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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.

2) “The admixture percentages you give are weird for population X.”

Someone who is more technically fluent than I can correct me, but I suggest that you be very careful about taking absolute percentages too literally. If you tell a statistical algorithm to push the genetic variation you’ve input into it into a certain number of boxes, it will do that, even if it has to squeeze them in all sorts of ways. In other words, modulating the parameters is an easy way to generate plenty of weird absolute proportions. Often it’s pretty obvious that deeply admixed populations are showing up as their own distinctive cluster…but that begs the question, when is admixture so distant that it shouldn’t count? Instead of focusing on absolute percentages, look at the relationships between individuals and populations. These too can be tweaked and massaged, but my personal experience is that they’re somewhat less volatile.

3) “The Nilotic cluster doesn’t map well onto Nilotic populations.”

The labels one gives, formally or informally, to a population cluster are for ease of recollection. They are not there to transmit to you real concrete information about the deep history of a population and its relationship. Additionally, there is always going to be a lot of confusion when you leverage geographical or linguistic terminologies which have only approximate relationships to genetic clusters. Don’t get so caught up in semantics that you forget that ADMIXTURE components are abstractions, useful for smoking out genetic variation, not for perfectly mapping onto some idealized set of ur-populations.

Now to my results. I used 200,000 markers. I combined Lithuanians and Belorussians into one pot as “Baltic,” and Syrians and Jordanians into another as “Levantines.” For the PCA I focused on African populations, and used the Yemeni Jews as the outgroup. Additionally, there is clearly structure due to some family relationships amongst the Masai. This is a problem in many runs with them. Even when you remove the “problem” individuals other clusters tend to crop up at higher K’s where the Masai are very numerous. In any case, for the purpose of these runs ignore the family clusters, and focus on the more typical individuals amongst the Masai.

Remember that the Tutsi is 3/4 Tutsi, 1/4 Hutu. It is N = 1. So is the Nubian. You see in many of the Horn of Africa populations that the Eurasian component has an affinity with Yemenis, not Europeans. In contrast, the Nubian does have some European-like component. That’s probably simply due to the fact that in this run Levantines themselves have that, and Egyptians who also carry that component are part of the heritage of the Nubian. The Tutsi does have the Southwest Asian component, which the Masai seem to lack.

To get a better sense, let’s look at a slice of individuals. The Tutsi is last. The family relationships of some of the Masai are also clear. Focus on the more typical Masai and the Tutsi:

Looking at the individual results it seems that the Tutsi can be placed with the range of combinations of ancestral components of the Masai, though not the Luhya. To get a different vantage point let’s look at some PCAs, which visualize the largest components of genetic variance in the data set.

The results are not cut & dry. I am less skeptical of some Afro-Asiatic element in the Tutsi heritage, though it still seems that the dominant affinity is with the Masai.

Note: I ran K = 7 to K – 10. There wasn’t anything different in the general pattern of the runs I did not show.

(Republished from Discover/GNXP by permission of author or representative)
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Paul Kagame with Barack and Michelle Obama

I first heard about Rwanda in the 1980s in relation to Dian Fossey’s work with mountain gorillas. The details around this were tragic enough, but obviously what happened in 1994 washed away the events dramatized in Gorillas in the Mist in terms of their scale and magnitude. That period was a time when the idea of “ancient hatreds” leading to internecine conflict was in the air. It was highlighted by the series of wars in the former Yugoslavia, and the Tutsi-Hutu civil wars in Rwanda, Burundi, and Congo. Of the latter the events in 1994 in Rwanda were only the most prominent and well known.

After having read Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa I am relatively conscious of the broader canvas of what occurred in Central and East Africa in the 1990s. Not only was there a conflict between Tutsi and Hutu in Rwanda, but a similar dynamic also flared up in Burundi. The tensions are more complex in Congo and Uganda, in large part because there are many ethnic players, and the Hutu role as the antagonists with the Tutsi is divided among many different populations. In trying to distill the complex ethnography of this region in setting the structural parameters of the landscape into which the violence of the late 20th century emerged many pundits have pointed to the role of the Belgian colonial authorities in crystallizing, sharpening, and perhaps even originating the distinction between Tutsis and Hutus. This is not totally unreasonable if you don’t know much. A quick “look up” will confirm that there is no linguistic or religious distinction between the two groups; they share a common culture in many ways. Rather, the differences seem more of class and ecology. The Tutsi minority had a much stronger pastoral element to their economy. The Hutus were conventional farmers, clear legacies of the Bantu expansion which swept from West-Central Africa east and south, all the way to the Cape of Good Hope and the Indian Ocean. As is not uncommon in the history of humankind the pastoral Tutsi tended to dominate the Hutu peasant. This is where the class dimensions are clearest, as the modest Hutu were traditionally ruled by the wealthier Tutsi aristocracy.

