Tag: Admixture

The genomic landscape of Brazil in 1950

Posted on by Razib Khan


A new whole-genome analysis out of Brazil has some interesting ancestry information. The preprint, Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (São Paulo, Brazil):

As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases….

Admixed populations are useful for a lot of reasons. But let’s observe some things about his Brazilian population.

First, it’s old. The average age is 72, so these are people born in 1950. This is the genetic characteristics of Brazil in 1950 in many ways, not today. This is why you see so many individuals who self-identify as Asian who are nearly 100% Asian. These individuals are the children of Japanese immigrants. In 1950 the endogamy of the community was high. Today the youngest generation of Japanese Brazilians is 60% mixed.

Second, most of the ancestry of self-identified Brazilian whites in this sample is mostly white. Like the Japanese, a large number of these individuals are probably the children of European immigrants. I suspect this accounts for many of the 20% of the “white” sample that has no trace non-European ancestry. But observe that around another 20% has trace proportions (~1%) of non-European ancestry, mostly African.  My supposition, in this case, is that these are “old stock” white Brazilians. That this, one or both of their parents descend from Portuguese Brazilians who settled in overwhelmingly European areas and retain some non-European admixture due to long-term residence in Brazil. The remainder is white Brazilians who have substantial non-European ancestry, with a small minority whose proportions are quite high from a North American perspective.

A point of comparison is probably useful. About 95% of non-Hispanic whites in the United States seem to have almost no detectable non-European ancestry using this sort of model-based clustering. This illustrates the massive demographic difference between the USA and Latin American nations. The vast majority of white Latin Americans look quite Iberian, but the majority also have far more non-European ancestry than 95% of North American whites. This is partly a reflection of the smaller population sizes of native peoples in North America, and, the nature of hypodescent for people of any African ancestry in the United States, so that mixed individuals were integrated into African Americans.

Third, the people who are “mixed” and black in Brazil are more European than you might expect. All the estimates of European ancestry I’ve seen for self-identified black Brazilians (a somewhat protean category due to social changes over the past few generations) indicate higher European ancestry fraction than among African Americans (~20% median in the latter). Self-identified “mixed” Brazilians have more European ancestry than anything.

The native category is interesting because most of these people have only a minor component of that ancestry. Additionally, a huge number of white, mixed, and black Brazilians have native ancestry. This is not surprising from previous work. Ancestry deconvolution indicates this is an old admixture, and mtDNA lineages are more native than Y chromosomes. There was a sex asymmetry in the early settlement, and native women married into the settler population. Both black and white Brazilians (and mixed) have lots of native ancestry.

Finally, though there is some overlap between these groups (despite their average differences), I assume that the overlap is much greater in contemporary cohorts in terms of genomic ancestry. It will be interesting to see when we get temporal transects in Brazil to see how assortative mating does, or doesn’t, work.

Looking forward to more of this from Latin America. So many opportunities for admixture mapping!

Indic civilization came to Southeast Asia because Indian people came to Southeast Asia. Lots of them

Posted on by Razib Khan

Reading Indonesia: Peoples and Histories. I selected it because unlike many books it wasn’t incredibly skewed to the early modern and postcolonial period. The author makes the interesting point that the Islamicization of western Indonesia and the rise of the great Javanese Hindu kingdom of Majapahit occurred around the same time. This, in contrast to the skein of Indic civilization which had been layered over maritime Southeast Asia for hundreds of years before the medieval period, starting around 500 AD with polities such as that of Kalingga.

As is usual in these sorts of books, it is emphasized that Indian civilization spread through cultural diffusion (in contrast to the fact that though Chinese trade was evident and present early on, the cultural impact was minimal). Any migrations are dismissed as legends, with the possible exception of a few elite religious functionaries.

I now believe this is wrong. I’ve discussed this extensively in the past, but the Singapore Genome Variation Project (SGVP) data set along with more Southeast Asians allows me to illustrate rather clearly the issues. The short of it is that it is highly likely that substantial South Asian ancestry exists within Southeast Asia, and that that ancestry is not just a function of colonial contact (e.g., as certainly occurred in Malaysia).

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Black ancestry in white Americans of colonial background

Posted on by Razib Khan

I stumbled upon striking photographs of “white slaves” while reading The United States of the United Races: A Utopian History of Racial Mixing. The backstory here is that in the 19th century abolitionists realized that Northerners might be more horrified as to the nature of slavery if they could find children of mostly white ancestry, who nevertheless were born to slave mothers (and therefore were slaves themselves). So they found some children who had either been freed, or been emancipated, and dressed them up in more formal attire (a few more visibly black children were presented for contrast).

