November 29, 2012

South Indian Y chromosomes (+ a little complaining about methods)

The table of haplogroup frequencies (left) may prove quite useful, but I am fairly disappointed with what appears to be the state of the art in recent published research on Y chromosome variation. This is not to belittle the tremendous amount of labor and money needed to collect and genotype large representative samples of individuals; only to express hope that better use of the collected samples could be achieved.

First of all, it is inconceivable to me how scientists can continue to use the 3x slower "evolutionary mutation rate" for their analyses of Y-chromosome ages on the basis of Y-STR markers. I have done my small part in my Y-STR series to show that this mutation rate is applicable only for a rather specific demographic history, and completely unsuitable to real growing human populations where Y-STR variance accumulates at close to the genealogical rate. And, my observations merely elaborated quantitatively what was already present in Zhivotovsky et al. (2006) but has been completely ignored since:
In simulations of a neutral process with average rate of increase m = 1, the number of surviving haplogroups rapidly decreased with time and corresponded well with the theory of mutant survival (Li 1955, p. 242), and the average size of the surviving haplogroups increased each generation by a value rapidly approaching 0.5 (data not shown), which agrees with asymptotic fraction of 2/t of haplotypes that survive at generation t (Athreya and Ney 1972, p. 19). The accumulated variance increased almost linearly (fig. 1), at a rate of increase about 0.00028 per generation; that is, the actual rate of accumulation microsatellite variation was about 3.6 times less than that predicted from the germ line mutation rate. This corresponds perfectly to the 3- to 4-fold difference observed between germ line and evolutionarily effective mutation rate.
The issue is all but resolved in the amateur "genetic genealogy" community, but even professional geneticists often use either genealogical or evolutionary rate, or take an agnostic stance by reporting results based on both rates. To arrive at strong conclusions about a topic on the basis of a mutation rate that is, to say the least, controversial, without even acknowledging the existence of a controversy is unsatisfactory. Y-chromosome researchers ought to copy the attitude of those working with autosomal DNA, where a corresponding mutation rate controversy was not swept under the carpet, but acknowledged (e.g., in the recent Meyer et al. high-coverage Denisova paper), with the implications of the uncertainty during the present "transitional" period quantified in the form of wider confidence intervals.

This "mutation rate" issue  notwithstanding, it was also recently shown that by Busby et al. that Y-STR based estimates have a dependence on the set of Y-STRs used, with markers exhibiting linear behavior across different time spans. This does not invalidate their use as molecular clocks, but highlights the need to not only select a bunch of Y-STRs, but also either (i) demonstrate that the selected set exhibits linear behavior for the time span of interest, or (ii) correct for deviations from linearity. Again, this type of modelling of microsatellite behavior was recently achieved for autosomal STRs by Sun et al.  Note that such deviations result in a slower rate than the genealogical one, but the mechanism whereby this is produced is completely different than the one proposed by Zhivotovsky et al.: it is not drift in a non-growing (m=1) population that reduces the effective rate, but rather "saturation" of the mutation process, whereby the variance at fast-mutating markers grows sub-linearly with time, because of physical constraints on their possible range of values.

I don't hope that Y-STR based age estimation will have much to offer in the coming years. But the third set of the 1000 Genomes Project is on its way, and this will include a variety of South Asian samples. Very soon we will be in a good position to study the time depth of common ancestry between e.g., European and South Asian Y-chromosomes within various haplogroups using point mutations, and these are not plagued by many of the problems associated with Y-STR variation and its interpretation.

Finally, I can't help but notice that this paper has not acknowledged the tremendous progress in resolving the Y chromosome phylogeny done by non-academic researchers. With the current state of our knowledge, the claim that haplogroup R1a1 is "autochthonous" in India is not tenable. Even if one discounts all the evidence made by SNP discoveries in the commercial testing world (and why should they?), finer-scale structure within this haplogroup has now been officially published and appears to be inconsistent with a South Asian origin of this haplogroup.

