Admixture

How Argentina became white

razib — Thu, 17 Dec 2009 12:42:55 +0000

How Argentina became white

Apropos of my skepticism of Census projections of 2050 demographic balances, there's a new paper out on Argentina which is relevant. Here's Wikipedia on Argentina's self-conception:

As with other areas of new settlement such as Canada, Australia and the United States, Argentina is considered a country of immigrants. Most Argentines are descended from colonial-era settlers and of the 19th and 20th century immigrants from Europe, and 86.4% of Argentina's population self-identify as European descent. An estimated 8% of the population is mestizo, and a further 4% of Argentines were of Arab or East Asian heritage. In the last national census, based on self-identification, 600,000 Argentines (1.6%) declared to be Amerindians (see Demographics of Argentina for genetic studies on the matter). Following the arrival of the initial Spanish colonists, over 6.2 million Europeans emigrated to Argentina from the mid-19th to mid-20th centuries Argentina was second only to the United States in the number of European immigrants received, and at the time, the national population doubled every two decades mostly as a result.

In contrast to Mexico, which is self-consciously a synthetically a "mestizo" nation which conceives of itself as a cultural and biological synthesis between European and native, I think it is fair to portray Argentineans as a settler society of Europeans in their self-image. As I have said before, this mythos goes a bit too far. The median Argentinean probably has enough indigenous ancestry to qualify as a Native American tribal member in the United States by the rules of blood quantum (on the order of 20-25%). Here's a multi-dimensional genomic window into this reality, Inferring Continental Ancestry of Argentineans from Autosomal, Y-Chromosomal and Mitochondrial DNA:

We investigated the bio-geographic ancestry of Argentineans, and quantified their genetic admixture, analyzing 246 unrelated male individuals from eight provinces of three Argentinean regions using ancestry-sensitive DNA markers (ASDM) from autosomal, Y and mitochondrial chromosomes. Our results demonstrate that European, Native American and African ancestry components were detectable in the contemporary Argentineans, the amounts depending on the genetic system applied, exhibiting large inter-individual heterogeneity. Argentineans carried a large fraction of European genetic heritage in their Y-chromosomal (94.1%) and autosomal (78.5%) DNA, but their mitochondrial gene pool is mostly of Native American ancestry (53.7%); instead, African heritage was small in all three genetic systems (<4%). Population substructure in Argentina considering the eight sampled provinces was very small based on autosomal (0.92% of total variation was between provincial groups, p = 0.005) and mtDNA (1.77%, p = 0.005) data (none with NRY data), and all three genetic systems revealed no substructure when clustering the provinces into the three geographic regions to which they belong. The complex genetic ancestry picture detected in Argentineans underscores the need to apply ASDM from all three genetic systems to infer geographic origins and genetic admixture. This applies to all worldwide areas where people with different continental ancestry live geographically close together.

I've outlined a reasonably plausible model for how this situation came out before. Strong male bias in European settlement and immigration. This would naturally result in the persistence of maternal indigenous ancestry, while at the same time contributing to the dominance of European ancestry. Dienekes points out:

European ancestry in mtDNA (44.3%) and Y-chromosome (94.1%) gives an estimate of 69.2%, compared to 78.6% for autosomal markers. Native S. American in mtDNA (53.7%) and Y-chromosome (4.9%) gives an estimate of 29.3%, compared to 17.28% for autosomal markers. Finally, African mtDNA (2%) and Y-chromosomes (0.9%) gives an estimate of 1.45% compared to 4.15% for the autosomal markers.

If one assumes serial matings between European men and mixed women the uniparental lineages would underestimate the total ancestral contribution of Europeans, as the "mixed" women themselves progressively became more European in ancestry. As for the African lineages, the proportions are small, but one could envisage scenarios whereby slave women have mixed-race children, and for whatever reason their sons marry out and reproduce to a greater extent than their daughters. This would eliminate African mtDNA from the population, but maintain the total ancestral contribution.

Let's see how the sample above relates to other world populations:

The people of Argentina are mostly European in ancestry, so these results match our expectation. Now let's visualize it in another way:

The Structure bar plot is small, but you can see the intra-population variance among Argentineans. A substantial proportion of the population of Argentina arrived within the last 100 years. But, a far smaller number of Argentineans have only ancestry from within the last 100 years. In other words, to have exclusively grandparents or great-grandparents who were only immigrants or only the children of immigrants must be relatively rare, looking at the detectable proportion of indigenous ancestry across most of the population. Since Argentina was a mixed-race society before mass immigration, as long as the roots of any given individual goes back to the period before mass immigration than it is likely that they will have some non-European ancestry.

Of course this doesn't really change anything. I have known of individuals who look European with less than 25% Native American ancestry who identify as Native American. I have known individuals who show their Native American ancestry on hindsight who don't identify as such. To say that racial identity is a social construction is ludicrous on the boundaries. An blonde Swede would not pass for a Sinhala. But there are plenty of gray lands in between, and the populations of Latin America often inhabit those domains. Someone who in Brazil identifies as white could be identified as African American in the United States. Someone whose forebears were part of the white racial aristocracy of Cuba two generations ago may now self-identify as a Person of Color in the United States (while at the same time being a participant in the racial discrimination which Afro-Cubans still suffer within the greater Cuban community.

The relevance for the United States is clear. I think the Census projections underplay the likely role of admixture in "whitening" the population. Though white-black biracial actors can not plausibly play white characters in American culture, white-Asian actors do. Those of partial Hispanic ancestry have long passed for their career's sake (and sometimes later come back out when social norms changed). Therefore, I think America may have a non-Hispanic white majority just a little longer in its own mind than what the genes and projections might tell us....