This illustrates that the media and elites have been using this ploy for a long time. I am talking about the Afghan girl photograph, or the foregrounding of blonde and blue-eyed Yezidi children. Recently I expressed some irritation on Twitter when there was a prominent photograph of a hazel-eyed Rohingya child refugee being passed around. Something like 1 in 500 people in that region of the world has hazel eyes! That couldn’t be a coincidence. Race matters when it comes to compassion.

But this post isn’t about that particular issue…rather, the images of enslaved white children brought me back to a tendency I’ve seen and wondered about: the old stock white Americans whose DNA results suggest ~1% or less Sub-Saharan ancestry. These are not uncommon, and I’ve looked at several of them (raw data). I’m pretty sure the vast majority at the 0.5% or more threshold are true positives, and probably many a bit below this (to my experience people from England and Ireland don’t get 0.3% African “noise” estimates with the modern high-density marker sets).

According to 23andMe’s database about 1 out of 10 white Southerners has African ancestry at the 1% threshold. It would be even more if you dropped to closer to 0.5%. And the DNA ancestry here understates the extent of what was going on: at about 10 generations back you are about 50% likely to inherit zero blocks of genomic ancestry from a given ancestor (assuming no inbreeding in the pedigree obviously). And this is exactly when a lot of the ancestry that is being detected seems to have “entered” the white population. In other words, for every person who is 1% African and 99% white American, they have a sibling who is 0% African and 100% white American, even though genealogically they share the same ancestors. Dropping the threshold to closer to 0.3%, and considering that even in the South there was migration from the North, and to a lesser extent Europe, after the Civil War, I wouldn’t be surprised if models of admixture inferred from the distributions we see indicate that over half the lowland Southern white population likely had genealogical descent from a black slave.

This all comes to mind because there aren’t too many records of people “passing” during this period. Those who deal in genealogy and encounter these cases of low fractions, which are nevertheless likely not false positives, almost never find a “paper trail” when they go look. And they look really hard.

The reason is obvious in the context of American history. Thomas Jefferson’s slave Sally Hemings had three white grandparents and one African slave grandparent. Several of her children are recorded to have been totally European in an appearance, and all except one passed into the white population (the two eldest married well into affluent white families in Washington D.C.). Passing as white was a way to escape the debilities of black status in the United States.

That being said, I think our Whig conception of the progressive nature of history sometimes misleads us in forgetting that the dynamics of race relations has had its ups and downs several times in the last few centuries in North America. If you read Daniel Walker Howe’s excellent What Hath God Wrought you observe that racial beliefs about the necessity and institutionalization of white supremacy in the early American republic evolved over time. Though the early republic would never be judged racially enlightened by modern lights, it was certainly far less explicitly racially conscious than what was the norm in the decades before the Civil War.

In particular, the rise of democratic populism during the tenure of Andrew Jackson was connected with much more muscular racial nationalism. To utilize a framework emphasized by David Cannadine in Ornamentalism, colonialism and Western civilization during the 19th and early 20th centuries can be viewed through the lens of race and class. Though the economic inequalities of American society persisted through the 19th century, men such as Andrew Jackson affected a more populist and rough-hewn persona than the aristocratic presidents of the early 19th century.* The white man’s republic had a leveling effect on the nature of elite culture.

But the attitudes toward racial segregation and mixing took decades to harden. Martin van Buren’s vice president, Richard Mentor Johnson, was well known to have had a common-law wife, Julia Chinn, who was a slave. He recognized his two daughters by her. He was vice president from 1837-1841 in the more racist of the two American political parties of the time. It is hard to imagine this being a viable “lifestyle” choice for someone of this prominence in later decades (after Julia Chinn’s death Johnson continued to enter into relationships with slaves).

Walter F. White, a black leader of the NAACP

Which brings us back to what was happening in the decades around 1800. Racism was a fact of life, necessitating the need for passing. But, beliefs about racial purity and the one drop rule had not hardened, so it would not be surprising to me that it was much easier for slaves or ex-slaves with mostly European ancestry to change their identity. Perhaps white Americans of that period were simply less vigilant about someone’s background because they were genuinely less concerned about the possibility that their partner may have had some black ancestry, so long as they looked white.

