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440px-Desembarque_de_Pedro_Álvares_Cabral_em_Porto_Seguro_em_1500I pay a subscription to The New York Times because it’s America’s premier middle-brow journal. Its science pages are decent, so my interest was piqued when I saw the the bold headline, Discoveries Challenge Beliefs on Humans’ Arrival in the Americas. But the article is a total mishmash, alternating between spotlighting paradigm challenging scholars, and crazy. Here’s the crazy:

Having their findings disputed is nothing new for the archaeologists working at Serra da Capivara. Dr. Guidon, the Brazilian archaeologist who pioneered the excavations, asserted more than two decades ago that her team had found evidence in the form of charcoal from hearth fires that humans had lived here about 48,000 years ago.

Dr. Guidon remains defiant about her findings. At her home on the grounds of a museum she founded to focus on the discoveries in Serra da Capivara, she said she believed that humans had reached these plateaus even earlier, around 100,000 years ago, and might have come not overland from Asia but by boat from Africa.

These are changing times in human evolutionary biology. But if humans couldn’t make it by boat to Madagascar until 1,000 to 2,000 years ago, there’s no way they made it to Brazil.

• Category: Science • Tags: Archaeology, Brazil 
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Credit: Dragon Horse

The Pith: Brazil is often portrayed as the second largest black nation in the world, after Nigeria. But it turns out that the majority of the ancestors for non-white Brazilians are European.

One of the more popular sources of search engine traffic to this website has to do with the population genomics of Latin America. For example, my post showing that Argentina is not quite as European a country as it likes to consider itself is regularly cited in online arguments (people of various “persuasions” are invested in the racial status of the Argentine people). But last week in PLoS ONE a paper looking at the patterns of ancestry in the Brazilian population came to a somewhat inverse conclusion as to the self-conception or perception of the preponderant racial identity of that nation. Let me quote from the conclusion of the paper:

Among the actions of the State in the sphere of race relations are initiatives aimed at strengthening racial identity, especially “Black identity” encompassing the sum of those self-categorized as Brown or Black in the censuses and government surveys. The argument that non-Whites constitute more than half of the population of the country has been routinely used in arguing for the introduction of public policies favoring the no-White population, especially in the areas of education (racial quotas for entrance to the universities), the labor market, access to land, and so on[36]. Nevertheless, our data presented here do not support such contention, since they show that, for instance, non-White individuals in the North, Northeast and Southeast have predominantly European ancestry and differing proportions of African and Amerindian ancestry. The idea that Brazil is majority non-white, that is black, is one I’ve seen elsewhere. Using the American model of hypodescent, where children inherit the racial status of their most stigmatized ancestral component, no matter its magnitude, well over half of Brazilians are “black.” On the other hand, there’s the persistent trend in the recent analyses which show that black Brazilians have a much higher load of European ancestry than black Americans, while white Brazilians have a much higher load of Amerindian and African, than white Americans.

Let’s jump to the paper first. The Genomic Ancestry of Individuals from Different Geographical Regions of Brazil Is More Uniform Than Expected:

Based on pre-DNA racial/color methodology, clinical and pharmacological trials have traditionally considered the different geographical regions of Brazil as being very heterogeneous. We wished to ascertain how such diversity of regional color categories correlated with ancestry. Using a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms we estimated individually the European, African and Amerindian ancestry components of 934 self-categorized White, Brown or Black Brazilians from the four most populous regions of the Country. We unraveled great ancestral diversity between and within the different regions. Especially, color categories in the northern part of Brazil diverged significantly in their ancestry proportions from their counterparts in the southern part of the Country, indicating that diverse regional semantics were being used in the self-classification as White, Brown or Black. To circumvent these regional subjective differences in color perception, we estimated the general ancestry proportions of each of the four regions in a form independent of color considerations. For that, we multiplied the proportions of a given ancestry in a given color category by the official census information about the proportion of that color category in the specific region, to arrive at a “total ancestry” estimate. Once such a calculation was performed, there emerged a much higher level of uniformity than previously expected. In all regions studied, the European ancestry was predominant, with proportions ranging from 60.6% in the Northeast to 77.7% in the South. We propose that the immigration of six million Europeans to Brazil in the 19th and 20th centuries – a phenomenon described and intended as the “whitening of Brazil” – is in large part responsible for dissipating previous ancestry dissimilarities that reflected region-specific population histories. These findings, of both clinical and sociological importance for Brazil, should also be relevant to other countries with ancestrally admixed populations.

