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Variation

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51qciM4cBhL._SS400_ A quick post to clarify things. When we talk about human variation and history we’re talking about phenomena which we need to decompose into different levels of analysis, because there are major differences in terms of methodology and questions we’re asking. Too often public presentation tends to melt them together and confuse separate strands.

First, there is the level of phylogeny. The question here relates to the history of human genes and populations. With the rise of genomic technologies it is trivially easy to identify human clusters, and not that much harder to infer historical-demographic events. This is important, because due to Richard C. Lewontin’s popularization of the correct point that most human genetic variation is partitioned within, not across, populations, the public is under the impression that population structure is trivial. It’s not. Some extant modern human populations may have diverged from the rest of our species as early as ~100,000 years ago (the Khoisan peoples of southern Africa). Gene flow between even Eurasian populations can be rather attenuated over the over of 50,000 years (e.g., Northeast Asians seem to have had minimal gene flow from other Eurasian populations over the past ~30,000 years).

Second, there is the question of variation in phenotype. Do biological traits vary by population? Yes. Is this variation heritable? Some of it is. This is where an understanding of phylogeny is important, because it turns out that some phenotype distributions are strongly divergent from phylogeny. For example, as early as 2007 it was clear that human pigmentation had been subject to regional selection events which decoupled ancestry from variation on those traits. Melanesians who have been separate from Africans as long (or longer in the case of West Eurasians due to admixture) as any other human population exhibit phenotypic and genotypic similarities to Africans, likely because of functional constraint at low latitudes. But this is not always the case. The peoples of Southeast Asia tend to be rather light skinned for their environmental conditions. But now we know that they are likely the product of recent migration due to human phylogenomic and archaeological results (i.e., in Southeast Asian for <4,000 years).

Third, there is the question of between group differences in complex traits. This where the first point, the triviality of between group differences as asserted in Lewontin’s Fallacy comes into play. If between group differences are not viable phylogenetically, i.e., human genetic history is not structured by divergences and fusions which are evident in the genome, then the whole argument collapses. But I think point one and two illustrate that the move into question three is not logically unsound, but must be gripped one empirical trait at a time. Complex traits are difficult to tackle, and we have to be cautious and not let prior conceptions cloud our judgment, but here’s a paper from a few years ago which illustrates where we might be going, Evidence of widespread selection on standing variation in Europe at height-associated SNPs:

By studying height, a classic polygenic trait, we demonstrate the first human signature of widespread selection on standing variation. We show that frequencies of alleles associated with increased height, both at known loci and genome wide, are systematically elevated in Northern Europeans compared with Southern Europeans…This pattern mirrors intra-European height differences and is not confounded by ancestry or other ascertainment biases. The systematic frequency differences are consistent with the presence of widespread weak selection (selection coefficients ~10−3–10−5 per allele) rather than genetic drift alone….

 
• Category: Science • Tags: Human Genetics, Human Variation, Variation 
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I notice that last summer Karl Smith asked “Why Are There Short People?” His logic is pretty good, except for the fact that the fitness variation seems to be much starker in males than females (there is some evidence I’ve seen that shorter women can be more fertile, though that’s balanced by the fact that larger women seem to be able to manage gestation better). In any case, height seems to be a fitness enhancing trait which is highly heritable, and yet the variation in height remains!

 

Karl’s readers offered some reasons. What do you think? Mind you, something which immediately comes to mind is that the logic presented for why everyone should be tall and vary only a touch is logic. Not all the assumptions need to hold. For example, has the advantage to height been invariant at all times and places? I have posited for example that the fact that humans became smaller after the Ice Age may have something to do with increased morbidity and declining mortality, where agricultural settlements “hugged” the Malthusian boundary more consistently than hunter-gatherers. In this sort of environment smaller individuals may have gained a fitness advantage because they required fewer resources to make it through the inevitable “starving times.”*

But more generally the fact that height seems widely distributed across the genome brings to mind the role that pleitropy might play. Genes of small effect in height may have larger effect in many other traits which are constrained from shifting in allele frequency too much. In other words, can it be that the G-matrix is somehow maintaining this quantitative trait? I’d be curious what those of you with a quantitative genetic background might have to say….

* Another obvious issue is that larger individuals may be more favored energenetically in cold environments. As the world warmed that constraint was released.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Genetics, Genomics, Variation 
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This morning I received an email from the communication director of the American Anthropology Association. The contents are on the web:

AAA Responds to Public Controversy Over Science in Anthropology

Some recent media coverage, including an article in the New York Times, has portrayed anthropology as divided between those who practice it as a science and those who do not, and has given the mistaken impression that the American Anthropological Association (AAA) Executive Board believes that science no longer has a place in anthropology. On the contrary, the Executive Board recognizes and endorses the crucial place of the scientific method in much anthropological research. To clarify its position the Executive Board is publicly releasing the document “What Is Anthropology?” that was, together with the new Long-Range Plan, approved at the AAA’s annual meeting last month.

