I have discussed the reality that many areas of psychology are susceptible enough to false positives that the ideological preferences of the researchers come to the fore. CBC Radio contacted me after that post, and I asked them to consider that in 1960 psychologists discussed the behavior of homosexuality as if it was a pathology. Is homosexuality no longer a pathology, or have we as a society changed our definitions? In any given discipline when confronted with the specter of false positives which happen to meet statistical significance there is the natural tendency to align the outcome so that it is socially and professionally optimized. That is, the results support your own ideological preferences, and, they reinforce your own career aspirations. Publishing preferred positive results furthers both these ends, even if at the end of the day many researchers may understand on a deep level the likelihood that a specific set of published results are not robust.

This issue is not endemic to social sciences alone. I have already admitted this issue in medical sciences, where there is a lot of money at stake. But it crops up in more theoretical biology as well. In the early 20th century Charles Davenport’s research which suggested the inferiority of hybrids between human races was in keeping with the ideological preferences of the era. In our age Armand Leroi extols the beauty of hybrids, who have masked their genetic load through heterozygosity (a nations like Britain which once had a public norm against ‘mongrelization’ now promote racial intermarriage in the dominant media!). There are a priori biological rationales for both positions, hybrid breakdown and vigor (for humans from what I have heard and seen there seems to be very little evidence overall for either once you control for the deleterious consequences of inbreeding). In 1900 and in 2000 there are very different and opposing social preferences on this issue (as opposed to individual preferences). The empirical distribution of outcomes will vary in any given set of cases, so researchers are incentivized to seek the results which align well with social expectations. (here’s an example of heightened fatality due to mixing genetic backgrounds; it seems the exception rather than the rule).

Thinking about all this made me reread James F. Crow’s Unequal by nature: a geneticist’s perspective on human differences. Crow is arguably the most eminent living population geneticist (see my interview from 2006). Born in 1916, he has seen much come and go. For those of us who wonder how anyone could accept ideas which seem shocking or unbelievable today, I suspect Crow could give an answer. He was there. In any case, on an editorial note I think the essay should have been titled “Different by nature.” Inequality tends to connote a rank order of superiority or inferiority, though in the context of the essay the title is obviously accurate. Here is the most important section:

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Last of the Spanish Habsburgs

The New York Times has a long piece out, Can the Bulldog Be Saved? To a great extent it is a parable of the problems with purebred dogs. Domestic dogs are much more homozygous than humans. That is, for their two gene copies they are much more likely to exhibit similarity than humans. This is usually due to inbreeding, where a few ancestral dogs with the required traits are bred, and then selection operates upon the progeny to reduce the effective population size even more. This means that many dog breeds are in danger of pedigree collapse, where they are so inbred that going back enough generations results in a convergence of the family tree.

But the story of the bulldog isn’t just about inbreeding: it’s about correlated response. If you select upon a trait of interest, you generally produce side effects due to pleiotropy. That is, you shift the allele frequencies at locus X, which produces the outcome you want on trait 1, but also incidental outcomes on trait 2 to trait n. As stated in the piece: “Bulldogs could be as outbred as mongrel dogs in the streets of Calcutta, but if they keep that phenotype, they are not going very far.” The bulldog is profoundly unnatural in shape and gait. In other words, the issues here are not just genetic, but they’re biophysical.

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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!

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Alexander Dumas, of mixed race

One of the reasons I post regularly on the genetics of mixed-race people and their physical appearance is that I don’t think the media does a good job. There’s a “freak show” element which titillates but does not illuminate. This in a period in the United States where the absolute number of people of mixed origin is increasing rapidly due to intermarriage. In fact for years I’ve gotten inquiries from the parents of mixed-race children about the scientific details of the genetics, because they are regularly questioned in depth as to how the children came to look how they look (the emails are always from women, more on that later). A relatively well written article in The New York Times illustrates some of the issues, insofar as the focus is totally on social context and dynamics, with not even a small nod to the science. The story is about a mixed-race woman (mother white and father black) who is married to a white man, whose children don’t “look black.” Specifically, her two daughters are very light-skinned, and the younger one is boldly blonde.

Here’s the jump off point of the piece:

“How come she’s so white and you’re so dark?”

The question tore through Heather Greenwood as she was about to check out at a store here one afternoon this summer. Her brown hands were pushing the shopping cart that held her babbling toddler, Noelle, all platinum curls, fair skin and ice-blue eyes.

The woman behind Mrs. Greenwood, who was white, asked once she realized, by the way they were talking, that they were mother and child. “It’s just not possible,” she charged indignantly. “You’re so…dark!”