If you don’t know, the cartoon cut-out is that the northeast of Brazil is the most African inflected region, while the far South is predominantly European. Amazonia has more Amerindian influence, while there is local variation in other parts of the country due to rural to urban migration. Because the ancestry components that the authors were looking for are very distinctive, with the parent populations being separated for tens of thousands to hundreds of thousands of years, I assume 40 well selected markers are sufficient. Over 900 individuals is a large number. I jumped to the detailed methods, and was a little curious as to possible sampling bias introduced by their locations of collection, universities. Nevertheless, after 10 years of these sorts of papers I am convinced that there really does seem to be a fair amount of admixture in the Brazilian population across color lines.

The authors focused on three major color categories, white, brown, and black. These are self-descriptions for most of the participants, though the methods indicate that the southern sample was classified visually by the researchers. To get a sense of the relevance of these categories quantitatively the book Race in Another America: The Significance of Skin Color in Brazil, is useful (the low stars given on Amazon to this book seem to do with the reviewers being dumb or angry that the author didn’t have a big enough axe to grind). Roughly, Brazil shakes out as a “layer cake,” with (on average) blacks on the bottom, whites on top, and browns in the middle.

To the left you see the excepted triangle plots, with each vertex representing an ancestral component. The apex is European on each triangle (don’t deconstruct that!), with African to the bottom left and Amerindian to the bottom right. The leftmost column consists of self-identified whites, the right-most column self-identified blacks, and the middle column browns. Each row consists of a set of samples from a specific geographic region. To get a sense of national patterns the authors report that a 2008 survey indicated that of Brazilians 48.4% identified as white, 43.8% as brown, 6.8% as black, 0.6% as yellow, and 0.3% indigenous. These are social constructs. In fact, it seems likely that the indigenous genetic contribution to the total Brazilian population is actually 10-15%, relatively evenly distributed across the white, black, and brown categories. Additionally, American sociologists have generally observed that while very light-skinned individuals with some African ancestry self-identify as black in the USA, in Brazil the same individuals would probably identify as white. That’s a function of the differences between North American and Brazilian societies.

In any case, as you can see above there are differences between the color categories. Whites have more European ancestry, blacks more African, and browns are more mixed, with those in the north having more Amerindian quantum than those elsewhere. Here are the summary statistics by region & self-identification:

Color Assignment
Region Ancestry White Brown Black
North European 0.78 0.69 0.52
African 0.08 0.11 0.28
Amerindian 0.14 0.21 0.2
Northeast (Bahia) European 0.67 0.6 0.54
African 0.24 0.31 0.36
Amerindian 0.09 0.09 0.1
Northeast (Ceara) European 0.76 0.73
African 0.13 0.14
Amerindian 0.11 0.13
Southeast (Rio) European 0.86 0.68 0.43
African 0.07 0.24 0.5
Amerindian 0.07 0.09 0.08
South (Rio Grande do Sul) European 0.86 0.44 0.43
African 0.05 0.44 0.46
Amerindian 0.09 0.11 0.11

There’s nothing that surprising in this. The rank order is as you’d expect…except that blacks in the far south, where they are a much smaller minority, have less, not more, European ancestry. This is counter-intuitive because the presumption is that in blacker regions the threshold for being white is lower, while in whiter regions the threshold for being black is lower. You see the first in Bahia, where the typical white is about 2/3 European in ancestry, vs. Rio Grande do Sul, where European ancestry is at the level of Argentina genetically. I don’t think the authors have a good explanation for this, and even at their N there might be issues with representativeness that is distorting the results.

