The history and geography of genomes

By Razib Khan | December 15, 2011 11:30 pm

A new paper in PloS Genetics sheds some light on issues which we were already familiar with through conventional history, Ancestral Components of Admixed Genomes in a Mexican Cohort. What we already know: Mexicans and people of Mexican descent predominantly derive from an admixture event(s) between Europeans and Amerindians, with a minor African component. The last is often a surprise to Mexicans themselves, but it is no surprise to those who are aware of the nature of Spanish colonialism in the New World. In some cases, such as in Cuba, the African slave economy which we’re familiar with the United States was the norm, but in many instances African slaves accompanied Spaniards as secondaries in their conquest of the indigenous populations. New Spain was a caste society with a Spaniard and Creole elite, and a productive base of indios from whom they extracted rents. But Africans served as junior partners to the European elites, and were a substantial demographic presence down to the 19th century. Their near total genetic absorption though seems to have resulted in their near elimination from the cultural folk memory of Mexico.

Most of the techniques in the paper should be somewhat familiar to you. In particular, there’s a lot of PCA, as well as some model-based clustering methods. The PCA takes all the genetic variation in the data set, and reduces it down to large independent dimensions which you can visualize on a two dimensional plot (e.g.., PC 1 vs. PC 2 represents the largest explanatory dimension vs. the second largest). It turns out that most of the largest dimensions of variation are pretty well explained by our intuitions of genetic distance. The model-based approaches are different. Instead of letting the algorithm generate the clusters hypothesis free (i.e., you put labels on the clusters after the fact) you specify a number of populations, K, and the method forces the data you input to fit that parameter. In other words, it’s kind of like a sausage. Sometimes the fit is good, and sometimes not so good (if you try and divide Swedes into 20 distinct populations, the algorithm will try and comply, but it should really tell you that’s you’re being crazy). But another way to go is to look at the structure of the genome itself in methods which focus on correlations across the chromosomes. While PCA and model-based methods can give you an intuition as to the average admixture of an individual, more fine-grained genomic methods which assign ancestry to segments across an individual’s genotype yield more information.

To get a better sense, here are two graphics generated from 23andMe’s Ancestry Painting.

Both individuals shake out as ~50% European and ~50% East Asian. On PCA and model-based clustering they’re not distinguishable. But when you look at the patterns on a more fine-grained chromosomal scale you see clearly that the individual to the left seems to show no evidence of recombination between “European” and “East Asian” segments, while the individual to the right shows many. That’s because Uygurs as a genetic group emerged at last 1,000 years ago, and perhaps earlier. There are literally dozens of generations over which recombination could break apart association. In contrast, someone who is an F1 hybrid won’t manifest that, because their parents are from “pure” populations. Recombination events will only result in the swapping of segments of the same ancestral origin.

What does this have to do with this paper? The authors extracted out the different ancestral segments from Mexicans, European, African, and Amerindian, and constructed “virtual genomes” out of this raw material. And then they used the other methods to analyze these virtual genomes! You can see the result below.

As you would expect, the segments assigned to Europeans, Africans, and Amerindians diverge from each, and Mexicans span the gamut in proportion to assumed admixtures. There’s no Amerindian population in the HapMap, but the position of the “virtual Amerindians” seems about right. Observe here though the importance of the nature of the input sample in PCA: the largest dimension of variation separates Amerindians from Europeans and Africans, not Africans from everyone else. The latter is the norm in most studies, but this data set is biased toward large numbers of Mexicans, and the Amerindian vs. European difference is what dominates that then. If your population is mostly Amerindian and European, then Amerindian vs. European differences will explain more variance than African vs. Amerindian or European difference. On the other hand, if you balanced the proportions somehow the African vs. everyone else difference should take its position as the largest independent dimension again (PC 1).

But the authors did find something interesting using this method that we didn’t quite know. The virtual genomes go where you’d expect on the coarse continental level, but here you see that Mexicans seem to have two sources of Amerindian ancestry. One from southwest Mexico, and another are Maya from the Yucatan. Observe the clear admixture among some of the indigenous groups, while the virtual genome budges far less. This supports the validity of their method, as their assignments obviously did avoid labeling European segments as Amerindian. In any case, this pattern of ancestry is in sharp contrast with African Americans, who seem to exhibit little inter-individual difference in African ancestry. Why the contrast? Obviously the stories about the anomie of slave family life are correct, as ethnic cohesion and family integrity were rapidly destroyed in the New World. In contrast, in Mexico the indios may have been helots, but they weren’t quite chattel. Their native communities persisted and maintained integrity in a way not possible with enslaved Africans.