(the countervailing trend would be the tendency of people will little, or rumored, Native American ancestry to identify as Native American)

Citation: Annals of Human Genetics doi:10.1111/j.1469-1809.2009.00556.x

razib Thu, 12/17/2009 - 07:42

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Anthroplogy

genetics

Admixture

Argentina

Census

race

To be Coloured in South Africa means being all of the above

razib — Sat, 05 Dec 2009 19:53:29 +0000

To be Coloured in South Africa means being all of the above

About six months ago I had a post up on the Cape Coloureds of South Africa. As a reminder, the Cape Coloureds are a mixed-race population who are the plural majority in the southwestern Cape region of South Africa. Like the white Boers they are a mostly Afrikaans speaking population who are adherents of Reformed Christianity. After the collapse of white racial supremacy many white Afrikaners have argued that it is natural and logical to form a cultural alliance with the Cape Coloureds because of the affinity of language and faith (Afrikaans speaking Coloureds outnumber Afrikaans speaking whites). For their own part, though a people of color who suffered under Apartheid, the Coloureds have an ambivalent relationship with the black majority and have supported several white dominated political movements since the end of Apartheid.

One of the reasons that the Afrikaners and Coloureds have a relationship is a genetic one: the white ancestry of the Coloureds is the same melange of Dutch, French Huguenot and German which gave rise to the Afrikaners. Though I am unaware of modern genetic studies, older genealogical research has concluded that on the order of 5% of Afrikaner ancestry is non-white, and almost certainly it is through the "passing" of Coloureds into the Afrikaner population. As the Coloureds share language and religion with the Afrikaners this would naturally not be particularly difficult if they could pass themselves off as unmixed European. Or, at least if on the frontier farms of the 18th and 19th century if the neighbors did not inquire too closely as to the provenance of an individual whose ancestry was probably mixed. It is because of the non-white genetic load, small, but not trivial, that individuals such as Sandra Laing emerged from Afrikaner pairings during the era of Apartheid.

But though the Cape Coloured derivation from Europeans and local Africans, a mixture of Bushmen, Khokhoi and Xhosa, is well known and attested, there are other groups who are in the mix, quite literally. The Cape Colony was a way station between the far flung holdings of the Dutch East Indies Company, the VOC, one of the first major joint-stock corporations in the world, and the mother country. Just as Europeans arrived from the north, so Asians were brought from the east, though in this case they were generally slaves or bonded laborers. Large numbers of Southeast and South Asians arrived to serve the Dutch and provide labor which the locals would (because they were free and outside of colonial control) or could not (they died of disease and maltreatment). The Cape Malay community, which is in some ways affinal to that of Cape Coloureds, serves as a cultural testament to the Muslims amongst those brought to Africa. But the Cape Coloureds themselves no doubt have Asian ancestry which has left fewer salient cultural marks than that of their European ancestors.

But recent genetic data is clarifying that ancestry. It seems plausible to assume now that Asian ancestry surpasses European ancestry among the Cape Coloureds, with African ancestry still retaining a plural majority. A new paper in Human Molecular Genetics confirms earlier findings, Genetic structure of a unique admixed population: implications for medical research:

Understanding human genetic structure has fundamental implications for understanding the evolution and impact of human diseases. In this study, we describe the complex genetic substructure of a unique and recently admixed population arising 350 years ago as a direct result of European settlement in South Africa. Analysis was performed using over 900 000 genome-wide single nucleotide polymorphisms in 20 unrelated ancestry-informative marker selected Coloured individuals and made comparisons with historically predicted founder populations. We show that there is substantial genetic contribution from at least four distinct population groups: Europeans, South Asians, Indonesians and a population genetically close to the isiXhosa sub-Saharan Bantu. This is in good accord with the historical record. We briefly examine the implications of determining the genetic diversity of this population, not only for furthering understanding of human evolution out of Africa, but also for genome-wide association studies using admixture mapping. In conclusion, we define the genetic structure of a uniquely admixed population that holds great potential to advance genetic-based medical research.

The name of the game again is population substructure in the service of medical research. In this case, the Cape Coloureds are relevant because of their highly diverse origins, and so their possible relevance for admixture mapping. If a genetic variant which causes disease differs greatly in frequency between two distinct populations, an admixed population would be ideal to explore that particular relationship. African Americans are a case in point, they are modeled easily as a two-way mixture between Northern Europeans and West Africans. The Cape Coloureds present a more complex case, because their admixture derives from several different very distinct groups.

Historically the Asians seem likely mostly to have been from the Indonesian archipelago, as well as from coastal southern India and Bengal. The African demographics of the Cape have changed considerably since the colonial era. The Khoisan groups, both Bushmen and Khoikhoi, have declined in numbers in relation to the Xhosa. Though the Xhosa themselves have clearly absorbed a great deal of the Khoisan, before, and after, that period. For this study the researchers used 20 Cape Coloureds, 20 Xhosa and 20 Indonesians, combined with HapMap and HGDP samples. They covered 900,0000 SNPs.

Here is a figure where they display the geographical origins of their samples:

You should be familiar with most of these; e.g., the South Asian samples are from Pakistan, from the HGDP, the Europeans are Utah Whites from the HapMap.

Below are pairwise genetic distance values:

I want to emphasize that these are pairwise values. The initials represent:

COL = Coloured
XHO = Xhosa
SAN = Bushmen
YRI = Yoruba
CEU = Utah White
CHB = Chinese (Beijing)
SAS = South Asian (Pakistan)
IND = Indonesian

The relatively close relationship between the Cape Coloureds South Asians should be viewed with caution, since there is evidence that South Asians themselves are a compound admixture between quasi-Europeans and an ancient East Eurasian population of Indians. Note the small distance between South Asians and Europeans in the table above.

An easy way to visualize relationships are principal component scatter plots. These plots show independent dimensions of variation within data, in this case genetic data. The points are individuals, and in 2-dimensional plots generally the x-axis illustrates the first component of variation while the y-axis the second component. These are respectively the independent dimensions which explain the most variation in the data set.