Certainly, not all is resolved; for example, the representation of tribal populations in commercial DNA testing is almost non-existent, and a sampling of their Y-SNP diversity is urgently needed. A very useful paradigm of research is that of recent work on the most basal clade of the Y-chromosome phylogeny (A00) in which the identification of very unique Y-chromosomes by genetic genealogists was combined with academic samples of "indigenous" peoples to produce new knowledge.

Much of population genetic research will benefit from such consilience between academics and amateurs. This is not an idle hope, but a recognition that this field is one in which the public not only has a substantial interest but can also do something about it. Many might be interested in Mars exploration, but without Elon Musk's bank account, most are consigned to being consumers of information about the Red Planet. Hopefully, better ways of combining the efforts of research scientists and the educated public can be identified and used in the near future.

PLoS ONE 7(11): e50269. doi:10.1371/journal.pone.0050269

Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System

GaneshPrasad ArunKumar et al.

Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed less than 20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.

Link

21 comments:

shenandoah said...

Re yDNA latest breakthrough; have you seen this already?

http://dna-explained.com/2012/11/16/the-new-root-haplogroup-a00/comment-page-1/#comment-1440

I'm pretty excited about it, although still trying to figure out what it all means.

Slumbery said...

"Finally, I can't help but notice that this paper has not acknowledged the tremendous progress in resolving the Y chromosome phylogeny done by non-academic researchers. With the current state of our knowledge, the claim that haplogroup R1a1 is "autochthonous" in India is not tenable."

The mere fact, that the frequency of R1a1 is clearly and significantly caste dependent, is a strong reason to think that it's presence does not pre-dates the caste system very much.

DOD879 said...

How come r1a1has a higher %than R in many cases?
I hope the data is accessible somewhere...

Nirjhar007 said...

''Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya,''
So the author is against the arya migration theory but the problem is we need direct indicators not these comparative methods.

DMD said...

The Busby et al (2011) study entitled “The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269” investigated how ASD (Averaged Square Differences) estimates changes when different combinations of STRs are used. Under the STR’s stepwise model of mutation, ASD linearly increase with time but this relationship is constrained by the maximum number of repeats a STR can sustain. In that study the authors estimated the durations of linearity for 15 STRs, which reflects when ASD will stop increasing linearly with divergence time. Among other conclusions, at the end of the Discussion section in page 7, the authors state that “the majority of Haplogroups dates based on such sets of STRs may therefore have been systematically underestimated”. We completely agree with this conclusion and they just reinforce the main point of our work: The time of divergence among the tribal and non-tribal groups in Tamil Nadu occurred much before the Varna system was introduced by the Brahmins into the region.

It is well known that the methods used for estimating time of divergence among populations are based on oversimplified models. Dating Y chromosome is also controversial and depending on which mutation rate one uses (genealogical versus evolutionary effective mutation rate), estimates can differ by a factor of three. These are the reasons why we were very careful to base our interpretations on the overall genetic patterns that were independent of the divergence time estimates. For example, the HG age estimates were associated to the STRs variances, but these variances can also be interpreted without timing then. Tribes are expected to exhibit higher STRs variances of the ‘Indian-autochthonous’ HGs (C5, F, H1) if these paternal lineages were recently introduced into the caste populations from the tribes. However, the opposite trend was observed for these HGs. Moreover, the patterns observed in the RM networks further support that the paternal lineages of these older HGs did not recently come from the extant tribes. In the same way, these RM networks also did not support recent mixing among tribes and non-tribes for the rest of the HGs. Finally, the similar divergence patterns among the groups and populations observed in the different BATWING runs also suggest that populations stopped sharing haplotypes during the same time frame (independently of the estimated time). Therefore, if our divergence time estimates are indeed underestimates, it does not negatively affect the conclusions presented in the manuscript: That both tribal and non-tribal populations share a common genetic heritage and they were affected by the same past demographic events. The Busby et al (2011) study just may indicate that the timings reported in our manuscript would be older and this rather reinforces the points we stated above and presented in the paper.

Dienekes said...

The Busby et al (2011) study just may indicate that the timings reported in our manuscript would be older and this rather reinforces the points we stated above and presented in the paper.

"Older" relative to the genealogical mutation rate estimate, and how older depending on the set of STR markers used.