In the future these techniques are going to get better, especially with whole genome analysis. This means we’ll be able to explore in more detail the contributions of various to groups to any given population. Specific elements of history will come into sharper focus. For example, we could ascertain the impact genetically of the Dutch, French (descended from Protestant refugees), and Germans, on the genomes of Afrikaners. This group clearly has non-trivial African and Asian ancestry, but perhaps a more intriguing anthropological issue is why the Dutch culture dominates over that of the French and German if the latter contributed so much biologically, as some historians have maintained.

Citation: Johnson NA , Coram MA , Shriver MD , Romieu I , Barsh GS , et al. 2011 Ancestral Components of Admixed Genomes in a Mexican Cohort. PLoS Genet 7(12): e1002410. doi:10.1371/journal.pgen.1002410

CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics
MORE ABOUT: Human Genomics
  • Mike Keesey


    “But Africans served as junior partners to the European elites”

    Reminds me of a scene in Werner Herzog’s Aguirre: der Zorn Gottes, where the conquistadores send a man of African descent out before them when raiding an Amazonian village. In the commentary, Herzog says this is based on historical sources: conquistadores would sometimes send a black man as a forerunner, under the rationale that his skin color would terrify the natives. (But I’m not sure why white skin wouldn’t have the same effect….)

  • Karl Zimmerman

    I find it interesting the differences between the Mexico City populations (which are about 2/3rds Indian, 1/3 white) and the Los Angeles population (which is around half and half).

    Historically, most U.S. migration from Mexico has been from the north. This has been changing, but southern Mexicans in the U.S., being more recent, are more likely to have various difficulties (language, documentation) which would probably make it harder to be study participants.

    I believe some earlier studies have confirmed that northern Mexican populations, which have generally been perceived as “whiter,” are in fact more European. This makes logical sense, as the population densities in northern Mexico were never as high pre-contact. It was also undoubtedly reinforced a bit due to large levels of white migration to Chihuahua.

    Regardless, I wish they had asked the study participants in Los Angeles where their ancestors had been located in Mexico.

    Which brings me to another thing they didn’t mention but is clear on the chart. The Mex2 population (Los Angeles) groups close to Guerrero but not to the Maya, which is again indicative of Northern/Central Mexican ancestry. On the other hand, there is no difference between the two on the European component, suggesting few people with extra-Iberian ancestry from Northern Mexico migrated to the U.S.

    To me, this suggests the following scenario is most likely:

    The original Northern/Central Mexican population was nearly a 50/50 White/Indigenous split. However, later in Mexican history, as Mexico City had explosive population growth, a substantial amount of people of largely Mayan descent from southern Mexico migrated in, which swung the population more firmly towards the indigenous side.

  • http://www.isteve.blogspot Steve Sailer


    Fascinating. That might help explain something that has puzzled me about Mexican-Americans. When I was young, the Mexican-American population was not large, but there were a moderate number of Mexican-American celebrities, people who had clawed there way from nowhere to considerable accomplishment and renown even in fields like country club sports.

    For example, Pancho Gonzalez, an East L.A. cholo who spent a year in Juvenile Hall in the 1940s, was the most famous tennis player in America from the 1950s into the early days of the tennis boom in the early 1970s. Lee Trevino was the 3rd most famous golfer in America after Arnold Palmer and Jack Nicklaus. Nancy Lopez was the most popular woman golfer of all time.

    While the number of Mexican-Americans in the U.S. has increased enormously, the number of celebrities has barely increased at all. While levels of individual ambition seem to be dropping, so has the violence rate.

    Whether the causal relationship is cultural or genetic or just a coincidence, it is obvious that Mexican-Americans tend to be more Amerindian these days than before. But, as this study points out, the Amerindian component also seems to changing from Southwest Mexican to Mayan, which may have behavioral implications.

    Former Mexican foreign secretary Jorge Castaneda’s recent book Manana Forever includes a tribute to the orderliness and lack of violence in the Yucatan capital of Meridia. Perhaps the Amerindian component of Mexican-Americans used to be similar to that of, say, Apaches, but is shifting over time toward descent from long-urbanized Mayans?

  • Antonio

    I agree a lot with your last paragraph, and I believe this approach can easily extended to the study of admixed populations elsewhere. However, I would also like to read about studies in which the focus is more on the history and politics of the populations changes and interaction rather than on the estimation of the ancestral components per se.


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