May 02, 2009

Fine-scaled human genetic structure (Xing et al. 2009)


Our picture of global genetic variation becomes ever more clear. In this study -the supplementary material of which are online- the researchers studied 240K loci in 554 individuals from 27 populations.

From the paper:

The African, East/Southeast Asian, European, and Indian individuals are correctly assigned to their self-identified continental groups without exception.

Some individuals show evidence of membership in multiple groups. South Indian upper- and lower-caste populations have ∼30% and 10% membership in the inferred European group, respectively. South Indian tribal Irula have a relatively high probability of membership in the inferred Indian cluster. Southeast Asians (Iban, Cambodians, and Vietnamese) have ∼10% membership in the inferred Indian cluster, and the African Hema cluster shares ∼15% membership with the inferred European cluster.


The Hema are Nilotic-speaking pastoralists from the Congo. The Alur, from the same region were also studied.

Social stratification based on "European" (more properly extra-Indian Cauasoid) ancestry in South Indian populations is not surprising; see my post on the Origin of Hindu Brahmins. Differential -based on caste- admixture with an exogenous element is not really compatible with an indigenous creation of the caste system, and is more in accord with the traditional theory of an exogenous origination of the upper caste populations.

The study also includes populations from the Caucasus (Stalskoe and Urkarah) from Daghestan, which group with HGDP Adygei (see Figure S3C) and are clearly (FRAPPE analysis in Figure 4, reproduced top left) transitional (as mentioned in my previous post) between European and Indian Caucasoids, although quite clearly more on the European side.

Genome Research doi:10.1101/gr.085589.108

Fine-scaled human genetic structure revealed by SNP microarrays

Jinchuan Xing et al.

We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

Link

20 comments:

Maju said...

Pretty interesting. Though K=7 is pretty much limited when studying the World, I guess.

The most intersting novel elements are the minority (substrate?) components (at K=7) in India and SE Asia, embodied best by the Irula and the Iban respectively. Also the presence of some 20% "European" (or is it West Eurasian?) component among Indian Brahmins (and not the rest) appears to confirm the Indo-European invasion model. This NW component is also found at similar apportions among the Hema of East R.D. Congo (where it should have arrived from North Africa or West Asia, I guess).

South Central Haplo said...

This is complete waste paper after all these days.
The data is atleast 5 year old or more.

Sampling Andhra Brahmins and Tamil Brahmins and comparing with Europe is like taking a set of Mascoites and interpreting to whole Europe.

Dienekes Jumps on these topics whenever interpretation tilts to Europe and keeps absolutely silent selectively when he publishes diversity proof of India.

A new term extra-Indian Caucasoid coined by Dienekes. All the socalled Indian caucasoids came from where?.

No answer from anybody so far.

The so called causcasoids(Indian or even others) came from east of caucasas. Which is part and parcel of Indian sub continent/South Asia. They did not come from some place different or far. Please expalin where is this European ancestry came from?. Dont throw ideas around?. Genetic , Linguistic , Cultural traces are all from east of caucasus. close to indian Sub continent.


1. Social startification is built on top of existing triabl caste structure. This is published by people who spend years on reserchinng Indian cast structure inlcuding Europian researchers. Half Knowledge Dienekes(on this subject) keep saying differently does not change the fact. Exogenous elelments has taken advantage themselves . Just becuase of that you can not say the structure is built by them. It is like saying Greek orthodox chuch represent Christian/Jewish orthodoxy from Jerusalem.

There is some advantage for tribes who are living close to Himalayas on people with fair skin getting advantage with in South India. It is not different in south India or Polynesia or any part of the world. In India they became Upper priestly class. Still the phenotype or what you call whether it is Pakistan or Kashmir or the majority mt haplogroup is 'M and with population mainly local F+H+R2/R1a and M+U.

You published a paper on the same forum Majority of North Indian lower casts/Untouchables are of R1a haplogroup. At that time you were completely silent on the cast strucure. If there is an Aryan Invasaion they copied the cast structure and some of them got divided into lower casts. whyy not lower cast is the proof of caste structure? After all they are single biggest block of cast in India.