In this paper they constructed a series of PC scatter plots where the axes display between group variation, upon which later groups are mapped upon. Below I've repurposed figure 2 a bit to fit on the screen. Here is the legend:

Figure 2. Principal components scatter plots. Indicating (A) our Coloured and isiXhosa samples across an African versus non-African axis, (B) a Bantu versus Bushmen axis, (C) European versus Asian (Han Chinese, Indonesian and South Asian) axis, (D) Chinese versus Indonesian axis and (E) European versus South
Asian axis.

In other words, what you're seeing are the Cape Coloureds being projected onto PC scatter plots where the axes are constructed from populations which resemble their putative parental populations.

And finally, bringing it all together:

The scatter of Cape Coloureds in the domains between these populations dovetails well with what intuition would suggest if they were in fact an admixture between all of these continental populations. But one issue is that because South Asians and Europeans are relatively close on a continental scale of genetic variation PC plots can only be somewhat definitive in establishing a contribution from that group, though figure 2E above comes close (showing that in relation to South Asian groups Cape Coloureds are shifted toward white Europeans).

To confirm a possible contribution from South Asians they used a regression method whereby the allele frequencies in the admixed population can be modeled as a combination of the frequencies from the non-admixed populations. Table 4 shows the results:

These align well with earlier results. But again there is an issue with the fact that South Asians and Europeans exhibit relatively small between population difference in gene frequencies (the methods rely in part on taking the difference between allele frequencies). They divided the Coloured genome into blocks and used a model where they included South Asians and left them out; the model with South Asians had much greater predictive value than that without South Asians. As I noted above the South Asians who were ancestral to the Cape Coloureds were likely Bengalis and South Indians, not the Pakistanis in the HDGP. Therefore using the model of some of the researchers in this paper the ancestors probably had an "Ancestral North Indian" (quasi-European ANI) component closer to 50% as against 70-80% in the case of the South Asian populations in the HGDP. Though even the ANI was at some genetic distance from modern Europeans, the fact that South Asians themselves can be modeled as an admixture of two populations, one very similar to Europeans, and one more similar to Indonesians than Europeans ("Ancestral South Indians", ASI), though still at a much further remove from Indonesians than the ANI from Europeans, I think explains the relatively modest Fst values between South Asians and Cape Coloureds. The Cape Coloureds in to some extent recapitulate an aspect of an the admixture event which produced South Asians (ANI:ASI::European:Indonesian).

One final dynamic confirmed by these results is that there was "female mediated Asian gene flow" and "male mediated European gene flow" in the emergence of a mixed-race group in South Africa. It is especially striking in the case of Indonesian ancestry, and to me surprisingly small in the case of the African ancestry. In the text the authors note that many marriages were contracted between whites and freeborn Africans, so what we may be seeing here is simply that sociological reality, prior to the further crystallization of a racial caste system African males were able to join the mixed-race community. By contrast Asians, disproportionately slaves, could not marry free whites. This resulted in much greater asymmetrical gene flow between white owners and female slaves.

I'll let the authors conclude:

In conclusion, using a novel method for computing degree of admixture, we demonstrate clear evidence of African (genetically close to isiXhosa), Indonesian, European and South Asian contributions in our recently ( 350 years) admixed Coloured samples. This agrees well within the historical evidence. Therefore the Coloured people represent a new class of unique genomes created from a divergent genetic background, including more than one of the described six major ancestral human genetic clusters...This admixture holds strong potential to offer new insights into complex gene-gene and gene-environment interactions, insight into human evolution and human disease evolution, and enabling medical research efforts unparalleled by any other population.

To those who assume that racial mixture leads to an indistinct and homogeneous mass, here is an extended family of Cape Coloureds:

One issue that a researcher on this paper pointed out to me is that there is a difference between the mix of populations ideally used to predict allele frequencies in populations, and the actually admixing proportions. This makes some sense when you note the difficulties involved in separating South Asian from European contributions because the two groups are the relatively similar in relation to the others. The Fst between the Bushmen and Xhoas is 3 times greater than between the South Asians and Europeans!

A final thought. We don't need to go South Africa for a very admixed population. How about Hawaii? At least 20% of the population in Hawaii apparently exhibits some sort of mixed ancestry (probably an underestimate because of various political issues related to Native Hawaiians).

Citation: Nick Patterson , Desiree C. Petersen , Richard E. van der Ross , Herawati Sudoyo , Richard H. Glashoff , Sangkot Marzuki , David Reich , and Vanessa M. Hayes
Genetic structure of a unique admixed population: implications for medical research
Human Molecular Genetics Advance Access published on November 18, 2009, DOI 10.1093/hmg/ddp505.

razib Sat, 12/05/2009 - 14:53

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Population Substructure

race

south africa

Sex differences in ancestry in the New World

razib — Wed, 25 Nov 2009 01:44:19 +0000

Sex differences in ancestry in the New World

A new paper in PLoS ONE, Evaluation of Group Genetic Ancestry of Populations from Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas, doesn't add much to what we know. They looked at a several hundred individuals who are self-identified as African American and European American, as well as 49 Senegalese from Dakar. Additionally, they reanalyzed data from Latin America from whites and blacks in Brazil, as well as a group of mixed Cubans. They found what you might expect to find, African and Native ancestry shows a female bias, European ancestry shows a male bias.