A common finding, which shows up in this research, is that there isn’t that big of a difference in the averages between some of the color categories in terms of ancestry. You can see that clearly in the figure to the left, from the paper Color and genomic ancestry in Brazilians: a study with forensic microsatellites. Again you have the three color categories, with their position on the y axis proportional to their “index of African ancestry.” The average rank order is perfectly correct, but there’s a great deal of overlap. The sample was from Sao Paulo. This is not typical in the United States. African Americans may be about ~20-25% European, with 10% being more than 50%, but the rate of non-European admixture in American whites is generally rather low. Only a small minority of American whites have anywhere near the median among of non-European ancestry among Brazilian or Argentine whites.

The main argument of the paper, which is in line with that of a long line of papers coming out of Brazil over the past ten years, is that assortative mating over the past 300 years has maintained phenotypic races, despite ancestral admixture. In other words, the physical difference between the color categories is much clearer than their ancestral quanta. Why? Because skin color, and perhaps traits like hair curl and nose form, as controlled by a small number of genes. In the case of skin color most of the variance is accounted for by less than half a dozen genes! We all know that among mixed-race siblings some individuals will resemble one race much more than the other, despite similar ancestral quanta. Rashida Jones regularly “passes” for white for her television roles, while her sister Kidada looks a bit more African American. As long as humans fix upon salient characteristics the “post-racial” idea is probably a delusion of idealism.

In any case, probably the most interesting and original aspect of the paper is the demographic one. I’ll quote:

We believe that the regional disparities in mtDNA ancestry were maintained because, once again, in the immigratory wave of Europeans there was a significant excess of males. When they admixed with the Brazilian women there was rapid europeanization of the genomic ancestry, but preservation of the established matrilineal pattern. There is demographic information to corroborate this possibility. First, of 1,222,282 immigrants from all origins that arrived in the Port of Santos in the period 1908–1936 the sex ratio (males/females) was 1.76…Second. the two most abundant immigrants, Portuguese and Italians, had sex rations of 2.12 and 1.83, respectively. census data of 1910 showed concordant results: there were 1,138,582 foreigners in Brazil, with a male/female ratio of 1.74, while there were 22,275,595 Brazilians with an even sex ratio of 1.0.

I’ve poked around for this sort of data before, and it is often hard to find. The Brazilian pattern, with a huge bias toward male migration, has probably been the pattern across much of human history with long distance travel. The United States is a great exception, with intact families settling New England early on (though the South exhibited a more Brazil like pattern, the admixed element was reabsorbed into the slave population). I think this has resulted in some weird inferences from historical population genetics derived from mitochondrial DNA, which passed through the maternal lineage (example: mtDNA of India didn’t predict very well how much closer Indians were going to be to West Eurasian populations when autosomal studies utilizing hundreds of thousands of markers came online).

Finally, a lot of these authors in these papers coming out of Brazil seem rather political when it comes to genomics, race, etc. I have no knowledge of the detailed back story, and I don’t believe that anything but conspiratorial manipulation could result in the consistent pattern in the data. But, in a heterogeneous population there’s always going to be worries about representativeness. From what little I know an awful lot of Brazilians are like Gisele Bündchen, the grandchildren or great-grandchildren of European immigrants. If so, they shouldn’t have any non-European ancestry. So I do wonder if there’s some conscious or unconscious undersampling going on because the researchers want to promote the idea of a racially admixed population.