As the databases grow larger we’ll get a better sense of the demographic and genealogical dynamics. My suspicion is that we’ll see that there wasn’t much diminishment of gene flow into the black-identified community over the past 200 years, as much as the fact that hypo-descent, the one-drop rule, became so powerful in the between 1850 and 1950 we can confirm that passing declined, before rising again in the 1960s as whites became less vigilant due to decreased racism.

* As a middle class New Englander John Adams obviously was no aristocrat, but he was no populist either.

Carving nature at its joints more realistically

Posted on by Razib Khan

If you are working on phylogenetic questions on a coarse evolutionary scale (that is, “macroevolutionary,” though I know some evolutionary geneticists will shoot me the evil eye for using that word) generating a tree of relationships is quite informative and relatively straightforward, since it has a comprehensible mapping onto to what really occurred in nature. When your samples are different enough that the biological species concept works well and gene flow doesn’t occur between node, then a tree is a tree (one reason Y and mtDNA results are so easy to communicate to the general public in personal genomics).

Everything becomes more problematic when you are working on a finer phylogenetic scale (or in taxa where inter-species gene flow is common, as is often the case with plants). And I’m using problematic here in the way that denotes a genuine substantive analytic issue, as opposed to connoting something that one has moral or ethical objections to.

It is intuitively clear that there is often genetic population structure within species, but how to summarize and represent that variant is not a straightforward task.

In 2000 the paper Inference of Population Structure Using Multilocus Genotype Data in Genetics introduced the sort of model-based clustering most famously implemented with Structure. The paper illustrates limitations with the neighbor-joining tree methods which were in vogue at the time, and contrasts them with a method which defines a finite set of populations and assigns proportions of each putative group to various individuals.

The model-based methods were implemented in numerous packages over the 2000s, and today they’re pretty standard parts of the phylogenetic and population genetic toolkits. The reason for their popularity is obvious: they are quite often clear and unambiguous in their results. This may be one reason that they emerged to complement more visualization methods like PCA and MDS with fewer a priori assumptions.

But of course, crisp clarity is not always reality. Sometimes nature is fuzzy and messy. The model-based methods take inputs and will produce crisp results, even if those results are not biologically realistic. They can’t be utilized in a robotic manner without attention to the assumptions and limitations (see A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots).

This is why it is exciting to see a new preprint which addresses many of these issues, Inferring Continuous and Discrete Population Genetic Structure Across Space*:

A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure….

The whole preprint should be read for anyone interested in phylogenomic inference, as there is extensive discussion and attention to many problems and missteps that occur when researchers attempt to analyze variation and relationships across a species’ range. Basically, the sort of thing that might be mentioned in peer review feedback, but isn’t likely to be included in any final write-ups.

As noted in the abstract the major issue being addressed here is the problem that many clustering methods do not include within their model the reality that genetic variation within a species may be present due to continuous gene flow defined by isolation by distance dynamics. This goes back to the old “clines vs. clusters” debates. Many of the model-based methods assume pulse admixtures between population clusters which are random mating. This is not a terrible assumption when you consider perhaps what occurred in the New World when Europeans came in contact with the native populations and introduced Africans. But it is not so realistic when it comes to the North European plain, which seems to have become genetically differentiated only within the last ~5,000 years, and likely seen extensive gene flow.

The figure below shows the results from the conStruct method (left), and the more traditional fastStructure (right):

There are limitations to the spatial model they use (e.g., ring species), but that’s true of any model. The key is that it’s a good first step to account for continuous gene flow, and not shoehorning all variation into pulse admixtures.

Though in beta, the R package is already available on github (easy enough to download and install). I’ll probably have more comment when I test drive it myself….

* I am friendly with the authors of this paper, so I am also aware of their long-held concerns about the limitations and/or abuses of some phylogenetic methods. These concerns are broadly shared within the field.

Why humans have so many pulse admixtures

Posted on by Razib Khan

The Blank Slate is one of my favorite books (though I’d say The Language Instinct is unjustly overshadowed by it). There is obviously a substantial biological basis in human behavior which is mediated by genetics. When The Blank Slate came out in the early 2000s one could envisage a situation in 2017 when empirically informed realism dominated the intellectual landscape. But that was not to be. In many ways, for example in sex differences, we’ve gone backward, while there is still undue overemphasis in our society on the environmental impact parents have on children (as opposed to society more broadly).