But Figure 3 is nice in that it illustrates how exceptional European Americans are: they are a New World population with very little admixture, that is, a "pure race." The data on people of white identification in most of Latin America, including in the European dominated southern cone, is that a non-trivial load of non-European genes exists in these populations (often indigenous ancestry down the maternal lineage). Similarly, African origin populations in the New World are invariably known to be admixed, more or less. Finally, even the "indigenous" generally show non-trivial European or African ancestry (this is evident in the regular notations of African or European ancestry being used to explain anomalous results).*

Citation: Stefflova K, Dulik MC, Pai AA, Walker AH, Zeigler-Johnson CM, et al. 2009 Evaluation of Group Genetic Ancestry of Populations from Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas. PLoS ONE 4(11): e7842. doi:10.1371/journal.pone.0007842

* Some escaped African slaves "went native" and assimilated into indigenous tribes. The symbiotic relationship between the Seminoles of Florida and escaped blacks is well known, but not exceptional. The case in the United States is exceptional in its magnitude in that most people of native self-identifications are mixed.

razib Tue, 11/24/2009 - 20:44

Tags

Population Substructure

race

White Americans from Philadelphia are unlikely to have any Native or African ancestry. Most are descended primarily from 19th or early 20th century Irish, Polish, Italian and Jewish immigrants.
Of course the amount of Native ancestry in Euro-Americans has been exaggerated by family legends, and the actual amount, where it exists, is often going to be undetectable by commercially available DNA tests.
If one is looking for such ancestry, it is best to look at French Canadians, as well as old-stock Americans with Scots and Scots-Irish roots, especially in the South and West. Scots were heavily involved in the colonial-era southeastern deerskin trade (likewise the later Canadian fur trade) and many of the early mountain men were of Scots-Irish descent.

The Euro-American results are false.
http://www.plosone.org/article/slideshow.action?uri=info:doi/10.1371/jo…
No Negroid mtDNA was found in the Euro-American sample. The only African mtDNA is two North African Caucasoid lineages. These are most likely from Southern Europeans.
None of the "Native American/Asian" lineages are Amerind.
http://www.plosone.org/article/slideshow.action?uri=info:doi/10.1371/jo…

Not surprising that a small proportion of North African mtDNA might be found in Euro-Americans from Philadelphia, given the number of Philadelphians of Southern Italian/Sicilian descent.
Among Euro-Americans in general, there is clearly less non-European ancestry than among the most "European" populations in Latin America (Argentines) or even among white Afrikaners (many of whom have minor African or South/Southeast Asian ancestry). But if one is looking for such ancestry among Euro-Americans, the sample used in this case is about the LAST place one would want to look.

Svante Paabo believes modern humans & Neandertals interbred

razib — Mon, 26 Oct 2009 16:25:25 +0000

Svante Paabo believes modern humans & Neandertals interbred

Neanderthals 'had sex' with modern man:

Professor Svante Paabo, director of genetics at the renowned Max Planck Institute for Evolutionary Anthropology in Leipzig, will shortly publish his analysis of the entire Neanderthal genome, using DNA retrieved from fossils. He aims to compare it with the genomes of modern humans and chimpanzees to work out the ancestry of all three species.
...
Paabo recently told a conference at the Cold Spring Harbor Laboratory near New York that he was now sure the two species had had sex - but a question remained about how "productive" it had been.

"What I'm really interested in is, did we have children back then and did those children contribute to our variation today?" he said. "I'm sure that they had sex, but did it give offspring that contributed to us? We will be able to answer quite rigorously with the new [Neanderthal genome] sequence."

The way Paabo is couching it, what he has found then seems likely to be evidence that humans who had just expanded Out of Africa contributed to the genomes of Neandertals. In other words, modern human introgression into Neandertals. Of course if the gene flow was from modern human to Neandertals exclusively, then it would be an evolutionary dead end since that lineage went extinct.

In any case, for several decades some fossil-based paleoanthropologists have been claiming that there are "intermediate" individuals in the record which indicate modern human-Neandertal hybridization. Most prominently Erik Trinkaus. If Paabo's finding becomes more solid, then it seems time to update the probabilities on these sorts of claims based purely on morphology.

H/T: Anthropology.net

Related: Neandertal introgression.

razib Mon, 10/26/2009 - 12:25

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but.... every case of fossil based hybrid has been retracted, as far as I know. Early H. sap and contemporary N's were just too similar to draw conclusions ...

What I would like to know more about (and this is coming) is the relationship (degree thereof) between European H. sap and living humans.

The Daily Telegraph (UK) had a nice typo with this story.

"I'm sure that they had sex, but did it give offspring that contributed to us? We will be able to answer quite vigorously with the new [Neanderthal genome] sequence."

Sex with neanderthals would be vigourous, but science should be rigourous.

http://www.telegraph.co.uk/science/evolution/6430494/Modern-man-had-sex…

Since the discoveries of Levallois technology tools in the U.S. recently, the migration theory and where neanderthals were all located is now in question,. Indiana,Texas, and Tenn. have all been yielding Mousterian style tools for the last six years. An entire lithic industry never seen before in the U.S. has been revealed. Every type of tool found on neanderthal sites abroad have been found in the U.S. Only to be ignored so far by main stream archaeology because it has been revealed to amatures. But the artifacts themselves speak to the truth of it. They are undeniably a prepared core design that until now has only been seen in lower and middle paleo sites abroad. It would serve Paabo, Trinkhaus,and the others well to take a close look at the recently assembled artifacts. These recent finds change everything as far as dispersals and migrations of at least the middle paleo cultures...rick doninger

I find it hard to believe that modern man didn't have sex with Neandertals -- after all, we will jump anything -- but whether it produced hybrids is a completely different question.

The genetic evidence so far hasn't shown any evidence for hybrids, but maybe the full sequence with. I haven't hard anything in that direction so far, though, and when I visited Paabo's group last month they didn't say anything about it, so if they have found it at least they are not revealing it to outsiders like me :)

I really look forward to reading the genome paper. Svante promised to send the draft when they have it, so I am waiting impatiently.

Of course, we are talking very low coverage sequence here, so even if the new sequence doesn't show any evidence for hybrids it doesn't conclusively rule out that we have left over Neandertal DNA in our genome. When we get deeper coverage over the next couple of years we should have a much better idea of it.

Comparing our modern genome with the Neandertal genome will of course only tell us if any Neandertal DNA entered our gene pool and survived till modern day. Getting a sequence from Homo sapience from ~30000-50000 years ago would be better, and it is possible to get that, even if contamination issues are harder to deal with for that than it is for Neandertals (and there it is hard enough as it is).