FYI: mala, madiga, dalit are so called un touchables. They have same admixture with So called caucasoids as brahmins in the same graph please see again.
That is Another proof this paper is waste of effort for India. If all the communities are from SOuth India and all of them including lower cast untouchables has the same Europian admisxture as per your own analysis . How do you make that basis for some social structure creation?.

Please learn little bit more about the subject you talk. Keep yourselfs to Europe and that will be good for you.
Also Follow the same logic for Albania/Greek or India. Dont change logic as per your own greek mythological beliefs.

Maju said...

A new term extra-Indian Caucasoid coined by Dienekes. All the socalled Indian caucasoids came from where?.

No answer from anybody so far
.

IMO from South Asia: they are native or mostly so. Indian people phenotypes appear mostly Caucasoid to me (a few in the far south may appear closer to Australoids maybe but they are both gradations in a continuum to a great extent, I think).

As far as I can tell, South Asian, East Asian and the various Sahulian phenotypes (and genotypes) diverged earlier at the first stages of Eurasian expansion. The expansion to the West (from South Asia) began precisely when the expansion to the East was being exhausted and the three (or four) eastern regions became pretty much isolated from each other.

But the flow to the west had just started and continued for a while. So the Western and Southern Eruasian phenotypes are much more similar, even ignoring recent flows like those from Neolithic or Bronze Age (which did reinforce the connection, of course), than they are to the Eastern Eurasian phenotypes (and genotypes).

This doesn't mean that there are not differences between the extreme Caucasoid types like North Europeans, North Africans or Southern Indians, but they all belong clearly to a continuum that has been flowing through the ages in both directions.

whyy not lower cast is the proof of caste structure? After all they are single biggest block of cast in India.

Precisely: their origins are quite diverse. They actually represent much better the bulk of Indians, because they make up (depending on what you call "lower caste", which is very unspecific for what I know) like 80% of the people, or maybe even more.

FYI: mala, madiga, dalit are so called un touchables. They have same admixture with So called caucasoids as brahmins in the same graph please see again.

They do have lower levels of the "European" cluster but you are right that they do have it pretty much visible anyhow.

I have read elsewhere that the famed Indoeuropean R1a1 is quite strong also among many low caste Indians, what implies that, even if it an outsider input, some IEs did end up as low caste. The reasoning I read is that they were originally of professions like leatherworkers, common among the nomads but considered impure in the Hindu caste system, but not sure if it's correct.

Please learn little bit more about the subject you talk. Keep yourselfs to Europe and that will be good for you.

I know this doesn't go for me but it's clear that we all should look everywhere, as our histories and destinies are interconnected. If you happen to know more about some area, maybe because you live in it or maybe because you have researched it in depth, you will be listened with interest by most (including Dienekes I believe). It's in exchange of information and also opinions where the real knowledge takes root and grows.

eurologist said...

I agree 100% with Maju.

Western expansion from northern Pakistan/India was late because the East was vast and easy. Modern humans needed to accumulate a much better tool set to make it in the western mountain valleys and plains, with their extreme seasonal changes in temperature and water availability, and with Neanderthals occupying some of the regions. Extreme Western Europe is only the genetic tip of the iceberg - from the beginning there was wider variability in western Asia, but decreasing westward, from Afghanistan, Turkmenistan, Iran, to the Caucasus and west - and that gradient is maintained until today - as shown in all published studies.

Except for the extreme south, modern Pakistani and Indians largely look Caucasoid/European because that is were Europeans originated from - not the other way 'round. How could anyone not see this?

Sure there were back migrations with agricultural advances and Indoeuropean expansion - but I would maintain that many of them came from adjacent regions with little phenotype or genetic difference from Northern Pakistan/India, in the first place.

Also, I am still not convinced that R1a1 is European (I think it is of Indian or northwest Asian origin), and so is R1b*, IMO. Those two just happened to dominate in the small, early groups that made it out of Northern Pakistan, and west from there.

Ponto said...

Don't agree with the theory, if that is what it is, of the origin of Caucasoids in the sub continent aka India/Pakistan/Bangladesh. Nor with the origin east of the Caucasus. Where does that theory come from? Mumbai perhaps. My interest when it comes to Caucasoids is confined to Europe and the Middle East. The Indid ones can go to hell in a pappadam, totally uninteresting. Only some Indians look Caucasoid.