Citation: Pena SDJ, Di Pietro G, Fuchshube-Moraes M, Genro JP, & Hutz MH (2011). The Genomic Ancestry of Individuals from Different Geographical Regions of Brazil Is More Uniform Than Expected PLoS ONE : 10.1371/journal.pone.0017063

• Category: Science • Tags: Brazil, Genetics, Genomics 
🔊 Listen RSS The populations of the African Diaspora have a particular interest in the new genomics, and its relationship to ancestry. Unlike other post-Columbian Diasporas they have sketchy, at best, knowledge of the regions from which their ancestors arrived. This probably explains the popularity of Roots and Henry Louis Gates Jr.’s various genealogical projects which have utilized cutting edge genomics. It may seem silly to hang one’s hat on one maternal lineage, but perhaps it seems silly if you are relatively assured of the broad outlines of your own genealogy. The fact that I am U2b is not very interesting to me, but I also happen to know that my maternal grandmother’s mother’s family were long resident in their region of Bengal (and, that her father was a migrant from northwest India). It would be a different matter if my ancestors had been enslaved and dispossessed of their heritage.

A new paper in PLoS ONE surveys the paternal (NYR), maternal (mtDNA), and autsomal (using 175 ancestrally informative markers), heritage of a range of African origin populations from across the Americans. Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas:

Our analysis revealed that both continental admixture and within-Africa admixture may be critical to achieving an adequate understanding of the ancestry of African-descended Americans. While continental ancestry reflects gender-specific admixture processes influenced by different socio-historical practices in the Americas, the within-Africa maternal ancestry reflects the diverse colonial histories of the slave trade. We have confirmed that there is a genetic thread connecting Africa and the Americas, where each colonial system supplied their colonies in the Americas with slaves from African colonies they controlled or that were available for them at the time. This historical connection is reflected in different relative contributions from populations of W/WC/SW/SE Africa to geographically distinct Africa-derived populations of the Americas, adding to the complexity of genomic ancestry in groups ostensibly united by the same demographic label.

There isn’t anything too surprising here. Blacks from Brazil have much more ancestry from the former Portuguese colonies of Angola and Mozambique. As we should expect. Because the New World African Diaspora dates to only the past 350-150 years even mtDNA should be a good snapshot of the genetic variation. And, because of the ability to construct clean genealogies due to lack of recombination, mtDNA can be even more informative than total genome surveys in terms of elucidating fine-grained geographical patterns. The map below illustrates the mtDNA results well:

But I was more interested in some patterns comparing the various African and European identified populations. In the figure which I stitched together below you have maternal ancestry on the left, paternal in the middle, and total genome ancestry to the right. The first panel has self-identified blacks from various nations, and the second has self-identified whites from Brazil and Philadelphia, USA. These results need to be taken with a grain of salt, because the samples from each nation need not necessarily be representative of the ethnicity for that whole nation (e.g., blacks in coastal Georgia have far less white ancestry than those in urban northern cities). But they give a rough picture of the differences and similarities.

Here the numbers with margins of error as well:

Self-identified black Self-identified white
African error European error Native error African error European error Native error
Brazil mtDNA 85 3 1 1 14 3 31 6 38 5 31 5
NRY 51 4 47 4 2 2 0 1 97 2 2 2
AIMs 58 30 12 20 64 17
USA mtDNA 93 1 5 1 2 1 6 5 92 7 2 1
NRY 77 2 25 2 0 0 2 1 97 2 1 1
AIMs 83 1.6 15 2 2 1 2 2 95 3 3 3

Similarities: a strong bias toward more male European ancestors, and more female African and Native ancestresses. This is what you’d expect. But look at the Brazil black sample. The disjunction between nearly total lack of female European ancestry and a substantial proportion of male European ancestry is rather striking. I think this is partly a function of the strong male bias of the Portuguese settler community. A process of “whitening” of the original mulatto and mestizo population of the colony probably occurred with each successive generation of male immigrants, who married into the hybrid communities and shifted the total genome content, though not the maternal background. The biggest difference of course is the much more clear and distinct difference between the races in the USA as opposed to Brazil. A minority of Brazilians identify as black, while a plural majority identify as white (the remainder are “brown” or mixed-race). And yet Brazilian blacks are ancestrally much whiter than American blacks, while Brazil whites are ancestrally much less white than American whites. Additionally, while Brazil perceives itself as a mulatto nation, there is a substantial Amerindian substrate which spans the black, white, and brown, populations.