BTW, about a year ago my impression from Svante was that there was no gene flow seen in the record. His belief at that time was that there was no gene flow but of course they had sex because, well, they would. So whatever new report of evidence of gene flow follows a moment when it seemed that there was no positive evidence of such.

greg, yes. he was unequivocal about it. the about-face means

1) there must be something compelling or

2) british newspapers are making stuff up again

"The genetic evidence so far hasn't shown any evidence for hybrids"

Apparently Neanderthals had the human version of FOXP2, yet the genomic estimates in humans are that the gene is something like 40,000 years old. Hard to come up with a scenario other than it having come from Neanderthals. Similarly for the 7R version of the D4 dopamine receptor.

Henry Harpending

Henry, are you sure about FOXP2?
It was my impression that it was a different gene, that for the variant of microcephalin, MCPH1, that is believed to be 42,000 years old and that this was NOT found in the neanderthal sequence.
The way I read the story is that there is a possiblity that neanderthal sequence reveals something that would have made hybridization with humans difficult - for instance a chromosomal difference (inversion, translocation etc). This would have greatly limited the chances of having fertile pairings between neanderthals and modern humans.

"Similarly for the 7R version of the D4 dopamine receptor."

Really?! Hadn't heard this. Very interesting.

A little google-foo lead me to this study:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117557/

From the study:

"we show by DNA resequencing/haplotyping of 600 DRD4 alleles, representing a worldwide population sample, that the origin of 2Râ6R alleles can be explained by simple one-step recombination/mutation events. In contrast, the 7R allele is not simply related to the other common alleles, differing by greater than six recombinations/mutations."

--This, obviously, makes 7R old. But the article goes on:

"Strong linkage disequilibrium was found between the 7R allele and surrounding DRD4 polymorphisms, suggesting that this allele is at least 5â10-fold âyoungerâ than the common 4R allele."

--Yep, this makes it young, at least in humans. So what this is implies is that this is a very old allele that did most of its aging in a population not represented as a subset of modern humans.

Sigmund said "Henry, are you sure about FOXP2?"

MCPH too, but also foxp2. See

http://mbe.oxfordjournals.org/cgi/content/full/25/7/1257

The Timing of Selection at the Human FOXP2 Gene
Graham Coop*, Kevin Bullaughey{dagger}, Francesca Luca* and Molly Przeworski*
MBE 2008 25:1257-1259

Henry

Hypertension, race, class & Puerto Rico!

razib — Wed, 09 Sep 2009 01:47:20 +0000

Hypertension, race, class & Puerto Rico!

Update: Author comments below.

PLoS ONE has an interesting paper out, Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico. They're exploring the topic of African ancestry and hypertension, which seems to have a positive correlation, but where there is dispute as to whether that correlation is driven only by genes, or environment, or a combination. Puerto Rico is characterized by a wide range in admixture between Europeans & Africans (with a minor but significant amount of Amerindian). Additionally, because most variance in between population complexion is controlled by only a half a dozen genes there is going to be a lot of noise in the correlation between skin color and ancestry. In this small sample of 87 individuals, 37 white, 31 brown and 19 black, assayed on 78 ancestrally informative markers, the correlation was 0.63. Moderately strong, but one variable can only explain 40% of the variance on the other (some more juice would no doubt be squeezed by more markers, as well as using a continuous skin color metric based on reflectance).

Here's the plots of ancestry across the three classes:

The means & standard deviations in African ancestry for the three classes were 0.19 & 0.10, 0.28 & 0.12 and 0.44 & 0.11. It is interesting that the black category in this community in Puerto Rico may very well be whiter than 90% of American blacks (10% of American blacks are 50% or more white).

The top line finding of this paper though is that once you control for the interaction of color with socioeconomic status the effect of African ancestry his sharply mitigated (to below statistical significance). There are some data from Brazil which also provide possible avenues of investigation into the interplay between perceived race coded through phenotype and the underlying ancestral quanta. Here is the regression table which lays out their model (I left one off because of how small the font is already):

And now here's a chart illustrating the interaction effect evident in the model above. What's going on here? This is showing you the interaction where higher SES among those coded as black seem to have higher blood pressure. They tiptoe around it in the discussion, but the implication is strong here that racism and negative life experience might have had some role to play in this. How this could play out concretely isn't too difficult to imagine. Years ago I read a book which was basically an ethnography of Brazilian culture, and in particular how blacks and whites related as a function of class. One of the illustrations of the travails of the lives of middle class blacks was a mother who told her children never to eat bananas in public, lest they be mocked by their white peers. The experience of racism by lower and middle class blacks was qualitatively different in this model. In particular, lower class blacks were often embedded in a predominantly black community and so could withdraw from interactions with whites, while middle class blacks were professionals who interacted with and lived with whites and so experienced stress and tension as a matter of course.

A possible novel finding in this paper was that taking into account the color X SES interaction they found a genetic association with hypertension. Association studies obviously have to account for population genetic substructure. Here they are suggesting that other environmental variables might be useful as well (in a world of infinite research dollars, of course!).

Nevertheless, I pointed out the fact that the blacks in this study aren't very black ancestrally to urge some caution (they do so as well). The sample size is small, and lots of variables are being manipulated and values coded (e.g., the racial classes are coarse). Who knows where the p-values might have fallen if the parameters were jiggled in another direction. The studies about people with African ancestry and hypertension include some nations where the overwhelming majority of the population is African ancestry (e.g. ,West Indies), but also there are data from African nations where hypertension isn't a problem. It seems likely that genes and environment are both a role in these sorts of "lifestyle" diseases, and that there are likely interaction effects at work.

Finally, instead of the racial angle, I wonder about the familial one. In these societies which are heterogeneous by origin siblings may be coded as different races. Dark-skinned siblings may be treated much worse than light-skinned siblings. It would be interesting to see the effect within families among siblings. These sorts of studies often get boiled down to "racism = bad health" in the American media, but I do suspect it's more complicated than that. Especially when other societies do not always have American conceptions of race.

