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Why is no one talking of sample size and sampling strategy of all the studies that have been done? MOst of these studies are poor in terms of design and not much generalisations can be made from them.== Tocharians == This article probably could benefit from some reference to (or at least a link to) the Tocharian people

Borderline if they can be included in the "south asia concept" but as india seems to belong here, and the Tocharians probably had some contact there on their way to the east of China....

Even if they did or did not in the end contribute many genes they can stand as an example of the migrations from Europe to Asia that were taking place. And it's nice that we have physical relics of them, mummies and colour depictions.

Then there are the genetics of the Berber people and the Guanche People, who also seem to have had that funny looking yellow hair and seem to have been lodged outside their normal realm, but they are in africa hence by far outside the scope of this article.

Would take a shot at it myself if I were not so lazzzzy.

Removed copy from Bamshad et al. study

A user 71.195.221.190 has copied a large portion from Bamshad et al. study. This is irrelevent here as the it was just one of the studies also the first one to explore it. The details of the study has been included under mtDNA and Y-chromosome headings. In fact, many of the data from the study is patently incorrect, such as mtDNA U2i as proved by the later Kivisild et al. study(2003). So we don't have to consider that primitive study as the final word on caste genetics.

Manjunatha (23 Apr 2006)

Removed the following:

It is certainly agreed upon by most antoropologists that most Indians, whether "Dravidian" or "Aryan" are still members of the Caucasiod race as per their skull-structure and genes.

Egon Freiherr von Eickstedt Template:Von E. Eickstedt racial definitions

--- skull-structure? and his theories are linked to some dodgy 'white race' page.. It should be clear that the existence of a specific genetic marker Haplogroup R1a1 (Y-DNA) does not necessarily relate to the appearance (skull-structure) or colour of skin of a person. Even though it is interesting to see how the genes distribution is consistent with the thus far lingustically theoretical Proto-Indo-Europeans But note that the article's links are considere pseudo-science and that this is a highly controversial field... As of 1999, most Physical Anthropologists disagreed that there are any physical existing 'races' that differentiate the human race.

Max Nemo 28/02/07

Text

Maybe this text (from Indo-Aryan migration article) can be merged here: There has been significant progress in genetic studies of the Indian caste populations in the last five years (as of 2006); this has implications for the Indo-Aryan migration/invasion theory. The studies could be broadly classified into pro-racial and pro-cultural.

The genetic studies are ongoing with conflicting results: those that support an infusion of genetic material {Bamshad et al.(2001), Spencer Wells, Journey of Man(2002), Basu et al. (2003), Cordaux et al.(2004)} (pro-racial) and those that don't {Kivisild et al.(2003), Sengupta et al.(2005), Sahoo et al.(2006)} (pro-cultural). A final picture will emerge after critical and comparative analyses of these studies.

The pro-racial construction studies maintain that there exists "Aryan" Y-lineages in Indian(especially upper caste) population. The age of these Y-lineages in India coincided with the putative Aryan invasion period in their studies.

The pro-cultural construction studies argue that the lineages identified with the "Aryan" are in fact more diverse in lower caste and tribal populations even though their frequency is lower. Their studies came to the conclusion that most of Indian Y-chromosomes date back to late pleistocene.

Interestingly, western Eurasian mtDNA haplogroup U2i in pro-racial Bamshad et al. study turned into Eastern Eurasian(mostly India specific) in pro-culture Kivisild et al. study.

However, there are still doubts exist over autosomal admixture analysis. It is also suggested that Indian marital traditions may have an impact on the calculation of age of Indian Y-haplogroups.

The genetic views on race differ in their classification of Dravidians. Most modern anthropologists, however, reject the genetic existence of race, like Richard Lewontin who states that "every human genome differs from every other", showing the impossibility of using genetics to define races. (Biology as Ideology, page 68). According to population geneticist L.L. Cavalli-Sforza of Stanford, almost all Indians are genetically Caucasian, but Lewontin rejects the label Caucasian. Cavalli-Sforza found that Indians are about three times closer to West Europeans than to East Asians. Genetic anthropologist Stanley Marion Garn considers the entirety of the Indian Subcontinent to be a "race" genetically distinct from other populations. Others, such as Lynn B. Jorde and Stephen P. Wooding, claim South Indians are genetic intermediaries between Europeans and East Asians. Recent studies of the distribution of alleles on the Y chromosome, microsatellite DNA, and mitochondrial DNA in India have cast overwhelmingly strong doubt upon any biological Dravidian "race" as distinct from non-Dravidians in the Indian subcontinent. This doubtfulness applies to both paternal and maternal descent; however, it does not preclude the possibility of distinctive South Indian ancestries associated with Dravidian languages.