The paper deals with many ethnic groups and racial affiliations not
just the bores from the sub continent. It is not a waste of paper but very informative. Most people want to know their true origins rather than a putative one based on prejudice and ignorance. Now when it comes to the origins of I.E languages the east of hell, sorry Caucasus, is fair enough.

R1a1 is European as far as age is concerned. Indian R1a1 is younger than Arabian R1a1. R1a is definitely Asian (from east of Europe), as it R1b, and I and just about every other haplogroup in Europe that is common there

Maju said...

@Eurologist: I think it was more a mere matter that the West was Neanderthal territory and they were much stronger and as smart as us... we needed to develope some skills or social organization to be able to face them with advantage, IMO. SW Asia was otherwise a good place to colonize and live in: it just had other owners.

@Ponto: "Caucasoid" is not a species but just a somewhat arbitrary phenotype category. It does not have to have a single orgin, as phenotypes also converge, not just diverge. The origin is nowhere but in coninuous interaction of people regionally.

But the origin of West Eurasians, excepting some minor inputs from elsewhere, notably Africa, is in South Asia by all the available genetic evidence. In fact, the origin of all original Eurasians, Sahulians and Americans. South Asia, and to a lesser extent SE Asia, were cradle of all non-Africans (and some Africans too).

IMO, the first flow was into the East and then the trend switched to the West as South and East Asia, as well as mainland Oceania went into relative isolation. So nearly all West Eurasian genetics come from South Asia (notwithstanding backmigrations) at a later period than East Asian and Sahulian ones. There are minor African and Siberian influences though but these belong to later periods and are not the core of any West Eurasian population.

R1a1 is European as far as age is concerned.

Only if you consider that east of the Volga is Europe. The Volga was the (admittedly arbitrary but consensual) boundary between Europe and Asia between the Caspian Sea and the Ural Mountains until some Russian Tsar decided otherwise.

For me it's East European/Central Asian (or West Steppary if you wish). There's no specific boundary between Europe and Asia overall much less in that region.

R1a is definitely Asian (from east of Europe), as it R1b, and I and just about every other haplogroup in Europe that is common there.

I could perfectly have began expanding in Europe (but not IJ). R1b has a West (SW) Asian origin by all accounts but R1a is probably South Asian by origin, as were the precursor stages R1 and R (and possibly P too).

Dienekes said...

The evidence is quite clear that these Indians have admixture with Western Eurasians (light blue; what I called extra-Indian Caucasoid). Moreover, this component is most prevalent in the Brahmins.

This parallels the situation for Brahmin Y-chromosomes which are about half to three quarters of Western Eurasian origin. As Western Eurasian mtDNA is much rarer in comparison, this translates to about 1/4 to 3/8 overall Western Eurasian admixture, which is precisely what we see in this study.

wolcupitol said...

Jesus Christ these God damn studies. This is the first time I've seen a result from an autosomal study that I just can't understand. They say that Brahmins have 20% European cluster, but other people in India don't? What the hell??? That flies in the face of everything found out about India so far. Rosenberg studied 20 groups from every corner of India and they were so homogenous they couldn't be told apart. And the distances between north and south were just 0,0050, not 0,0121 as in the other God damn study found between Dravidians and non-Dravidians. And that other study also found that the distance to Europeans ranged from 0,0250 in north India to 0,0500 in south India!? that's just insane. That just doesn't make sense. These people are more homogenous than Europeans. Europeans have a genetic distance of at most some 0,0070 FST from corner to corner. These results are just ridiculous. God damn it. This is the first time I really can't understand the results of an autosomal study. These results simply don't fit. they don't add up. So there's hundreds of millions of Brahmas or whatever those things are walking around who are 20% European and the rest of the country has 0% of this European ("European") cluster??? How did they manage this for 3,000 years ??? What the hell?? God damn study. This is actually kind of making me mad! Ha ha. It's messing up the nice picture I've built up of the genetic make-up of the world. This is just bizarre. Nothing makes sense. God damn it...

One of these 2 studies seems to not know very well how to use that STRUCTURE program. The one with the Mexicans, whenever it shows a STRUCTURE result, it's ok for the first few K, but then at the end it adds a couple of K layers in which the new clusters are bizarre garbage that runs like a ghost line in the background of all the samples. Do these people know what they're doing?