Let us take haplogroup R1a1 in the BRH sample, which you claim as "autochthonous" (despite the recent Y-SNP evidence placing it as a twig in the R1a1 tree), and which you date as 13,387 years using the Zhivotovsky rate.

This translates to 3,718 years when taking into account the 3.6x inflation factor (Zhivotvsky et al. 2006). In this time frame, most STR markers -except the very fast mutators- exhibit very close to linear behavior.

So, rather than being pre-10ka, Brahmin R1a1 Y-chromosomes coalesce to the Bronze Age, and very close to the period where the Indo-Iranian unity broke down and the linguistic ancestors of the Indo-Aryans migrated into the Indian subcontinent from Central Asia.

Tribes are expected to exhibit higher STRs variances of the ‘Indian-autochthonous’ HGs (C5, F, H1) if these paternal lineages were recently introduced into the caste populations from the tribes. However, the opposite trend was observed for these HGs.

That is not what is expected if the greater part of the aboriginal population of India was absorbed into the caste system, and the tribes represent the bottlenecked remnants of a few populations that were not absorbed into this system.

A very good analogy is with Latin American Mestizos vs. unmixed Amerindians; most of the native population of the Americas was absorbed into the Mestizo population, and -in most countries- a few unmixed tribes remain that represent a very small subset of the original Amerindian population. We do _not_ expect the Amerindian tribes to exhibit higher STR variance, because most Amerindian Y-chromosomes became incorporated into the Mestizo fold; we expect the opposite.

The same applies to India as well. The tribes represent a small minority of the population; most "native" Y-chromosomes were incorporated into castes, and a smaller number of them persisted in tribes. Hence, the "number of copies" of a particular indigenous lineage within the castes is higher than within the tribes, and, correspondingly it possesses higher STR variance.

DMD said...

Your analogy of latino populations is perfect and the data and text support your interpretation. I do not see any contradiction on the previous comments.

Both Latino and unmixed Amerindians share the same ancestral gene pool but they have been affected by different demographic processes: one being isolated and experienced strong bottle necks (Amerindians) and the latino group originated from a amalgamation of multiple paternal lineages from different sources. Indeed, what we are observing in the tribal groups is a small subset of the past genetic diversity for these lineages.

About R1a1: Indeed it appears at high frequencies in Brahmin populations. However, RM networks, coalescent analyses and STRs variances, all suggest that these lineages were not introduced in Tamil Nadu during the Brahmin migrations. Tamil Nadu has historical records pointing when Brahmins arrived to the region (1000 years ago). The variances observed in non-Brahmin populations is higher than in Brahmins. Our data suggest that R1a1 has been in the region before the historical migration of Brahmins to the region, independently of the mutation rate estimate we used. Age estimates based on STRs are very controversial and this is the reason why you should rather focus on the overall Y chr. patterns than in just in the age estimates.


I really appreciate your comments and constructive criticism since this is the correct way to improve our knowledge . I would like to suggest you to read again the paper from a different angle and have some time to digest the information there.

The origins of R1a1 are far from clear and the paper you cited is only a small representation of the global R1a1 diversity. The sample size is very small and they only genotyped Malaysian Indians. As our paper suggests, we cannot infer the whole genetic landscape of a subcontinent with just studying small groups in India. The diversity in this region is very high and each group has its own history reflecting very complex demographic events for a long period of time. Saying that R1a1 origin is clear now, it reflects how little we really understand the Indian genetic landscape and the importance we give to papers with biased samplings.
Our earlier conclusions after genotyping the data were very similar to the ones you are suggesting. However, these conclusions changed after a deeper look of the data and the different analyses we applied and identifying the null hypothesis to test for each of the cases.

Dienekes said...

The origins of R1a1 are far from clear and the paper you cited is only a small representation of the global R1a1 diversity. The sample size is very small and they only genotyped Malaysian Indians.

Hopefully the samples collected for your study can be tested for Y-SNPs at some future time. You should not overlook, also, the existing evidence in Underhill et al. (2009), the abundant samples of which placed all Indian R1a-related lineages within the R-M17 clade, while both R1a*-M420 and R1a1*-SRY10831.2 existed outside India.