Possible error

From the mtDNA section:

Virtually all modern Central Asian MtDNA M lineages seem to belong to the Eastern Eurasian (Mongolian) rather than the Indian subtypes of haplogroup M, which indicates that no large-scale migration from the present Turkic-speaking populations of Central Asia to India (and vice versa) could have occurred (Kivisild 2000).

This might be clarified. Migrations were sometimes mostly comprised of males, esp if migrations of conquest, Therefore the lack of Turkic mtDNA does not necessarily mean there was n;t any substantial migration of Turkic men into India Hxseek (talk) 08:36, 20 January 2008 (UTC)

this is correct. we cannot draw our own conclusions. we need to phrase this along the lines of "Kivisild (2000) conclude ..." provided the conclusion is in the paper. Otherwise remove. dab (𒁳) 09:18, 20 January 2008 (UTC)

Bunch of stuff

Transfering incoherent material from Indo-Aryan migration#Physical anthropology. Some of it seems to be in the article already; whether any sense can be made of the rest remains to be seen.

However (Kivisild 2003a; Kivisild 2003b) have revealed that a high frequency of haplogroup 3 (R1a1) occurs in about half of the male population of Northwestern India and is also frequent in Western Bengal. These results, together with the fact that haplogroup 3 is much less frequent in Iran and Anatolia than it is in India, indicates that haplogroup 3 found among high caste Telugus did not necessarily originate from Eastern Europeans. The high diversity of haplogroup 3 and 9 in India suggests that these haplogroups may have originated in India (Kivisild 2003a). Studies of Indian scholars showed the R1a lineage forms around 35–45% among all the castes in North Indian population (Namita Mukherjee et al. 2001) and the high frequency of R1a1 present in the indigenous Chenchu and Badaga tribes of South India making the association with the Brahmin caste more vague. However, a model involving population flow from Southern Asia into Central Asia during Paleolithic interglacial periods with a subsequent R1a1-mediated Neolithic migration of Indo-European-speaking pastoralists back into Southern Asia would also be consistent with these data. A further study (Saha et al 2005) examined R1a1 in South Indian tribals and Dravidian population groups more closely, and questioned the concept of its Indo-Iranian origin. Most recently Sengupta et al. (2006) have confirmed R1a's diverse presence including even Indian tribal and lower castes (the so-called untouchables) and populations not part of the caste system. From the diversity and distinctiveness of microsatellite Y-STR variation they conclude that there must have been an independent R1a1 population in India dating back to a much earlier expansion than the Indo-Aryan migration. The pattern of clustering does not support the model that the primary source of the R1a1-M17 chromosomes in India was a single entry of Indo-European speaking pastoralists from Central Asia. However, the data are not necessarily inconsistent with more complicated demographic scenarios involving multiple entries in both Paleolithic and Neolithic periods and two-way population flows into and out of South Asia. In addition, there remains a difference in haplogroup prevalence between present day Indo-Aryan and Dravidian speakers and between upper and lower castes. The preponderant haplogroup amongst a proportion of Indo-Aryan populations and upper castes is R (both R1a and R2) and, amongst tribal groups and lower castes, to a higher extent Dravidian ones, it is haplogroup H (Y-DNA). The high prevalence of haplogroup R1a (around 50-60%) combined with the relatively low prevalence of haplogroup H in the northwestern portion of the subcontinent (northwestern India and present-day Pakistan) also suggests an affinity between this part of the subcontinent and the Central Asian steppes, perhaps brought about by longstanding two-way population flows. The absence of haplogroup R1b (Y-DNA) in Indo-Aryan and Dravidian populations which is found in all other Indo-European populations, in especially large proportions in western Europe, may suggest significant levels of native genetic base for the Indo-Aryan peoples compared to other Indo-European peoples. However, it must be noted that R1b is also not present in significant levels in Slavic and Central Asian populations.