And the inclusion of the totally mixed-up people of Mexico is kind of a dumb thing to do. There's 3 times as much Spanish dna in the Mexican samples then in the Spanish samples, so if the STRUCTURE program identifies a Spanish-specific haplotype, it will assign it instead to the yellow Indian cluster, since it will be more common in the Mexico samples than in Spain.

But it doesn't end there! No!! They even split India into 2 clusters, a Dravidian and non-Dravidian cluster. Jesus Christ. So now India is a super-heterogenous country?? A 180º change from all studies up to now, that were saying it was the most homogenousplace in the world, more than Europeans?!? Where the hell did all this come from? Did they confuse the samples with another continent ?? Did I say god damn about these studies, already?


argiedude (grrr...)

Maju said...

So there's hundreds of millions of Brahmas or whatever those things are walking around who are 20% European and the rest of the country has 0% of this European ("European") cluster???.

That is not what the graph shows: it shows that southern Bramins have like 20-30% of the Euro (West Eurasian probably in fact) component and that Dalit samples in the same area have c. 10% (10-20% in the case of Madigas), the Dalit groups also have somewhat more East Asian component among them than the Brahmins. The only exception are the Irula tribe who appears as the best representative of the "pure" South Asian comonent, with almost no presence of Euro or Eastern components.

An issue that may have been ignored here is that Dravidian brahmins are mostly of northern ancestry. AFAIK Dravidians were never really structured into castes properly and their kings and warriors were all sudras (that elsewhere would be the low caste). Sudras take all social positions among Dravidians except that of Brahmins, which are essentially a foreign (northern) caste. Hence their greater ammount of Euro genetics may be (also) because they are northerners (by origin) and not just because IEs "tainted" the brahmin blood with "foreing impurities". It may reflect a north-south cline rather than a caste cline.

Also the lack of sudras (nearly 80% of Dravidians are Sudra) or other middle castes, really limits the scope of the comparison, as these groups can only represent at most 25% of the population, and are their extremes not any middle sample.

Dienekes said...

That flies in the face of everything found out about India so far. Rosenberg studied 20 groups from every corner of India and they were so homogenous they couldn't be told apart."This result differs somewhat from that of a previous study in which little genetic structure could be detected among 15 Indian populations (Rosenberg et al. 2006). Several factors may be responsible for this difference. First, the number of markers used in the Rosenberg study (1200) was much smaller than the number used in our study. Second, because all individuals sampled in the Rosenberg study were Indians living in the United States, their data set was likely biased toward upper-caste individuals and thus less likely to detect the effects of caste or tribal membership. Finally, the Rosenberg sample contained individuals from all regions of India, while our sample was derived only from South Indian populations."

Polak said...

argiedude,

The STRUCTURE graph in the Auton et al. study only goes up to K=5.

The supplement has K=6 and K=7 included to show that they're of no practical use in this case.

homerun43 said...

Lol these studies always make me laugh! I’m not a geneticist, however understanding the research you have to take into a vide variety of factors to know how it was contrived. A number of scholars have done thorough and accurate research into the genetics of South Asia.

Being from Canada, and our family from upper castes in Panjab and Uttar Pradesh ..Let me tell some of you none-South Asians who correlate eye or skin colour, or some studies with genetics…

…Even though our family has always been from India, people always assume my mom is Scottish or European (because she has a slight accent, red hair because she uses henna, her skin is white (white white) and features similar to Russians (nose ears jawline, etc, etc.). Her eye colour is also a mix of brown-violet-blue but is very dark like brown, and even some of my cousins have green eyes. It’s common in North India and Pakistan, Parts of Iran to have light eyes like light brown, hazel, green eyes, and we even know lots of people who have dark blue eyes from Panjab. It’s kind of like how some Italian families have 2 siblings. One has blonde hair and brown eyes and the other one I know has dark brown hair, light brown skin, but green eyes, but looks Italian. And also read the “Real Eve: Modern Man's Journey Out of Africa” by Oxford University scholar Stephen Oppenheimer. Case Closed.

Polak said...

^ WTF?

These markers test genetic ancestry, not pigmentation traits.

For pigmentation you'd need to look at genes like HERC2, and not just any SNPs all over the genome.

Although genetic ancestry does correlate with pigmentation to a large degree, it doesn't determine the precise results for individuals.