Citation: Gravlee CC, Non AL, Mulligan CJ, 2009 Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico. PLoS ONE 4(9): e6821. doi:10.1371/journal.pone.0006821

Addendum: I assume someone might quibble with my translation of the terms above as "white," "brown" and "black." So be it.

razib Tue, 09/08/2009 - 21:47

Tags

genetics

Admixture

race

This is going to be fairly hard to prove that it is mostly biological because HP varies quite a bit within and between races.

This links to a study done back in 2005:

http://thestudyofracialism.org/viewtopic.php?t=5874&highlight=blood+pre…

It clearly shows...obviously African Americans and especially Caribbean blacks have lower levels of blood pressure than many Europeans. It is also pretty clear to anyone aware that blacks have a larger percent of their community concentrated in the lower income levels (in Latin America and the U.S.) and in the U.S. those blacks specifically have a "Southern" eating tradition which is much less "heart-healthy" on top of eating more junk food, etc. How does one sort through all that noise? My personal theory is it has to do with latitude and skin color. It may be environmental stress is less on blacks the closer they are to the equator (then add in societal stress of poverty, racism, etc).

Population
Total (%)
Men (%)
Women (%)

African-origin populations

-Nigeria
13.5
13.9
13.1

-Jamaica
28.6
23.4
31.8

-US black
44.0
43.1
44.8

European-origin populations

-US white
26.8
29.7
23.9

-Canada
27.4
31.0
23.8

-Italy
41.5
48.0
35.1

-Sweden
38.4
44.8
32.0

-England
41.7
46.9
36.5

-Spain
46.8
49.0
44.6

-Finland
48.6
55.7
41.6

-Germany
55.3
60.2
50.4

Thanks for highlighting our paper, Razib. A few points of clarification:

You mention the correlation between ancestry and skin color (r=.63) and suggest that the correlation might be higher using a reflectance-based measure. That is, in fact, what we did. Skin pigmentation isn't the focus of the PLoS ONE paper; see an earlier paper in Am J Public Health; which shows that blood pressure is associated with social classification but not with skin pigmentation, as measured by reflectance spectrophotometry. The purpose of mentioning the modest correlation between pigmentation and the genetic-based estimate of ancestry here is to reinforce the point that skin pigmentation is only a very rough proxy for genetic ancestry.

A related issue that may get lost here is that our approach to measuring "color" differs from standard approaches. Our measure is designed to estimate how people are perceived by others in terms of "color" during everyday social interaction. To get such an estimate, we used ethnographic data about how people categorize others by "color" in southeastern Puerto Rico (see Gravlee 2005; the emphasis on locally relevant color categories is an important reason to avoid translating them as you did). So, yes, the categories are coarse, but we think they approximate the way people are perceived in day-to-day interaction -- which, as you argue, shapes exposure to racism and other social stressors related to blood pressure.

Thanks again for the nod to our paper. I look forward to other comments, questions, and criticism.

Dr. Gravlee, great paper. I'm annoyed at how few scientists have attempted this kind of methodology.

Perhaps I missed this in the paper, but my question concerns the correlation between socio-racial classification and education reported in your paper.

Did you check to see if genetic admixture predicted any economic or educational outcomes over and above what was explained by socially classified race?

Zeeb,

"Additionally, because most variance in between population complexion is controlled by only a half a dozen genes there is going to be a lot of noise in the correlation between skin color and ancestry. In this small sample of 87 individuals, 37 white, 31 brown and 19 black, assayed on 78 ancestrally informative markers, the correlation was 0.63."

Just to clarify (or reiterate Dr. Gravlee), "color" in this paper didn't refer to skin color, but to socio-racial classification from overall appearance -- which would probably involve many more genes of small effect related to facial variations (And probably to indicators of social class in the portraits, if racial classification in Puerto Rico is like some other non-US countries).

Racial admixture from skin color alone typically has a much weaker association with ancestry (average = .20), consistent with the small number of genes involved.

Scratch that, the association is higher than I remembered. Identical to the overall appearance association in Puerto Rico even:
"In the samples that were measured with the DermaSpectrometer, we observed a significant positive correlation between melanin index and Indigenous American or West African ancestry, but the strength of the relationship was quite variable: Puerto Rico = 0.633; African Americans = 0.440; African Caribbeans = 0.375; Mexico = 0.212".

"Years ago I read a book which was basically an ethnography of Brazilian culture, and in particular how blacks and whites related as a function of class. One of the illustrations of the travails of the lives of middle class blacks was a mother who told her children never to eat bananas in public, lest they be mocked by their white peers. The experience of racism by lower and middle class blacks was qualitatively different in this model. In particular, lower class blacks were often embedded in a predominantly black community and so could withdraw from interactions with whites, while middle class blacks were professionals who interacted with and lived with whites and so experienced stress and tension as a matter of course."

Thank you for stating this. I can tell you from first hand family experience that this type of thing also goes on in the United States. In fact, I have long argued that the black people in America who are so incensed by racism are not poor blacks, but middle class ones. In my experience (I am a black American) most poor blacks might believe there is racism, but often, outside of work their environment is completely black, so most of the time they do not speak about or probably think about racism. Middle Class blacks often associate with whites or in predominately white environments (especially upper middle class) most of the time, not just at work. They always have the experience of walking into a room that is predominately white, interacting with whites in the grocery store, restaurants, etc.

@Jason: We weren't focused on educational outcomes, and our data are limited to educational attainment (years or degree) and household income. But I just ran some quick-and-dirty analysis to look at how educational outcomes are associated with genetic ancestry and social classification. The short answer is that, once you include social classification, there is no association between genetic ancestry and years of education. Ditto for household income.

@Longman: I appreciate your comments about the unique stressors faced by middle class African Americans. There's a growing body of research that underscores your point. You may also be interested to know that my colleagues and I are doing new ethnographic research now on the types of stress blacks of varying socioeconomic backgrounds face in their day-to-day lives. We will use what we learn to develop better measures of stress exposure among African Americans, and within a couple of years, we should be able to say more about how the experiences you mentioned (e.g., being in predominantly white environments) relate to the risk of high blood pressure and other stress-related outcomes.