Bafflegab at its finest. rudra (talk) 07:19, 22 January 2008 (UTC)

Haplogroup L

There is a whole paragraph that looks as self-research (and obviously lacks of any sources):

Most of the pro-migration papers imply that R1a1 is the genetic marker that is representative of a migration, due to its high frequency in Eurasia. But an equally likely genetic marker is haplogroup L. This haplogroup is present in Greek, Turkish, Lebanese, Iranian, Central Asian, and Indian populations (and Europe, see Kivisild). This marker is found in locations where written sources record the presence of Indo-European languages and people: i.e. Greeks, Hittite, Mitanni, Iranians and Indians. Its peak frequency is found in Indo-Iranian populations. The 'Western Eurasian' components that are found in Indian mtDNA show a distribution closer to that found in the Southern Caucasus and Middle East than to that found in Eastern Europe. There is also the question of why one should assume only one Y haplogroup is representative of the Aryan gene pool. R1a1, R1b, J2, L and H - all of which are present in India and Central and West Asia - are all possibilities. However, haplogroup L has a very low level of diversity in the Punjab. This is suggestive of a recent migration or expansion event in the area, and is supported by the fact that the diversity of R1a1, J2 and haplogroup C is higher in the region. Haplogroup C is supposed to be the remmants of the "Out of Africa" migration of humans, but still retains a high level of diversity. Haplogroup L is also found in South India at relatively high freqencies and has been associated by some (along with J2) with the spread of farming and Dravidian languages. However haplogroup L1 is the dominant one in southern India, hence may represent an expansion event in the South (or elite dominance from the North).

Haplogroup L does exist in Western Asia (Iran, Turkey) , but it is quite rare. It doesn't seem to justify the hypothesis expressed above and in any case, it should not be self-research but the elaboration of an academic opinion.

H is not present (except maybe erratics and the well known case of the Roma people) outside of South Asia.

And I really don't understand why macrohaplogroup C (most common in NE Asia and Oceania) is even mentioned in that context, really.

Overall the paragraph looks a very good candidate for deletionist practices. --Sugaar (talk) 08:25, 10 March 2008 (UTC)

Rosenberg et al.

This article has the much-reproduced graph of populations vs. 7 genetic clusters (Image:Rosenberg2007.png) from the recent Rosenberg et al. paper but the article text has no discussion of the results of the paper.

It is based on 1200 polymorphisms across the whole genome, while all the genetic discussion currently in the article is based on very restricted, much smaller sets of DNA that are only inherited through matrilineage (mtDNA) or patrilineage (Y-DNA); or on single autosomal genes. Including it would modernize this article into the genomic era.

Here are some representative quotes:

• "Populations from India, and groups from South Asia more generally, form a genetic cluster, so that individuals placed within this cluster are more genetically similar to each other than to individuals outside the cluster. However, the amount of genetic differentiation among Indian populations is relatively small. The authors conclude that genetic variation in India is distinctive with respect to the rest of the world, but that the level of genetic divergence is smaller in Indians than might be expected for such a geographically and linguistically diverse group."
• "We found that allele frequencies in India showed detectably greater similarity to populations in Europe and the Middle East than to those in East Asia (Figure 4). This result is consistent with the fact that the cluster corresponding to India in Figure 2A subdivides a previously obtained cluster corresponding to Europe, the Middle East, and Central/South Asia ."
• "The only population whose Fst values within India substantially overlapped those of either Europe/Middle East or East Asia was the Parsi population."
• "Compared to groups that speak Indo-European languages, the groups in our study that speak Dravidian languages (Kannada, Malayalam, Tamil, and Telugu) did not show noticeably different patterns of pairwise F_st values, and in particular, they did not show a greater F_st from populations of Europe and the Middle East (Figure 5)."
• "European allele frequencies are often reasonably predictive of frequencies in India, particularly for microsatellites (Figure 7A and 7C). The correlations are increased by using a linear combination of allele frequencies with ~2/3 contribution from Europe/Middle East and ~1/3 contribution from East Asia (Figure 8). At the same time, however, the separate cluster for India in population structure analysis indicates that allele frequencies in India are distinctive, so that predictions obtained based on European and East Asian groups cannot fully explain allele frequencies in Indian populations. This comment applies particularly for the indels (Figure 7B and 7D)"

--JWB (talk) 00:12, 8 August 2008 (UTC)