Finally, going back to the main theme of the paper, African population structure, one of the main rationales is for purposes of medical research where stratification of ancestry within an aggregate pool may lead to spurious associations. In other words, mixing blacks with ancestry from Angola with those from ancestry from Nigeria may result in false positives in GWAS due to differences in predispositions of traits between these populations, which also track their genetic differences. The authors bring up the fact that African populations are the most genetically diverse in the world. But let me resurrect a comment from geneticist Nick Patterson:

I want to comment on Africa’s genetic diversity. There is a great deal of genetic diversity within many African populations. For instance more diversity within Yoruba than within Europe. But many African populations are quite similar. For instance divergence between Kikuyu (Kenya) and Yoruba (Nigeria) is just a little more than (Spain, Holland). This is of course caused by the Bantu expansion as Razib explained.

In other words, the great African genetic diversity is more a function of the intra-population variance, than inter-population variance. This sort of work is important for reasons of intellectual interest, but may not be quite so important for GWAS.

Citation: Stefflova K, Dulik MC, Barnholtz-Sloan JS, Pai AA, & Walker AH (2011). Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas PLoS ONE : 10.1371/journal.pone.0014495

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The term “BRICs” gets thrown around a lot these days. At least it gets thrown around by people who perceive themselves to be savvy and worldly. In case you aren’t savvy and worldly, BRICs just means Brazil, Russia, India and China. The huge rising economies of the past generation, and next generation. Here’s a summary from Wikipedia:

The BRIC thesis recognizes that Brazil, Russia, India and China…have changed their political systems to embrace global capitalism. Goldman Sachs predicts that China and India, respectively, will become the dominant global suppliers of manufactured goods and services, while Brazil and Russia will become similarly dominant as suppliers of raw materials. It should be noted that of the four countries, Brazil remains the only nation that has the capacity to continue all elements, meaning manufacturing, services, and resource supplying simultaneously. Cooperation is thus hypothesized to be a logical next step among the BRICs because Brazil and Russia together form the logical commodity suppliers to India and China. Thus, the BRICs have the potential to form a powerful economic bloc to the exclusion of the modern-day states currently of “Group of Eight” status. Brazil is dominant in soy and iron ore while Russia has enormous supplies of oil and natural gas. Goldman Sachs’ thesis thus documents how commodities, work, technology, and companies have diffused outward from the United States across the world.

But there are big quantitative differences between these nations as well. Below the fold are some charts which I think illustrate those differences.

• Category: Science • Tags: Brazil, BRICs, China, Data Analysis, Indian, Russia 
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adriana-limaA few months ago I was thinking a fair amount about the Neandertals. One issue which became more stark to me due to that particular finding, that a few percent of the human genome seems to have derived from Neandertal populations, is the reality that genetic distinctiveness can persist long after cultural coherency is no longer a reality. That made me reconsider one of the facts of contemporary scholarship, that the Amerindian populations of the two most populous nations of the New World, the United States of America and Brazil, have disappeared or been totally marginalized demographically.

I’ve observed before it looks like that about 15-20% of the ancestry of the Argentine population is Amerindian, despite the nation’s proud identity as a European settler offshoot (i.e., more like the United States or Australia, than Mexico, which has an explicit hybrid identity). But I realized that Brazil was perhaps the bigger catch.

Only 0.4% of Brazilians identify as Amerindian. That’s about 700,000 people. But we know that a substantial number of white, brown and black Brazilians have Amerindian ancestry. Assuming for argument’s sake that the 700,000 Amerindians have undiluted indigenous ancestry, how much of the distinctive Amerindian genome in modern Brazil is to be found in this segment of the population?

There was a paper which came out in an obscure Brazilian journal last year which can help answer this question, DNA tests probe the genomic ancestry of Brazilians. For the purposes of the paper they needed to find a small number of ancestrally informative markers which would allow them to partition the ancestries of the individuals in their data set into European, African, and Amerindian, segments. Luckily these are three very distinctive populations. They cross-checked the utility of their markers against the HGDP data set. In other words the precision and accuracy of the 40 markers they selected should be assessed by how well they can distinguish these three “pure” populations. Their Brazilian subjects consisted of self-identified whites from various regions, as well as black men from Sao Paulo. Brazil’s racial taxonomy has a brown (pardo) category which is large, but judging from the very high proportion of African ancestry among the blacks in their sample I don’t think they included self-identified mixed-race people in that group (some scholars lump mixed and black Brazilians together into the black category).