South Central Haplo said...

The Irula are the major source of proof for southern migration theory. A nomadic tribe. With majority Y haplo C and mt haplo M.

So they are mostly Indian. that is the ridiculeness of this paper.

Brahmin has some or majority R1a/R2 so they are 1/4 West Eurasian admixture. Even if that R1a/R2 is of local source.

I remember Dienekes calling Mongoloid influenced R1a some time back. By that logic East Europe is 1/2 South Asian/ Asian Admixture.

Maju said...

Y-DNA R2 is not West Eurasian. In fact R as whole is most likely South Asian.

MtDNA M is a macro-haplogroup but anyhow there are few places other than South Asia where is more common.

By that logic East Europe is 1/2 South Asian/ Asian Admixture.

Nope. Even if R1a is South Asian (at some point in the deep past) Y-DNA does not normally reflect well the overall ancestry. MtDNA normally does that much better. Y-DNA is too much subject to drift and male-only founder effects (sex biased by elite dominance - or just a nice face and arse maybe). Female heritage cannot drift so much ever.

I generally have the following rule of thumb when autosomal data is not clear: 1/2 of total ancestry are represented by mtDNA, up to 1/4 by Y-DNA maybe, and the rest is unknown.

So if your Eastern Europeans are 50% R1a (what is not real, it's more like 40% maybe) and (we assume) R1a is South Asian by origin, they would be only 10% South Asian (not more than 20% in any case) by my system.

Anyhow all West Eurasians are ultmately of South Asian origin, except for minor African and East Asian inputs. It's not like we evolved here for millions of years, you know.

homerun43 said...

Sorry Polak, I should have said it more clearly but was in a hurry to get to class.

I was just trying to get the point across that people for a few hundred years have basically rewrote history to their definitions.

Mainstream consensus among scholars is that the modern "Out of Africa" theory is the correct one. Read Stephen Oppenheimer's book. Genetics and Archeology are firmly established.

Just like how the foundations of Calculus are now mostly agreed upon by academics to have originated in India (same as the numeral system, first surgical text, and how about the evidence of teeth being drilled close to 10,000 years old found in Pakistan?) and electric generation was known more than a 1000 years earlier by the former Persian Empire (in Babylon I believe), and the list goes on....

It's called Eurocentrism and has been a problem for a couple of centuries. Just like people assume India and China were always poor, when the facts are they were the richest regions historically over the last 2000 years (at least)(Maddison).

Things take time, like the Genetic discussion, but will get corrected.

Ponto said...

To get away from the Indians, yawn.

I was please to see the Cambodians accurately displayed showing both the Indian component and the Australoid component.

The Stalskoe inhabitants, Kumiks, show their Mongoloid component. It is surprising to see an Australoid component in Europeans.

Maju said...

It is surprising to see an Australoid component in Europeans.

What "Australoid" component? There're no Australoids sampled - at most Negritos (arguably the Irula, though the pics I've seen they look Caucasoid for the most part), what is surely a totally different thing.

Anyhow, Australo-Melanesians do show phenotypic traits that are also visible among West Eurasians, like prominent noses in Papuans or blond hair in Australian Aborigines and Island Melanesians. Western mtDNA shows some long distance connections (like N2, of which W is derived - but there are a few more) with Australia.

Not so surprising, assuming (what is a lot to assume) that the blue component dominant at the Irula and important through South Asia can be called "Australoid". More surprising IMO is to find it among some African peoples.

pconroy said...

Maju,

I'm not surprised that the "blue" is found among East Africans, in small amounts. As there was a great deal of circum Indian Ocean trade in times past.

Also, I've read reports of Australoid or Veddoid types being found in the Hadhramaut region of Yemen, and it is from around there that much of the Indian Ocean trade was mediated, with stop overs all along the East African coast, like Zanzibar, where an admixed (East African + some Yemeni) population arose speaking Swahili.

homerun43 said...

This study is pretty bogus, as the analysis of many other studies, it's not impartial.

Where is the West Asian, Middle Eastern, and Central Asian inputs??? That's would probable bridge this gap. How about individuals samples and results of this cluster analysis??

This cluster sample would seem more plausible - http://upload.wikimedia.org/wikipedia/commons/f/f9/Rosenberg2007.png