But genes do not determine everything, obviously. Several years after reading The Blank Slate I read Not by Genes Alone: How Culture Transformed Human Evolution. In this work Peter Richerson and Robert Boyd outline their decades long project of modeling cultural variation and evolution formally in a manner reminiscent of biological evolution. Richerson and Boyd’s program does not start from a “blank slate” assumption. Rather, it is focused on broad macro-social dynamics where cultural variation “swamps” out biological variation.

Recall that in classic population genetic theory a major problem with group level selection is that gene flow between adjacent groups quickly removes between group variation. One migrant between two groups per generation is enough for them not to diverge genetically. For group selection to occur the selective effect has to be very strong or the between group difference has to be very high. Rather than talking about genetics though, where the debate is still live, and the majority consensus is still that biological group selection is not that common (depending on how you define it), let’s talk about human culture.

Here the group level differences are extreme and the boundaries can be sharp. Historically it seems likely that most groups which were adjacent to each other looked rather similar because of gene flow and similar selective pressures. Even though in medieval Spain there was a generality, probably true, that Muslims were swarthier than Christians*, there was a palpable danger in battle of identifying friend from foe because the two groups overlapped too much in appearance.

This brings up how one might delineate differences culturally. In battle opposing armies wear distinct uniforms and colors so that the distinction can be made. But obviously one change uniform surreptitiously (perhaps taking the garb from the enemy dead). This is why physical adornment such as tattoos are useful, as they are “hard to fake.” Perhaps the most clear illustration of this dynamic is the Biblical story for the origin of the term shibboleth. Even slight differences in accent are clear to all, and, often difficult to mimic once in adulthood.

Biological evolution mediated through genes is relatively slow and constrained compared to cultural evolution. Whole regions of central and northern Europe shifted from adherence to Roman Catholicism to forms of Protestantism on the order of 10 years. Of course religion is an aspect of culture where change can happen very rapidly, but even language shifts can occur in only a few generations (e.g., the decline of regional German and Italian dialects in the face of standard forms of the language).

Cultural evolution as a formally modeled neofunctionalism is credibly outlined in works such as Peter Turchin’s Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth. That’s not what I want to focus on here. Rather, I contend that the reality of massive pulse admixtures evident in the human genome over the past 10,000 years, at minimum, is a function of the fact that human cultural evolutionary processes result in winner-take-all genetic consequences.

A concrete example of what I’m talking about would compare the peoples of the Italian peninsula and the Iberian peninsula around 1500. The two populations are not that different genetically, and up to that point shared many cultural traits (and continue to do so). But, a combination of geography and history resulted in Iberian demographic expansion in the several hundred years after 1500, whereby today there are probably many more descendants of Iberians than Italians. This is not a function of any deep genetic difference between the two groups. There aren’t deep genetic differences in fact. Rather, the social and demographic forces which propelled Iberia to imperial status redounded upon the demographic production of Iberians in the future. In addition, the New World underwent a massive pulse admixture between Iberians, and native Amerindians, as well as Africans, usually brought over as slaves, due the cultural and political history of the period.

The pulse admixture question is rather interesting academically. To some extent current methods are biased toward detection of pulse admixtures, and even fit continuous gene flow as pulse admixtures. A quick rapid exchange of gene flow and then recombination breaking apart associations of markers which are ancestrally informative haplotypes is something you can test for. But I think we can agree that the gene flow triggered by the Columbian Exchange was a pulse admixture, and there’s too much concurrent evidence from uniparental lineage turnover in the ancient DNA to dismiss the non-historically corroborated signatures of pulses as simply artifacts.

Nevertheless continuous gene flow does occur. That is, normal exchange of individuals between neighboring demes as a slow simmer over time. But the idea that we are a clinal ring species or something like that isn’t right in my opinion. Part of the story are strong geographical barriers. But another major part is that cultural revolutions and advantages introduce huge short-term demographic advantages to particular groups, and the shake out of inter-group competition can be dramatic.

Therefore, I make a prediction: the more cultural evolutionary dynamics a species is subject to, the more pulse admixture you’ll be able to detect. For example, pulse admixture should be more important in social insects than their solitary relatives.

* Not only was some of the ancestry of Muslims North African, Muslim rule was longest in the southern and southeastern regions, where people were not as fair as in the north.