It was not the first time someone had demanded an explanation from Mrs. Greenwood about her biological daughter, but it was among the more aggressive….

Of course it’s possible. The science behind this is trivially plain. The biological mother has alleles which code phenotypes distinctive of Europeans and Africans. Because her father is African American she is even likely to have more European ancestry than African ancestry (median African American is ~80% African and ~20% European). Genes which control variation in skin pigmentation at the scale of racial differences are distributed across half a dozen loci, but with blue vs. brown eye color there’s really only one locus which explains most (though not all) of the variation. That probably explains how both the daughters have blue eyes. The mother is probably a heteozygote, and the father is a homozygote. That means that any one of their children has a ~50% chance of having blue eyes and a ~50% chance of having brown eyes. So the chance of both daughters turning out to have blue eyes is ~25%. But obviously the science isn’t the meat of the piece. I just wish they’d given a quick explicit nod to it so that people would know why the outcome is as it is. It’s not rocket science.

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Dienekes has already commented on this, but I thought I would go over Ewen Callaway’s piece, Aboriginal genome analysis comes to grips with ethics. It’s not surprising that this was written. Even if you take Keith Windschuttle’s position when it comes to Aboriginal-European contact you can’t escape the reality that Aboriginals did not fare so well in the interaction. In fact, they don’t fare so well today in Australia. The life expectancy gap between Aboriginals and non-Aboriginals in Australia is most conservatively estimated at 10 years (do remember that the majority of indigenous Australians are mixed-race). In the racialized physical anthropology of the early 20th amongst the colored peoples Aboriginals occupied the lowest circle of hell. Because of the robustness of their physiques it was argued they were the most primitive exemplar of humanity. Perhaps relic H. erectus.

Here are some interesting sections of Callaway’s article:

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Just realized. The Science paper has some interesting dates which allows us to make the above inference.

- Separation between Europeans and East Asians 25-38 thousand years before present.

- Gene flow between proto-East Asians and proto-Australians before the Native Americans diverged from the former 15 thousand years before the present.

- A conservative first landing in Australia 40-45 thousand years before the present.

The Native American result, where they share some derived variants unique to East Eurasians (mutations which emerged after the separation from West Eurasians) with Aborigines, pegs a minimum date of admixture ~15,000 years ago. But, obviously the admixture had to occur after the divergence of West and East Eurasians. Let’s say ~30,000 years ago. Even assuming that the gene flow between East Eurasians and proto-Australians occurred immediately after the separation 38,000 ago, there were anatomically modern humans in Australia for thousands of years already! The implication is that the first Australians by necessity can not have contributed in totality the ancestry of modern Aborigines. The AJHG paper gives a 50:50 estimate for the ratio of proto-Australian and the Andaman Islander/Malaysian-Negrito related population. We don’t need to be certain of the exact value to assume that numbers like this imply considerable admixture above trace levels.

Of all the dates I’m probably most confident about the archaeological ones about the settlement of Australia by anatomically modern humans. 46,000 years ago the megafauna started going extinct. That’s an immediate tell that humans have been let into the garden.

The Pith: The Bushmen branch of the human family tree diverged ~130,000 years ago. The non-Africans branched off from the Africans ~50,000 years ago. The Europeans and East Asians diverged ~35,000 years ago.

One of the terms in paleoanthropology which can confuse is that of archaic Homo sapiens (AHS). This is in contrast to anatomically modern humans (AMH). A simple Out of Africa “recent-origin-with-replacement” model allowed to sidestep the semantic imprecision in tossing disparate populations into a generic category such as AHS (similarly, the term “animal” as opposed to “human” has some colloquial utility, but it’s not scientifically useful). But the possibility of admixture from archaic lineages in modern human populations forces us to grapple with the dichotomy between AHS and AMH, as modern humans may be a compound of these two categories (not to mention the idea of behaviorally modern humans, who are a subset of AMH).

I assume that fleshing out the details of a new paradigm which is both precise and accurate will be a project for the coming years. But before we move on we need to fix more sturdily our understanding of the genealogical relationships of contemporary human populations. Over the past few years there have been major strides in this domain, confirming the broad outline of a dominant African heritage for modern humans. Geneticists have moved from classical markers to SNP data, focusing on hundreds of thousands of genetic variants. But now they’re shifting to whole genome sequences, which with errors excepted encapsulate the totality of the lowest order aspect of human genetic variation.* Earlier this summer I reviewed a paper in Nature which was a foretaste, Inference of human population history from individual whole-genome sequences. Today Nature has published another, Bayesian inference of ancient human demography from individual genome sequences.