The problem is when one makes recourse to Platonic thinking when population thinking would be more useful. There are certain average differences between the Tutsi and Hutu, but there is a great deal of overlap. Not all Tutsi were wealthy pastoralists, and not all Hutu were peasant vassals. There was a caste system of a sort, but it was semi-permeable, and the identity of an individual as Hutu or Tutsi was partly conditional on social, economic, and personal circumstances. The key word here is partly. Additionally, the semi-permeability of identity does not imply that these categories emerged from a previously aggregate population.

An example of what I’m talking about would be the blood nobility of France in the late 18th century. The vast majority of the hereditary aristocracy derived from those who had been promoted in previous centuries from the gentry class of commoners. A division between the aristocracy and the commons in France in the 18th century, which loomed so large, and later gave raise to racialist theories, was almost totally a function relatively recent social forces. At this point some of you may point to the international connections of the French aristocracy. For example, the nobility of Normandy not only had Norse ancestors, but also centuries long connections with England. This is wrongheaded. Because aristocratic lineages tend to keep relatively punctilious records it is clear that turnover was so high that over the centuries ethnically based aristocracies melted into the population, and the nobility of the future itself was more than likely not either of novel foreign origin, or uplifted from the local stock (or, as in the case of Hungary, the elites imposed their identity upon the masses, who later seem to have replaced them if ancient DNA surveys of cemeteries are any clue).

The application of this sort of framework then seems natural to the Tutsi-Hutu dichotomy. Because this topic is of great interest there’s an independent entry on this question in Wikipedia, Origins of Tutsi and Hutu:

The colonial scholars who found complex societies in sub-Saharan Africa developed the Hamitic hypothesis, namely that “black Europeans” had migrated into the African interior, conquering the primitive peoples they found there and introducing civilization. The Hamitic hypothesis continues to echo into the current day, both inside and outside of academic circles. As scholars developed a migration hypothesis for the origin of the Tutsi that rejected the Hamitic thesis, the notion that the Tutsi were civilizing alien conquerors was also put in question.

One school of thought noted that the influx of pastoralists around the fifteenth century may have taken place over an extended period of time and been peaceful, rather than sudden and violent. The key distinction made was that migration was not the same as conquest. Other scholars delinked the arrival of Tutsi from the development of pastoralism and the beginning of the period of statebuilding. It appears clear that pastoralism was practiced in Rwanda prior to the fifteenth century immigration, while the dates of state formation and pastoralist influx do not entirely match. This argument thus attempts to play down the importance of the pastoralist migrations.

Still other studies point out that cultural transmission can occur without actual human migration. This raises the question of how much of the changes around the fifteenth and sixteenth centuries was the result of an influx of people as opposed to the existing population being exposed to new ideas. Studies that approach the subject of racial purity are among the most controversial. These studies point out that the pastoralist migrants and pre-migration Rwandans lived side by side for centuries and practiced extensive intermarriage. The notion that current Rwandans can claim exclusively Tutsi or Hutu bloodlines is thus questioned.

The idea that people have “pure” Tutsi or Hutu “bloodlines” is so easily refuted that we can dismiss it and move on. Even species can hybridize, so the notion that populations which were spatially coexistent for centuries would be able to maintain pure distinctiveness seems ludicrous. But this idea was proposed by Europeans in the 19th and early 20th centuries, influenced by the racialist paradigms ascendant at the time, whereby the Tutsis were conceived as an intrusive Eurasian population which imposed its will upon the primitive Bantu Hutu. Interestingly these same concepts were resurrected by Hutu demagogues after independence, though the valence of division was altered, insofar as the Tutsi were now no longer vectors of civilization, but alien interlopers who brought contagion.

Most of these models are ridiculous on the face of it. But the converse extreme position is that the Tutsi-Hutu division was purely a cultural revolution, and that the Tutsi are as native as the Hutu in terms of the time-depth of their biological ancestry in the region of Rwanda-Burundi. A common observation here is that one couldn’t tell a Tutsi from a Hutu. This sentiment was put into the mouth of Joaquin Phoenix’s character in Hotel Rwanda. But this is obviously wrong. Some Hutu become Tutsi, and some Tutsi become Hutu, and some people have mixed ancestry but undivided identity, but the reality remains that on average the Hutu and Tutsi do look different. This was obvious in Hotel Rwanda itself, the Hutu protagonist’s Tutsi wife was played by a half-white actress. The preconception is that Tutsis are taller and have narrower features. Paul Kagame, the de facto ruler of Rwanda since 1994, and an ethnic Tutsi, is a perfect exemplar of the prototype Tutsi. He is tall, slim, and has relatively narrow features.

No matter the line promoted by the government of Rwanda after the genocide the people of the region are quite aware of Tutsi distinctiveness, or at least the ideal distinctiveness of the Tutsi. In Dancing in the Glory of Monsters the author observes that illiterate peasants in the eastern Congo will routinely express skepticism of an individual by bringing up the French form of the word morphology. This scientific term, which describes the exterior and structural phenotype of an individual illustrates the depth of a racial understanding of the difference between the Tutsis and other populations of this region.

