fuzzy set theory too. It’s possible to make statements like “sub-Saharan Africans are more likely to suffer from sickle cell anemia” without assuming that labels like sub-Saharan African and European are discrete and mutually exclusive. Fuzzy logic is incredibly powerful, elegant and subtle, and it has a wide range of applications to people.

  7. now that i re-read this i have a question: from her perspective, does she care whether the shared genes came from “an ancient indigenous group which has somewhat closer affinities to East Asians” or East Asians since they’re roughly the same genes?

  8. I don’t think any of that the idea of discrete “races” a very helpful or useful concept.

    no shit.

    i use isolation by distance models in my research, so chill on the talk-to-them-like-they’re stupid 😉

  9. An illustration – my daughter is half mostly-northern-Chinese and half mostly-northern-European. On a global PCA plot, she clusters with Uyghurs and Hazara.

    I’m also getting sick of reading/discussing genetics of race, and so is my daughter.

    I would like to see the origin of the Chinese fleshed out a lot more, but probably not much more than that.

  10. Fair enough Razib. My frustration is more with Wade and that isn’t reflected in my comments. Cheers.

    And yah Sandgroper, I hear you. I’m pretty much just standard northern European, yet I have many cousins with mixed ancestry originating on four different continents. I’m skeptical that my own family is off a different “race” than I.

  11. I’m skeptical that my own family is off a different “race” than I.

    as per your own comment this is only an issue if you have a platonic conception of race. obviously my daughter (half s asian, half n european) has a genome which reflects her evolutionary history which is different from her parents, insofar as its net is far wider.

  12. CupofSoup: It was very informative for my daughter and me to get genotyped. My wife declined on the grounds that she “knew she was pure Han and did not need some laboratory person to tell her.” Turns out to be not quite that simple, which was amusing, and I think now she regrets not doing it. Aside from anything else, it’s a lot of fun, and if you get ‘done’ with family members, the explanatory power is greatly enhanced. It has been enjoyable to see my wife’s mind opened to the science which, far from offending her, she has found enlightening – genes elucidate human history.

    My daughter wound up majoring in Biochemistry and Genetics, and now has no problem with dealing with the ‘race’ thing, but she has just gone beyond pop. gen., it is no longer very interesting to her for its own sake, and she finds the endless debates/arguments to be off the point, pointless and tiresome. Her focus/interest/job now is in medical science research. It is no mystery to her why there is a department next to where she works that is titled “Asian Cancers”, and the ‘are races real?’ question is one she regards as in the ‘not even wrong’ box – if something has utility in real life terms, then it has a genuine altruistic purpose.

    I have an ongoing amateurish interest in unravelling ancient human history and migrations, simply because it is interesting to me for its own sake – the truth is interesting simply because it is the truth, and I wish to know it. The accompanying background noise does indeed become hugely tiresome.

  13. FWIW, when Jennifer Raff trots out the old “someone who experiences the stress of racism may be more likely to develop high blood pressure and hypertension than someone who does not”, she is actually doing people a real disservice, but I honestly can’t be bothered. Yes, someone who drinks, someone who smokes, someone who has a poor diet, someone who does not get enough exercise, someone who is subjected to all kinds of environmental and working stress, someone who has a certain genetic predisposition can all be more likely to develop high blood pressure and hypertension, and you can map this genetically, at least it can be highly heritable, and all of these things are more tangible than the stress arising from being subjected to some form of social prejudice some time, but she trots this out, when I do not believe she is qualified to know, and she gives no citations. When someone is so ideologically disposed that they repeat stuff that is actually unhelpful to people’s health, it deserves a riposte, but I’m not going to make it. If she doesn’t get the point, she doesn’t.

  14. “What we actually care about in groups of human beings most importantly is precisely how they fare on socially important traits.”

    What if average relatedness and patterns of relatedness are socially important?

  15. Grey says:

    “I’m also getting sick of reading/discussing genetics of race, and so is my daughter.”

    I think the breaking of the wall over race as (mostly) a geographical construct will eventually lead to massive improvements in medical treatment.

    I think in the future the idea that testing meds on people from one geographical population and then prescribing them for a different population will be seen as crazy (both at the race scale and lots of lower regional scales also).

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