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I’ve been chewing on the modern human range expansion into Neandertal territory paper for a few days now. But I haven’t been able to bring myself to say much. There are two reasons. First, it’s a simulation paper, and I don’t exactly know what I can say besides being skeptical of the plausibility of some of their results and their assumptions, unless I bother to replicate their simulations. There’s something of a “black-box” aspect from the outside operationally in the case of these sorts of research. Second, Ed Yong has boiled down the paper to its essence rather well, while John Hawks and Dienekes have offered their critiques. Dienekes and John get at one of my gnawing worries about all these sorts of models about deep history. Here’s John:

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I’m going to address two points in this post. The next possible target for getting an undersampled population, and the Malagasy results.

First, lots of great submissions in regards to populations which are undersampled. Some of them are actually already in the data sets. For example, the Burusho and Kalash are in the HGDP. There has been a major dump of data from the Americans recently as well. Zack Ajmal at HAP has the most systematic description online about where to find these that I know of. Additionally, I’m looking for stuff which is interesting where N = 1 would make a difference. I think that was the case for the Tutsi sample, as well as the Malagasy. When you have no prior information, adding one data point is notable. Obviously I can’t afford the money, time, and energy, required to get a good representative sample from a given region. Though I hope researchers who have a gusher of grant money might look at the above thread for ideas.

I think the next population to look for is someone with Ainu ancestry. This is easier said that done, so I need to think about it (both because of dilution and the language barrier). But then again, the Tutsi and Malagasy requests had a much more positive and faster turnaround than I had expected. So I’m not going to get all down about the likelihood.

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A month ago I asked for a Malagasy genotype. Almost immediately I received a response from someone that was 33% Malagasy. More recently I have sent a genotyping kit to someone who is Malagasy. Those results should come in within a month or so. But a few days ago I received a contact from a person of the Merina ethnic group of highland Madagascar. So of course I ran their data.

Here are the technical logistics. I wanted to look at their genotype through an African and a Southeast Asian lens. So I created an African loaded data set with 400,000 markers. Unfortunately the Southeast Asian data set I have has only 56,000 markers, and only 18,000 in common with this genotype. I ran ADMIXTURE on the former data set, K 2 to K 11. But at only 18,000 markers I think there just isn’t enough to run ADMIXTURE and make inferences of the grain which I want to make. So I ran EIGENSOFT to generate PCA’s. I did this for the African data set too. From dimension 1 to dimension 10.

I uploaded all the files to Google Docs. You can look at the Southeast Asian weighted PCA’s there. I’m not going to post them. The Asian ancestry of the Merina individual does look to be similar to that of Malays. What you’d expect. Below are K = 10 and PC’s 1 and 4.

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“There were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare [children] to them, the same [became] mighty men which [were] of old, men of renown.”

- Genesis 6:4

The Pith: Pygmies and Khoisan have admixture from a distinct population at the level of ~2%. This population diverged from the other ~98% of their ancestry ~700,000 years before the present, and the hybridization occurred ~30-40,000 years before the present. Most other African groups have only traces of this element, with some West Africans lacking it.

I have read the paper in PNAS which I referred to below. There isn’t that much I can add at this point. A lot of the guts were pushed into the supplements, which aren’t on the web yet. I was correct that the Mbuti Pygmies of the eastern Congo likely have a special place in this possible admixture event. In particular, they seem to possess the diverged variants found in the western Pygmies, the Biaka, and the Khoisan populations of southern Africa. As assumed the pattern of admixture seems to be such that the two Pygmy groups and the Khoisan exhibit elevated signatures of archaic contributions, while other African groups manifest admixture in direct proportion to their known admixture to the aforementioned populations. For example, the Bantu group with the highest proportion of admixture are the Xhosa, who also have the most Khoisan ancestry of non-Khoisan populations. The West African Mandenka seem to have trivial admixture from this archaic group. What does this mean?

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In my post below, Tutsi probably differ genetically from the Hutu, there were many comments. Some I did not post because they were rude, though they did ask valid questions. I will address those issues, but let me quote one comment:

That’s an interesting possibility, but this admixture run didn’t split the non-hunter-gatherer Africans that well. In one of your previous analyses on East Africa you managed to get a pretty accurate ‘Afro-Asiatic/Cushitic’ and ‘Nilotic’ cluster. Is it possible that you could run this Tutsi sample using the same admixture settings as in the ‘Flavors of Afro-Asiatic’ blog post to see if he carries a significant Nilotic component or is mainly Bantu & Cushitic derived?