"The short answer is that, once you include social classification, there is no association between genetic ancestry and years of education. Ditto for household income."

Thanks! You realize that that has important implications for sociology. I would strongly recommend publishing it.

LongMa

Interesting observation. What immediately came to my mind was Seasonal Affective Disorder where incidence of seasonal depression increases with increased latitude I have not seen racial breakdowns for this.
Since the causes are unknown and open to armchair theorizing.
I would imagine that other non-depressive symptoms might be found as well.
It is well know that in our Society, while myriads of findings of racial differences may be noted, any attempt to generalize such differences evoke the Thought Police.
We do know that identification with Tribe is quite important in Africa. But little studied is the . And psychological effects of separation from one's tribe. And whether this varies by race. Differences in anxiety level while in alien corn would produce differences in hypertension.

Clarence C. Gravlee:

That would be a very interesting study that I look forward to reading. I think one area you might look into with middle class blacks (and up) is the work place, especially if they are white collar workers, specifically when blacks interview for jobs with white hiring managers. Also, when blacks are up for promotion. When blacks are concerned with appearing not to understand something so they keep quiet and may only mention it to another minority or some white person they trust. I have known blacks that are fairly paranoid in the office about how they are perceived, especially black men. For example, I know quite well that most African Americans feel that their negative behavior will be seen as more threatening or just far more negative than a comparable white person so they are often on guard. They feel they can not afford outbursts for example, even if a white man who is fairly popular in the office acts like this. As my friend once said, "we all know what we can get away with and what we can't compared to them". Blacks also worry about being discriminated against in terms of the assignments they are given or the career path they might feel they are being pushed into (often dead end grudge work). Some times it is just as simple as not being invited to lunch by white colleagues. I know one guy who has kept the fact his wife is white to himself for fear his predominately older white male management will respond negatively to him. I realize some of these things might sound paranoid or silly, but if one of these things happens to you once, you stay on guard and it is reinforced by the stories of other peers.

You might also look into blacks that have a significant number of white friends and when something is brought up, often race-related or even possibly about president Obama and his/her white peers have a different perspective what is their response. In my experience they often feel whites don't understand and keep it to themselves or maybe respond the opposite and get vary emotion. Most of the time the whites just defer for fear of appearing racist. I think this factor is a major reason why many blacks often do not associate with whites and specifically seek out other blacks to associate with even if they have to go out of their way, because they don't feel as stressed about interacting, the same might be true of whites as far as their association with blacks as well.

Argentina, the indigenous foremothers

razib — Mon, 24 Aug 2009 22:08:21 +0000

Argentina, the indigenous foremothers

Dienekes points to a new paper, Amerindian mitochondrial DNA haplogroups predominate in the population of Argentina: towards a first nationwide forensic mitochondrial DNA sequence database:

The study presents South American mitochondrial DNA (mtDNA) data from selected north (N = 98), central (N = 193) and south (N = 47) Argentinean populations. Sequence analysis of the complete mtDNA control region (CR, 16024-576) resulted in 288 unique haplotypes ignoring C-insertions around positions 16193, 309, and 573; the additional analysis of coding region single nucleotide polymorphisms enabled a fine classification of the described lineages. The Amerindian haplogroups were most frequent in the north and south representing more than 60% of the sequences. A slightly different situation was observed in central Argentina where the Amerindian haplogroups represented less than 50%, and the European contribution was more relevant. Particular clades of the Amerindian subhaplogroups turned out to be nearly region-specific. A minor contribution of African lineages was observed throughout the country. This comprehensive admixture of worldwide mtDNA lineages and the regional specificity of certain clades in the Argentinean population underscore the necessity of carefully selecting regional samples in order to develop a nationwide mtDNA database for forensic and anthropological purposes. The mtDNA sequencing and analysis were performed under EMPOP guidelines in order to attain high quality for the mtDNA database.

Unlike Mexico or Venezuela Argentina does not conceive of itself as a mestizo nation. In fact, it is not even primarily a Spanish-ancestry nation, because of the large contingent of Italians, as well as significant minorities of immigrants from Western and Northern Europe. And yet this is not an isolated finding, a large proportion of the mitochondrial lineages of Argentines seem to be of Amerindian origin. How can this be with the known waves of immigration and Europeanization of the country in the 19th and 20th centuries? I've discussed the likelihood of strongly male-biased immigration, replacing the indigenous autosomal and Y chromosomal genetic material, and leaving much of the direct-line female lineages intact.

Cite: International Journal of Legal Medicine, 2009 Aug 13, DIO:10.1007/s00414-009-0366-3

razib Mon, 08/24/2009 - 18:08

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Obesity inversely correlated with European ancestry among African Americans

razib — Fri, 22 May 2009 06:23:09 +0000

Obesity inversely correlated with European ancestry among African Americans

It is well known that different ethnic groups vary when it comes to diseases such as Type II Diabetes. Or, more specifically they vary in terms of risk, all things equal (if you use an online Type II Diabetes calculator you'll see immediately as they sometimes have a parameter for ethnicity). American blacks for example are heavier than American whites. This seems to be true even when you control for socioeconomic status (though as Oprah once said, "You don't need to do a 'study' to figure that out"). There has been research on genetic loci correlating to obesity in European populations before, but there is now a new one which looks at African Americans, and tries to ascertain whether some of the loci might be unique to them because of their racial ancestry.

Admixture Mapping of 15,280 African Americans Identifies Obesity Susceptibility Loci on Chromosomes 5 and X:

Obesity is about 1.5-fold more prevalent in African Americans than European Americans. To determine whether genetic background may contribute to this observed disparity, we scanned the genomes of African Americans, searching for genomic regions where obese individuals have a difference from the average proportion of African ancestry. By examining genetic data from more than 15,000 African Americans, we show that the proportion of European ancestry is inversely correlated with BMI. In obese individuals, we detect two loci with increased African ancestry on chromosome X (Xq13.1 and Xq25) and one locus with increased European ancestry on chromosome 5 (5q13.3). The 5q13.3 and Xq25 regions both contain genes that are known to be involved in appetite regulation. Our results suggest that genetic factors may contribute to the difference in obesity prevalence between African Americans and European Americans. Further studies of the regions may identify the causative variants affecting susceptibility to obesity.