The evidence from the R1a Project suggests that India has a limited subset of R-M17 itself (R-Z93). Perhaps this is not the case, but this is the evidence at the current time.

About R1a1: Indeed it appears at high frequencies in Brahmin populations. However, RM networks, coalescent analyses and STRs variances, all suggest that these lineages were not introduced in Tamil Nadu during the Brahmin migrations. Tamil Nadu has historical records pointing when Brahmins arrived to the region (1000 years ago).

That is not directly relvant, because the time when a lineage arrives at a new region does not correspond to its TMRCA within that region. The TMRCA of European American Y-chromosomes is in the many thousands, and yet Europeans arrived in the New World in the last five centuries.

We would expect some correspondence with the 1000-year figure, if the Brahmins of South India were founded by a single male in that time frame; if they were founded by multiple males whose TMRCA was already old, then their TMRCA would show no correspondence to the time they migrated to South India.

Analysis of Y-STR variance can only take us so far, because there are many assumptions involved in its interpretation. Two examples of this are admixture of divergent populations (which increases Y-STR variance relative to the mixing populations), and different demographic trajectories: for example, if A spawns B and A remains "static" (m=1) and B grows (say, m=1.05), perhaps as it expands into a new territory, the B will have higher Y-STR variance than A, even though A spawned B.

the sample size is very small and they only genotyped Malaysian Indians.

There are other samples in the R1a1 and subclades project and the general picture is that the South Asian gene pool exhibits a small subset of global R1a1 variation (see comments above). Your group has many more samples, so their future placement within the Y-chromosome phylogeny can be achieved, and that will resolve whether R1a1 is auto- or allochthonous in India.

Davidski said...

I'm not aware of a single R1a xZ93 lineage from South Asia to date.

Every sample tested for Z93 and downstream markers from India and Pakistan has tested positive, and that includes samples from all relevant FTDNA projects (not just the R1a and Subclades Project) and 1000 Genomes.

If there happens to be some R1a xZ93 in India or Pakistan, then I'd say it's of very recent origin, possibly from Iran or even England.

So it looks like there was an invasion of South Asia by R1a males from the north during or after the Bronze Age, followed by some massive expansions of their descendants.

By the way, many Malaysian Indians are from South India, so if South Indian tribals carry ancient xZ93, which I really doubt, then surely something like that would've popped up in the Malaysian Indian sample from Pamjav et al. 2012, even if only once or twice.

DOD879 said...

It is important to remember that even today, the lower castes/tribals of India do not have good economic prospects to migrate out of the country or pay for genetic tests. For this reason, only data collected right at source will reveal whether there is any Z93- samples in Indian tribals. My suspicion is that there definitely is a sizable amount. Recent introduction through Iran, England or elsewhere can definietly be ruled out because of well documented historical reasons over the past 2000+ years. We just have to wait and see for either this group or some one else to bring to light the complete snp variation of Indian tribal populations.

Davidski said...

It'll be easier to get a Yeti to spit into a 23andMe test tube than to find native R1axZ93 in South India.

South Central Haplo said...

All technical discussions aside, like to mention the following
(Hope science will definitely determine the R1a origin one way or the other eventually).

From The Heading:
Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System

The discussion is between two people.

1. Group of Indian scientists trying to correlate Indian lineages with caste system. which is against Aryan Invasion Theory.
They are better equipped to deal with the question. They are more in tune with Indian caste system, demography, history etc. Hopefully science will drive the conclusion more than other goals.

2. Group of Non Indians who like Aryan Invasion theory and strongly believe it created caste system. On the scale of 1-100 their familiarity with complex Indian cast structure is between 20-30.
Again lets hope science answers everything eventually. Political goals come into Analytic interpretations.

Depends on where you like to put the data.........

There is definitely ANI spread in India on ASI substrate. Is it Aryan Invasion? Not really or we are not sure..

There is definitely attempt by Non Indians to create a scientific argument in support of Aryan Invasion theory. Lot of new arguments etc. Always trying to hold on to caste system.

Caste system existed in every country just like last name indicating profession. It got complicated due to skin color. which can direct to autosmal content.