So I replicated ADMIXTURE runs for many of the same populations as I did in my post, Flavors of Afro-Asiatic. I also pared down the population set and generated a PCA with EIGENSOFT. Before I get to those results, let me tackle the questions.

1) “Are the Luhya suitable proxies for the Hutus?”

Probably. The reason is that Bantu-speaking populations, from the Congo to South Africa, are surprisingly similar. Not only that, but these populations are very distinctive from groups which are close them geographically, but linguistically different (e.g., Khoe, Sandawe, Masai). The Luhya  are not exceptional. I’ve run the Henn et al. data sets enough to be convinced that they’re exactly as they should be. They are pretty much what you’d expect from Kenyan Bantu. A predominant element which ties them back to an East-Central African point of origin, with some admixture with other East African elements (similarly, South African Bantu exhibit Khoisan admixture). The Hutu may be peculiar, but we don’t know, and my null is that they’re mostly Bantu with some admixture, as is the case with most Bantu speaking populations (this one Tutsi seems to be an exception in that context, as they are presumably Bantu speaking). If you think that the the Luhya are not suitable, I invite you to download the HapMap Luhya, and merge them with some of the Henn et al. data sets (or HGDP or Behar data sets). I think that should convince you.

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A few people have pointed me to Charles Murray’s comment at The Enterprise Blog, The Debate about Heritability of General Intelligence Radically Narrows, which alludes to the recent finding of genomic confirmation of the behavior genetic heritability measure for intelligence. Murray indicates that this should end the “debate” on the heritability of intelligence as a quantitative trait. As I implied earlier much of this debate had more to do with rhetoric and ideology than reality, in that I doubt many people support a very low heritability measure for intelligence ( < ~0.30) in developed societies when they don’t have strong ideological commitments. These commitments being that social policy can homogenize environments enough that only the genetic components of variation of a trait value will be important in the future, so that heritability values will go from ~0 to ~1.0.

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A new paper in Molecular Psychiatry has been reported on extensively in the media, and readers have mentioned it several times in the comments. I read it. It’s titled Genome-wide association studies establish that human intelligence is highly heritable and polygenic. But the fact is that I read this paper last year. Back then it was titled Common SNPs explain a large proportion of the heritability for human height. I kid, but you get the picture. The new paper establishes for intelligence what we already suspected: most of the genetic variation in this heritable trait is accounted for by numerous genes of small effect. You inherit variants of these numerous genes from your two parents, and your own trait value is to a large extent a combination of the parental values. The issue is not if intelligence is heritable, but the extent of that heritability.

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The Pith: Natural selection is a quick & dirty operator. When subject to novel environments it can react rapidly, bringing both the good and the bad. The key toward successful adaptation is not perfection, but being better than the alternatives. This may mean that many contemporary diseases are side effects of past evolutionary genetic compromises.

The above is a figure from a recent paper which just came out in Molecular Biology and Evolution, Crohn’s disease and genetic hitchhiking at IBD5. You probably have heard about Crohn’s disease before, there are hundreds of thousands of Americans afflicted with it. It’s an inflammatory bowel ailment, and it can be debilitating even to very young people. The prevalence also varies quite a bit by population. Why? It could be something in the environment (e.g., different diet) or genetic predisposition, or some combination. What the figure above purports to illustrate is the correlation between Crohn’s disease and the expansion of the agricultural lifestyle.

But don’t get overexcited Paleos! There are many moving parts to this story, and I need to back up to the beginning. The tens of thousands of genes which you inherited from your parents are embedded within the genome and aligned in a set of sequences, one after the other. On the one hand for the purposes of conceptualizing evolutionary dynamics, such as natural selection or random genetic drift, focusing on a single gene is useful. It has power to illustrate some basic and elementary principles.  But sometimes you need to take a more synoptic view, and look at genes in their broader context. In this post I’ll avoid molecular or statistical epistasis, gene-gene interaction. Rather, let’s just consider the static landscape of the genome, where genes are physical concrete entities which are embedded in a particular spatial relationship to other genes, upstream or downstream in the genetic code. These physical or statistical associations of genes can form a de facto supergene through linkage, and their variants combine to form haplotypes, sequences of markers across small stretches of the genome. But recall that these associations are counter-balanced by genetic recombination, which tears apart physical sequences and sows them to the opposite DNA strand.

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