The sample here is ~20% European in ancestry, in line with a large body of research on African Americans. Additionally, there is variance in the black community in terms of how much European ancestry an individual has (e.g., a rule of thumb is that around 10% of black Americans are actually 50% or less African in ancestry). This study find a weak but statistically significant negative correlation between European ancestry and Body Mass Index (BMI), Ï = â0.042 & P = 1.6Ã10^â7. Here's the figure (modified to fit on the screen) which illustrates it:

Let's jump to the part on where they find associations between obesity and particular genetic variants:

The residual association of local ancestry with BMI after adjusting for genome-wide ancestry remained significant at both Xq13.1 (P = 1.9Ã10â7) and Xq25 (P = 4.1Ã10â6) (Model 2 in Table 3), indicating that local ancestry had an effect on BMI above and beyond genome-wide ancestry. Both associations were nominally genome-wide significant (P = 1.9Ã10â4 and P = 4.1Ã10â3) after conservatively correcting for 1,000 hypotheses tested. A naive analysis suggests that each additional copy of a European ancestral allele at either the Xq13.1 or the Xq25 peak is independently associated with a BMI decrease of ~0.1 Z-score units on average (equivalent to ~0.64 kg/m2 and accounting for 0.3% of the variance in BMI, after adjusting for age, age-squared, sex and study). The true genetic effects are expected to be somewhat weaker because of discovery bias.

There was a weak correlation between total European genome content in African Americans. But here what they have found are possible genetic regions with elevated European ancestry, that is genes which are distinctively European in form which some African Americans carry. These genes seem to correlate with reduced BMI. The key point is that you have to zoom in on a finer grained level genomically because total ancestry isn't always going to be a good predictor. But here's an interesting find:

The association at the 5q13.3 peak was particularly interesting in that it did not achieve statistical significance until the genome-wide estimate of European ancestry was added into the analysis. This was presumably because the locus effect was in the opposite direction to the genome-wide ancestry effect (thus, the effects cancel in the unadjusted analysis). Each additional copy of a European ancestral allele at 5q13.3 was significantly (P = 5.8Ã10â7) associated with an increase in BMI of 0.09 Z-score units (naively equal to ~0.59 kg/m2, accounting for 0.3% of the variance in BMI), which was nominally significant (P = 5.8Ã10â4) after correcting for the approximately 1,000 independent hypotheses tested.

In other words, the overall trend obscured this particular signal. In any case the authors note that there is research which suggests that obesity is ~40% heritable, so those heritable genetic components may vary between populations (as well as within). Studies in diverse populations, including admixed ones, obviously are going to be important pieces of the puzzle.

Citation: Cheng C-Y, Kao WHL, Patterson N, Tandon A, Haiman CA, et al. (2009) Admixture Mapping of 15,280 African Americans Identifies Obesity Susceptibility Loci on Chromosomes 5 and X. PLoS Genet 5(5): e1000490. doi:10.1371/journal.pgen.1000490

razib Fri, 05/22/2009 - 02:23

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Studies such as this are needed in the fight against disparities in the African American community. As a diabetes educator I am often asked why African Americans develop type 2 diabetes at a greater rate then their European counterparts....this helps to answer that question.

And I wonder if the European ancestry they have is Northern European.

I really don't think obesity is related to race. It's just related to your diet. So right diet is the most important. Here is about Chinese holistic diet.
http://www.healthy-chinese-recipe.com/obesity-diet-recipes-low-fat-low-…

Hey Mary,

1) What you 'think' -- or believe you must think -- is not a good reason to criticise a paper, you need to come up with different proof, i.e. scientific research, backed up with logic and plausibility. You don't do that. ("Chinese holistic diet".. Are you kidding me?)

2) Low-fat & low calorie diets never work in the long run. You'll always be hungry and finally you will eat again -- move back to your old weight (and then some.) If blacks want to lose weight for real, they should, like any obese human, move on to a high fat/protein diet.

But, but, but I thought that Sandra Scarr disproved that percent European ancestry was a relevant explanatory variable with her sample of size 144! How could these thought criminals have decided to include it as a colum in the regression equatoin?

I will give you a real possibility, sorry no stats. I remember when a marshmallow was a marshmallow, do you? Have you tried to roast a marshmallow lately, good luck? What has happened to the good old marshmallow, the same thing that has happened to most of our food. When we were not paying any attention they took the marshmallow out of marshmallows but kept the price moving gradually upward. What is in the marshmallow today, artificial colour, artificial flavour, corn syrup, dextrose, gelatin, modified corn starch, sugar, tetrasodium pyrophosphate, sounds like a gut bomb to me. It still looks like a marshmallow and they still call it a marshmallow but it is obviously not. This kind of slow changing of ingredients has gone on food industry wide; it remindes me of the Trojan horse. Now suddenly everyone is noticing that gee, we have an obesity epidemic and a whole lot of other epidemics. Genetics is the weak answer medical science wants you to buy into so they can research it and make more drugs. Besides, how does the genetics of an entire country change in a matter of years? I am sure that your doctor cares but does the industry care? Why should they care; more sick people means more money in their pockets. Try this; on a piece of paper write down 10 diseases you can think of then do a Google search of each one of them and add the word epidemic to it. You will see that the majority of them are at epidemic numbers of 1 in 4 people will get this disease. If you think that this is ok; then you must be on a lot of drugs yourself. Paul

This post sure seems to be attracting interesting comments, so let me throw one out also: we don't know if the difference in BMI is due to difference in fat mass or the fact that white folk have flat asses. More European ancestry may well just mean a couple pounds less muscle in the glutes.