Regarding the statement "individuals placed within this cluster are more genetically similar to each other than to individuals outside the cluster" I don't think that is correct. Individuals within the same cluster are more similar to a specific "typical" genotype than to any other specific "typical" genotype. On an interindividual level individuals within a cluster may well be more similar to an individual in a different cluster than they are to an individual in their own cluster. Witherspoon et al (2007) say that clustering analyses use population level data to classify and not individual level data. When pairs of individuals are compared clusters look a great deal less convincing. Witherspoon et al (2007) conclude "The fact that, given enough genetic data, individuals can be correctly assigned to their populations of origin is compatible with the observation that most human genetic variation is found within populations, not between them. It is also compatible with our finding that, even when the most distinct populations are considered and hundreds of loci are used, individuals are frequently more similar to members of other populations than to members of their own population." (emphasis mine). Where did the quote come from? Alun (talk) 08:03, 12 January 2009 (UTC)

Ah, I see, it's a quote from the Rosenberg paper. What a shame that people writing these sorts of papers themselves don't appear to understand exactly what they are measuring. No wonder others get confused. Alun (talk) 18:07, 12 January 2009 (UTC)

Name

What's the notability of this subject? Most of the references eem to discuss India and not South Asia. The introduction is no introduction at all, it doesn't establish the notability of the subject, and there is no attempt to explain exactly what the article is about as a specific coherent subject. There are several articles called "Genetic history of ..." (e.g. Genetic history of Europe, Genetic history of the British Isles). I suggest that we rename this article Genetic history of India (or Genetic history of South Asia). I think it will hang together better then. I'll move to that name in a week or so unless there are any serious objections. Alun (talk) 08:02, 12 January 2009 (UTC)

Any sensible Y-chromosome studies?

My comment applies more to the research papers than this article. I know such comments are against Misplaced Pages policy, but I do pose one relevant request:

Please post link(s) to relevant research paper(s), if any.

Correlations between Indian caste and Y-haplogroup would be interesting to study. Too bad so many of the studies are flawed; in some cases the flaws appear to be deliberate and have political motivation. I'll mention the most obvious.

(1) Is it politically incorrect in India to distinguish Kshatriya and Vaisya castes? If not, why are these lumped together in so many DNA studies? And, if we must lump, why, in heaven's name, is Kshatriya lumped into "Middle Caste" in some studies and "Upper Caste" in others?

(2) Since some surveys combine Upper vs Middle studies with different definitions into single Upper vs Middle summaries, one might even guess that the Kshatriya confusion is deliberate! ... to enhance the appearance of "genetic homogeneity."

(3) As shown in my own crude summary (at http://james.fabpedigree.com/hindu.htm) R1a is common among both Brahmin and Sudra but not the "Middle Castes"; in my page I provide a reason for this. Yet some studies ignore this and use a flawed statistic to derive "genetic homogeneity" from the Sudra fact!

(4) Many papers describing Y-chromosome research by caste discard, unreported, the haplogroup information altogether. giving only a closeness statistic! Need I explain why this is silly?

(5) mtDNA studies concluding genetic homogeneity of castes are too laughable for words. Castes are inherited from the father; mtDNA from mother.

What I would like to see is raw data summarizing three facts about test individuals: caste, region, haplogroup. Note that the region information has much importance since, as the caste system spread to new regions, different indigenous groups might be rewarded with higher status. (And please let's don't lump Kshatriya with either Brahmin or Vaisya depending on which lumping produces the politically desired statistic!)

For example, there is a very strong

    Kshatriya = R2 haplogroup

effect in Northeast India, but this would be invisible in a region-agnostic study like Sengupta's, even without Sengupta's unfortunate equation of Kshatriya and Vaisya.

Jamesdowallen (talk) 06:17, 17 June 2009 (UTC)

Section on Autosomal markers

The section on Autosomal markers is just a collection of unrelated non continuous cunks of information. Please let me know if somebody can make sense out of it and could put it as a palatable section. Else it is up for deletion. nihar (talk) 05:34, 10 July 2009 (UTC)

Done the needfull nihar (talk) 11:27, 22 July 2009 (UTC)

Reich study

New study Indian ancestry revealed, likely to have important implications for genetic history of South Asia. Some of the material has social political implications related to the Indian caste system. Basically the study suggests an ancient mixing of two distinct populations, one population similar to central and western Eurasians, and another population related to the Andaman Islanders. Wapondaponda (talk) 18:06, 23 September 2009 (UTC)

"Sharma et al (2009)"