Analyzing lineages of Cast system more in South India in local communities may help determine this point to rest. where skin color/features are not different between communities. except for Brahmins. which the authors took as one of the basis.

For Non Indians two points.

1. South Indian Upper casts and lower casts share same lineages.

2. North Indian lower casts are as fair as Upper casts and share same lineages. Actually they are majority R1a more than any upper cast sampled so far.










South Central Haplo said...

"It'll be easier to get a Yeti to spit into a 23andMe test tube than to find native R1axZ93 in South India."

People foud F*, K*, P* in Europe on this forum. With that mindset nothing is impossible.

wagg said...

@South Central Haplo : "1. South Indian Upper casts and lower casts share same lineages."

Not really, at least not at all in the same percentage.
The figures on the table are incorrect due to a mistake.

Here's the figures from the original work of the authors :

picture 1

picture 2

You can read here for here for a proof of what I'm saying (the 2nd paragraph.


"2. North Indian lower casts are as fair as Upper casts and share same lineages. Actually they are majority R1a more than any upper cast sampled so far. "

No, see above.


"Group of Non Indians who like Aryan Invasion theory"

"like"? Be a little less self-centered and you'll understand that it doesn't have anything to do with India, the goal is to find a convincing explanation to the spread of the diverse indo-european language family. This theory must include indo-aryan in the gloabal picture, somehow.

Sorry for your ego, but there is basically no chance that the proto-indo-european language appeared in India, Which means that the ancestor of indo-aryan didn't either, since Indo-aryan group is also derived from it.

The people that "like" the Aryan invasion theory are just taking linguistics, archeology and, yes, even genetics into account in order to obtain a credible convincing theory.


"There is definitely attempt by Non Indians to create a scientific argument in support of Aryan Invasion theory."

And now, you know why.

bmdriver said...

"There is definitely attempt by Non Indians to create a scientific argument in support of Aryan Invasion theory."

And now, you know why.


ITS WELL KNOWN IN INDIA. Their are many many texts from Colonial Europeans showing hatred and anger at any suggestion of Indians migrating out of India. And if you take the preceeding 600years of slavery, occupation of 90% of the known world, take into consideration the Three world lineage of Noah which is core ideology of Caucasion Abrahamnic Faiths christianity and islam, its very easy to see the racism that is inbred in the imperialistic slave traditions of the West.

Its amazing to see how europeans of today, know nothing of the vast literature that exist in India by Europeans promoting white skin invasions of Europea from the tribe of Shem and Japeth, btw both christ and mohammed descend from Shem, this is everywhere in colonial Indian texts.

So yes their is DEFIANTE attempt by White Europeans, who enslaved people of color, promoted that they where savages, and barbarians, and this has morphed into Aryan theory. Which is nothing more than White Caucasion racism.

The huge attempt to reverse geneflow is amazing, africa, north and south american, australia are all COLONIES of Europeans. Their is no NATIVE culture left in any of them. India was occupied to be converted to Abrahamic rule, via Islam or Christianity. Roman beleived in Mithra, Mithra is main beleif of Persia, and Mithra first written about in the Vedas!

Dhryus, or the Druids of Europe, are also written about, also mentioned them leaving India and migration to the north.

Indian civilisation extends from North west India (afghanitan and pakistan) through to central and West asia.

West asia is now being paraded around as Arab genome. If you know history of religion, history of man then its VERY VERY EASLY to see the legacy of colonial racism, supported by religious superiority over coloured non caucasions.

So South Central Haplgroup is correct, the west wants their ideology to be presented as truth and democracy while they want Indian scientitist to be branded as right wing!..lmfaoo..


Its like the Nazis talling the jews that their version of their history is right wing, yet a nazi laced version is the truth.


VERY easy to see the deception.

Davidski said...

It'll be interesting to see how these scientists and the Genographic Project backtrack when they start testing the relevant SNPs, many of which are already known to everyone except them.

Debunking their own work will be difficult I'm sure, so let's hope they can do with some style and not hold back too much.

South Central Haplo said...

Wagg,

I am not sure you read my post. clearly you dont understand it.
So I repeat.