First, let’s see how well the markers allow for us to distinguish populations’ whose ancestry we’re pretty sure about.


No that bad. Observe the trailing off of Europeans and Amerindians along their axis of variation. From previous papers using SNP chips with hundreds of thousands of markers It seems that the HGDP Amerindian sample has non-trivial European ancestry, so it isn’t just a limitation of their marker set. This shouldn’t be that surprising in light of the history of Latin America, and the centuries of racial fluidity which occurred. Additionally, I assume that it would be more difficult to find markers which vary between Europeans and Amerindians than between these two groups and Africans (remember that Africans have more genetic diversity, and non-African populations can be thought of as simply one branch out of Africa).

The following chart shows the outcome from the markers across various regions of Brazil. I assume that the core American readership will be pretty ignorant of the regions, so this map will help. Southern Brazil is white. The rest of the country far less so. Gisele Bündchen and Alessandra Ambrosio are from Rio Grande do Sul in the far south. Adrianna Lima, pictured above, is from Bahia in the northeast. All of the panels are for whites (through self-identification) except for the last.


Despite the limitations of 40 markers I think the results here are probably pretty good. The South region has the whitest whites. This was an area with massive immigration, and fewer non-whites to start with. It is in the northeastern region that you see more Amerindian than black ancestry among the whites. From what I have seen in other papers the brown category in Brazil is more skewed toward European ancestry than panel F, so that’s why I assume that these are men who self-identify as black.

But for the purposes of my original question we need to assess ancestral contributions within these groups from Amerindians. The following table does just that.


The authors note a curious fact: there’s no statistically significant difference between the regions in terms of Amerindian ancestry for self-identified white Brazilians. This resembles the pattern we saw with Neandertal admixture, and I assume the explanation is the same: the integration of Amerindian ancestry occurred early in the history of the white Brazilian population and has now distributed throughout it via generations of intermarriage except for those with undiluted white immigrant heritage (e.g., Gisele, who comes from a German town). The figure for blacks from Sao Paulo is about the same as whites as well.

Let’s assume 10% Amerindian ancestry and 200 million Brazilians to make the math easier. Since it is about 10% in whites and blacks, I suspect it will be 10% in those who identify as mixed race as well. Where does that leave us? That would mean 20 million Brazilians of Amerindian ancestry! As you can see around 95% of the Amerindian genome in Brazil is found among those who do not self-identify as Amerindian.

For Americans (citizens of the USA) it is then interesting to wonder how much of the Native genome is found in whites, particularly old stock colonial descended whites, and how much in self-identified Native Americans. Looking at the genetic studies I believe that the Amerindian proportion is much lower among white Americans than 10%. Additionally, while 700,000 Brazilians identify as Amerindian, 2.4 million Americans do (though I believe that a much larger proportion of American Native Americans are of mixed ancestry than Brazilian Aboriginals). I think that the odds are that more ancestry which is pre-Columbian in the USA does reside within the white population than within the self-identified Native American tribes, but it may be a close thing. And of course there are Latino populations which need to be added into the equation, whose Amerindian ancestry is significant (in the case of Mexican Americans possibly preponderant), though it is of Mesoamerican origin.

But doing those sums is for another post.

Note: A preemptive apology to those who feel I’ve used the wrong term for any particular ethnic group. I have preferred the more Politically Correct (though less popular) term Native American in the context of the USA, but feel that Amerindian is technical or scholarly enough to evade charges of insensitivity.

Image credit:

• Category: Science • Tags: Brazil, Culture, Genetics, Genomics, Mixed-Race 
Razib Khan
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