What article is this? If it's this, it's very hard to fathom how it even passed peer and editorial review. Much of it, of course, is very similar in style to so many other articles of its type that are flooding various "journals" these days, in that the authors make portentous claims without ever, even once, stating the actual null hypotheses tested. (Hey, anyone, including my sainted grandmother, can use fancy shmancy statistical software and charting packages. That is still no substitute for actually making sense or being relevant.) But this article hits a new low for sheer shoddiness. Look at Table 1. Half of the rows have percentages which amount to non-integral numbers of persons: e.g., of the 30 West Bengal Brahmins sampled, apparently 1.67 (5.56% or 1/18 of 30) were H1, 21.67 were R1a1 and 6.67 were R2. Never mind the typos (e.g. the first two columns for Gujarat Brahmins should be 3.13, not 3.33) And then, under "RESULTS AND DISCUSSION", without explanation, the sample size switches from 621 in the first section to 510 in the second (the apparent data for which is tucked away in the supplementary document, as "supplementary Table 1"), literally from one paragraph to the next. Why is this agglomeration of graduate student GIGO being cited at all? rudra (talk) 18:19, 16 January 2010 (UTC)

Even better (or worse) they cite/quote Poliakov's Aryan Myth for allegedly philological and anthropological "models" and "evidence". Are these clowns for real? rudra (talk) 18:27, 16 January 2010 (UTC)

In a footnote: "Received 17 August 2008; revised 30 October 2008; accepted 6 November 2008; published online 9 January 2009". Revised!? Unbelievable. This journal is no longer being published through Springer. Does it have any credibility left? rudra (talk) 01:06, 17 January 2010 (UTC)

R1a(1) being indigenous to India is also attested by Underhill (2009). If you had cared to read the article in question you would know that the 621 referred to all subjects tested whereas the only time the number "510" appears is when the authors are discussing the Y-chromosomes of the Brahmins in question. Content on this page should not be discussed in isolation of content on the related article Haplogroup R1a (Y-DNA) (which presently favors a South Asian origin of R1a based on many more studies than this one). GSMR (talk) 03:15, 17 January 2010 (UTC)

Have you read the articles or are you parroting your favorite blog-warrior? A full-text search reveals that the number "510" occurs exactly once in the entirety of the paper, footnotes and all. It is not explained. According to "supplementary table 1" this 510 consist of, as far as can be made out, 256 "Brahmins" and 254 "Tribals". So it is not about the "Y-chromosomes of the Brahmins in question" as 510 also includes 254 Tribals. As for the 621 that conveniently and promptly dropped out of sight, they had 367 "Brahmins", 227 "Tribals" and 27 "Scheduled Castes". So, not only is the 510 not explained, the 256 and 254 parts of it are not explained either. Care to explain how the numbers match up? And while you're at it, try explaining how "72.22%" of 30 West Bengal Brahmins is a whole number. This paper is utter and total garbage from beginning to end. As for Underhill, don't claim. Produce a direct quote. (The paper isn't about what you would like it to be about) rudra (talk) 04:10, 17 January 2010 (UTC)

1. Bindon, Jim. University of Alabama. Department of Anthropology. August 23, 2006. <http://www.as.ua.edu/ant/bindon/ant275/presentations/POST_WWII.PDF#search=%22stanley%20marion%20garn%22>.
2. Lewontin, R.C. Biology as Ideology The Doctrine of DNA. Ontario: HarperPerennial, 1991.
3. Sailer, Steve. "Interesting India, Competitive China". xbiz. Retrieved 2006-09-12.
4. Robert Jurmain, Lynn Kilgore, Wenda Trevathan, and Harry Nelson. Introduction to Physical Anthropology. 9th ed. (Canada: Thompson Learning, 2003)
5. Garn SM. Coon. On the Number of Races of Mankind. In Garn S, editor. Readings on race. Springfield C.C. Thomas.
6. Robert Jurmain, Lynn Kilgore, Wenda Trevathan, and Harry Nelson. Introduction to Physical Anthropology. 9th ed. (Canada: Thompson Learning, 2003)
7. Jorde, Lynn B Wooding, Stephen P. Nature Genetics. Department of Human Genetics. 2004. <http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html>.
8. Bamshad, M.J. et al. Human population genetic structure and inference of group membership. Am. J. Hum. Genet. 72, 578−589 (2003).
9. Rosenberg, N.A. et al. Genetic structure of human populations. Science 298, 2381−2385 (2002).
10. Sitalaximi, T "Microsatellite Diversity among Three Endogamous Tamil Populations Suggests Their Origin from a Separate Dravidian Genetic Pool" Human Biology - Volume 75, Number 5, October 2003, pp. 673-685