The “What Is Anthropology?” statement says, “to understand the full sweep and complexity of cultures across all of human history, anthropology draws and builds upon knowledge from the social and biological sciences as well as the humanities and physical sciences. A central concern of anthropologists is the application of knowledge to the solution of human problems.” Anthropology is a holistic and expansive discipline that covers the full breadth of human history and culture. As such, it draws on the theories and methods of both the humanities and sciences. The AAA sees this pluralism as one of anthropology’s great strengths.

Changes to the AAA’s Long Range Plan have been taken out of context and blown out of proportion in recent media coverage. In approving the changes, it was never the Board’s intention to signal a break with the scientific foundations of anthropology – as the “What is Anthropology?” document approved at the same meeting demonstrates. Further, the long range plan constitutes a planning document which is pending comments from the AAA membership before it is finalized.

Anthropologists have made some of their most powerful contributions to the public understanding of humankind when scientific and humanistic perspectives are fused. A case in point in the AAA’s $4.5 million exhibit, “RACE: Are We So Different?” The exhibit, and its associated website at www.understandingRACE.org, was developed by a team of anthropologists drawing on knowledge from the social and biological sciences and humanities. Science lays bare popular myths that races are distinct biological entities and that sickle cell, for example, is an African-American disease. Knowledge derived from the humanities helps to explain why “race” became such a powerful social concept despite its lack of scientific grounding. The widely acclaimed exhibit “shows the critical power of anthropology when its diverse traditions of knowledge are harnessed together,” said Leith Mullings, AAA’s President-Elect and the Chair of the newly constituted Long-Range Planning Committee.


Up until the last paragraph this is an anodyne statement. Who could disagree with: “Anthropology is a holistic and expansive discipline that covers the full breadth of human history and culture. As such, it draws on the theories and methods of both the humanities and sciences. The AAA sees this pluralism as one of anthropology’s great strengths.” But the explosion of anger from biologically and scientifically oriented anthropologists on the web is drawn from a deeper layer of lived experience. On a raw level many of them feel that some factions in cultural anthropology are obscurantists who are fluent in rhetoric which they utilize in power-plays and politics. There are anthropologists who do deny the deep insights of the scientific method in illuminating reality. In fact, they reject the naive realism at the heart of science as it is practiced. For them science is a swear-word, and connotes an affinity with oppression and all the negative abstractions in fashion at a given time (e.g., patriarchy, heternormativity, capitalism, Eurocentrism, etc.). Of course as I note above scientific anthropologists are not given to tolerating the verbal circumlocutions and incantations of their non-scientific colleagues with much grace themselves. There is a deep cultural chasm, and these sorts of arguments over words in obscure institutional documents are only triggers for a persistent roiling debate.

As for the last paragraph, it illustrates the selectivity of a discipline which attempts to contextualize, and often has a skeptical relationship toward a positive framework. I believe that race is a social construct. The Hispanic identity, which consists of people of indigenous Amerindian, European, and African ancestry, and all their combinations, has been racialized. The Islamic identity has also been racialized. Benjamin Franklin stupidly contended that only the English and Saxons were true whites, with all other Europeans, including Nordics, being swarthy.

But just because a construct has a social element does not mean it has only a social construct. Because of the Left-liberal anti-racist egalitarian bias of anthropology, the academy in general, and the dominant narrative of Western society as a whole, there is a strong tendency to assert flatly that “race does not exist” as a biological concept. There is no interrogation of the concept of race except to refute its utility. This is not a case of agnostic skepticism washing away illusions, but a case of skepticism applied in a fashion to obtain a clear and distinct objective result which corresponds to reality. When it comes to race many become naive realists who accept that biological concepts can be falsified or verified in a simple and straightforward fashion. There is all of a sudden one Way of Knowing which presents us with indubitable truths.

Here is L. L. Cavalli-Sforza (my question in italics):

7) Question #3 hinted at the powerful social impact your work has had in reshaping how we view the natural history of our species. One of the most contentious issues of the 20th, and no doubt of the unfolding 21st century, is that of race. In 1972 Richard Lewontin offered his famous observation that 85% of the variation across human populations was within populations and 15% was between them. Regardless of whether this level of substructure is of note of not, your own work on migrations, admixtures and waves of advance depicts patterns of demographic and genetic interconnectedness, and so refutes typological conceptions of race. Nevertheless, recently A.W.F. Edwards, a fellow student of R.A. Fisher, has argued that Richard Lewontin’s argument neglects the importance of differences of correlation structure across the genome between populations and focuses on variance only across a single locus. Edwards’ argument about the informativeness of correlation structure, and therefore the statistical salience of between-population differences, was echoed by Richard Dawkins in his most recent book. Considering the social import of the question of interpopulational differences as well as the esoteric nature of the mathematical arguments, what do you believe the “take home” message of this should be for the general public?

Edwards and Lewontin are both right. Lewontin said that the between populations fraction of variance is very small in humans, and this is true, as it should be on the basis of present knowledge from archeology and genetics alike, that the human species is very young. It has in fact been shown later that it is one of the smallest among mammals. Lewontin probably hoped, for political reasons, that it is TRIVIALLY small, and he has never shown to my knowledge any interest for evolutionary trees, at least of humans, so he did not care about their reconstruction. In essence, Edwards has objected that it is NOT trivially small, because it is enough for reconstructing the tree of human evolution, as we did, and he is obviously right.