So what’s the truth here? I can now contribute a little to the elucidation of this question, because I have run the genotype of an individual who is 3/4 Rwandan Tutsi and 1/4 Rwandan Hutu. An N = 1 is not much, but it is far better than 0. There are some genetic studies of these populations, but they don’t use hundreds of thousands of SNPs. I did. More specifically, a little over 400,000 SNPs.

I first ran this individual in a trial set of populations using both ADMIXTURE and Eigensoft. The former partitions the ancestry of an individual into K components, weighted by the contribution of each component. These are not to be taken literally. In this case focus rather on the relatively comparison across populations, rather than the absolute values of each individual. Eigensoft generates PCA plots, which extract out the largest independent dimensions of genetic variation in the population. These dimensions are ordered from larger (1st component) to smallest (nth component).

Eventually I discarded most of the non-African populations, as well as the Mozabites. My main focus was on East Africa. I have no Hutu samples, but I do have Luhya from the HapMap. They are a Bantu group from western Kenya, and so presumably relatively good proxies for the Hutu. In the following analyses you should substitute “Hutu” implicitly when you see “Luhya.” The other groups are rather straightforward. I included some Yoruba as a West African outgroup, but left them out of the ADMIXTURE plot because at higher K’s internal structure began to show up. This didn’t change the overall results, but they don’t inform for the Yoruba. The Sandawe are a Tanzanian group which speaks a language with possible affinities to the Khoe.

[zenphotopress album=305 sort=sort_order number=5]

The figure to the left shows all the individuals in the ADMIXTURE run labeled by population (except the Yoruba). Near the bottom I’ve placed a red marker to point to the Tutsi. Both the PCA and the ADMIXTURE indicate that this Tutsi individual has a strong resemblance to the results for the Masai. Unsurprisingly this individual is shifted somewhat toward the Luhya in the PCA, further confirmation of their Hutu ancestry. We can probably reject an Afro-Asiatic ancestry for the Tutsi, as is claimed by some. This individual consistently shows much closer affinity to the Nilotic Masai than to the Semitic or Cushitic samples from the Horn of Africa. Also, notice the profile of the Bantu of Kenya. These are likely good proxies for the ur-Hutu. The Tutsi individual is far outside of the range of this population.

What does this mean? I think the title says it all: the Tutsi were in all likelihood once a Nilotic speaking population, who switched to the language of the Bantus amongst whom they settled, and from whom they extracted rents. The relationship of the Tutsi and Hutu is not exceptional, and does not require European colonial intervention or meddling. It is a representative of a range of relationships whereby mobile pastoral populations dominate sedentary farmers because of their superior martial prowess (farmers are “sitting ducks”). Quite often this division has some ethnic connotation, such as the Scythian dominion over various sedentary populations in the Ukraine ~2,000 years ago, or Turkic hegemony in late medieval and early modern Russia. Neither the Scythians nor the Turks emerged from the sedentary substrate. Rather, they were intrusive to the region. Despite the interaction and intermarriage between these sorts of populations they generally remain aware of their disparate origins, and conscious of it. The fact that the Tutsis and Hutus do should not surprise that much in this context.

When it comes to some scientific questions, such as the genetic basis of intelligence, the science isn’t quite there to resolve the issues to the satisfaction of all in the room. I believe it will, but it will take time. But in the cases of ethnic identity and its relationship to biology we have the technology. The Tutsis and Hutus in all likelihood derive from two distinctive biological groups, who have not become divided, but rather have amalgamated somewhat over time (culturally and biology). That’s a lot to derive from one 3/4 Tutsi sample, but we have more to go on than just this sample. There has been long a suspicion about the Tutsi’s non-Bantu origins due to phenotype, oral history, and lifestyle. I’m basically confirming what is evident to anyone who has eyes.

The reason that the Rwandan authorities don’t emphasize the differences between the Tutsis and Hutus (despite the current Tutsi domination of the government) is because of the history of ethnic violence and genocide in the region. But I do not believe that the genetic differences that are clear here are sufficient or necessary for genocide. This is famously illustrated by the Yugoslav conflicts of the 1990s, where very biologically similar groups engaged in wars based on their putative differences. Within Africa itself there is no shortage of genocide between groups which are much closer biologically than the Tutsi and the Hutu (e.g., the havoc wrought upon the Bantu Matabele in the early 1980s by the Bantu Shona dominated movement led by Robert Mugabe). It is not the truth we have to fear, but the mythologies which humans distort from the fragments of the truth in furtherance of their own perverse aims.

Note: thanks to everyone who spread the word about my quest for a Tutsi genome. I think we just did something really cool here.

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