L. L. Cavalli-Sforza contends that between population genetic variation is not trivially small. This is clear from the fact that one can discern village-to-village genetic distinctions in Europe. Human variation exists, and it is not trivial. It is useful for phylogenetics, significantly impacts salient phenotypes, and, risks for particular diseases. The social construction of race has real biological raw materials. At one end, the transformation of white European converts to Islam through changes in personal appearance into de facto “People of Color” are matters of social construction in totality. In contrast, the blackness of a Dinka from Sudan is a matter of biological categorization. The categorization of Egyptian Arabs with obvious African admixture as “white” in the US Census is a matter of social construction due to bureaucratic contingency, and illustrates the intersection of biological reality and social fluidity. It is well known that when foreign Arabs with obvious black admixture visited the American South there was often a debate as to whether they were subject to segregation, illustrating the tensions between social norms (which would have coded them as black), bureaucratic function (which coded them as non-black usually), and biological reality (where they were an amalgam of a minor black African component with a dominant white Arab component).

Of course it is true that on any given trait variation can span populations. But even in the case given above, of sickle cell, the correlations with ancestry and population are striking. A lower boundary value is that 75% of sickle cell suffers are of mostly African ancestry, despite only 15% of the world’s population being of mostly African ancestry. These statistics refute a platonic model of race, but they do not refute the population-thinking which is at the heart of much of modern biology, pure and applied.

All that said, the word “race” is fraught with a lot of historical baggage. Therefore to study population wide variation you need to focus on “fine-scale population structure” and what not. This trend would be something of interest for cultural anthropologists of science to study. Race is just a word. Even a term as widely accept as species exhibits a fair amount of flexibility on the margins. But the underlying biological patterns, and the instrumental utility of those patterns, can not be denied.

Addendum: I often use “human” or “humankind” where earlier norms would be to use “man” or “mankind.” My main rationale is I don’t want annoying comments objecting to the term. The concept which I’m pointing to is the same no matter the pointer, and so I don’t mind changing it to facilitate my intent to communicate clearly and without undue extraneous baggage.

(Republished from Discover/GNXP by permission of author or representative)
 
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Last year a paper came out in Science which made a rather large splash, The Genetic Structure and History of Africans and African Americans by Tishkoff et al. Since it’s more than a year old I recommend that those of you curious about the details of the paper and don’t have academic access go through the free registration, as you can then read it in full. Unlike Reich et al. the Science paper didn’t unveil a new method of analysis. It was the standard bread & butter, with PCA’s & STRUCTURE plots & phylogenetic trees. But the coverage of populations within Africa was massive. They had a lot of results and relationships to cover, and ended up with a 100 page supplement.

I commend the whole paper to you. But there are two elements I want to highlight. First, a three dimensional PCA plot. It has the first, second and third principal components of variation. In other words, the three largest independent dimensions in terms of explanatory power of genetic variation. Panel A includes all world populations, and panel B just Africans.


3DPCA

For panel A, PC1 = 20% of the variance, PC2 = 5%, and PC3 = 3.5%. For panel B the PCs didn’t drop off quite so much, PC1 = 11%, PC2 = 6%, PC3 = 5% and PC4 = 4%. In case you don’t know, the Hazda are Africa’s last obligate hunter-gatherers, and speak a language with clicks in it, just as the Bushmen do. The big division highlighted in this paper is that between the “indigenous” relict populations, the Hazda, Sandawe, Bushmen and Pygmies, and those who belong to the more widespread agriculturalist and pastoralist societies of Africa. Implicit within the paper is the model of a Bantu Expansion of farmers, as well as a possible later Nilotic expansion (which brought the Tutsi and Masaai) of herders, in a north-south direction. In the process they assimilated/and or/displaced the indigenous populations, of whom the aforementioned peoples are relict islands persisting in ecologically isolated or unfavorable domains.

324_1035_F5The map to the left shows the population coverage within this paper of African groups. The pie graphs simply show ancestral quanta as inferred by STRUCTURE. You can read the paper for the blow-by-blow. But ultimately it seems there will be need for a finer-grained coverage to the south of the equator. If the Bantu expansion is as recent as archaeologists and linguists assume, on the order of ~2,000 years ago, then the gradients of genetic signals should persist. From what I can tell it is assumed on both genetic and phenotypic grounds that the Xhosa have a higher load of Khoisan ancestry than the Zulu or Tswana. The Bantu Expansion is recent enough that the semi-legendary Phoenician circumnavigation of Africa would have encountered many Khoisan peoples along the eastern coast.

Below are a selection of figures from the above paper. After selecting an image it is probably best to hit F11 for “Full Screen” if you aren’t a on a very big monitor (you can copy image location and view it in a separate window as well).

[nggallery id=5]

(Republished from Discover/GNXP by permission of author or representative)
 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"