2. Issues: Caste system and Aryan invasion theory.

1. caste system.-
The article is about

Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System

and they concluded

minimal genetic impact of the Varna (caste) system on lineages.

I also said it is upto science not you and me couple of times. Is it Ego? Your post represents your ego.

Please see the data you presented and remove the new migrants to south like Brahmins and analyze your self. The authors point is minimal genetic impact of the Varna (caste) system on lineages.
and
I put it bluntly

South Indian Upper casts and lower casts share same lineages.

None of the people making posts here understand Indian Demography.

It is important to compare apples to apples " Local communities please" you can not compare Russians to Yakuts.

So take the authors data, conclusion and it is upto you.


2. Aryan Invasion theory:

You did not provide any data about north Indian lower casts. Your link points to this article only. google north indian lower cast haplogroups. or get some data.

The context is about India in this article.
If the goal is to find a convincing explanation to the spread of the diverse indo-european language family and if you want to include indo-aryan in the global picture.

Sure go ahead knock your self out but give due correct representation and analysis in data. " show me the data".

Again Science and non political analysis provides answers.

Wagg and BMDriver are the two sides of a coin. We dont want to leave it the coin.

Nirjhar007 said...

Dienekes said- ''Even if one discounts all the evidence made by SNP discoveries in the commercial testing world (and why should they?), finer-scale structure within this haplogroup has now been officially published and appears to be inconsistent with a South Asian origin of this haplogroup.''
There is no need for it to originate in south asia as our business deals with the R1a-Z93 now which is more globally present compared to Z280,Z283etc.
Davidski said-''So it looks like there was an invasion of South Asia by R1a males from the north during or after the Bronze Age, followed by some massive expansions of their descendants.''
your reasoning is sound and of course usual:) but practically from the archaeological data of south asia it is confirmed that the subcontinent enjoyed almost a 5000 years of archaeological continuity(4500-600b.c.) and since archaeology have detected neolithic intrusions of 6000b.c.,4500b.c. and of iron age 600b.c. and all the other historically known intrusions after! so if Z-93 is coming from outside then it is bound to happen before 4500b.c. as you have said the massive expansion theory of Z93 carrying ''male kurgans'' then unless they were using vimaanas(ancient flying machines depicted in scriptures) of course;)they must be creating some sort of marks on the soil with their 'rapid ventures' to south asia.
And yes one last thing don't forget R1a's brother R2a too which peaks around with 80% presence in certain south asian populations and in iranian kurds around 20%.

wagg said...

south central haplo:
" Wagg, I am not sure you read my post. clearly you dont understand it."

I did misread some things in your post, indeed. Sorry for the mistake.

That being said, you did write:

- "Group of Non Indians who like Aryan Invasion theory and strongly believe it created caste system".

This seems to imply that some non-indians "like" (<- that's a feeling) this idea for no reason (or bad reasons), on no scientific basis at all, which is an unfair view of the situation (that's where my comment on proto-indo-european, the state of linguitics, archeology and genetics research shows up as a reminder that this attempt to makes the indo-aryanization of India fit into a global process is not completely devoid of scientifical arguments, like you seem to allege with this sentence)).
As for the correlation of the bronze age Indo-aryan culture and the creation of the caste system, it derives from the archeological and philological observations (On one hand, what we can observe in the IVC doesn't seem to fit with a caste system AFAIK and OTOH the type of culture of the early indo-aryan speakers appeared to have (-> rgVeda), shows no ambiguity in this matter).


- About Indians being "more in tune with Indian caste system, demography, history etc."

Fine, but who knows what the caste system (before widely recorded history) was in its infancy? I've read that there are good reasons to think that, at first, there were likely more mobility (up and down) than now, which allowed for lineages to cross the social barriers (even though it doesn't seem reasonable at all to consider this as the reason for the main reason for the trans-caste lineage-sharing).

- "South Indian Upper casts and lower casts share same lineages."

The current haplogroup apportion could also depend of what kind of population was at the orgin of the spreading of the Indo-aryan group in India. I can't see why it couldn't be an already admixed population that started spreading this language family in north-western India (in the context of this "aryan invasion" theory)), partly explaining why a a lot of the major lineages are present in the upper-stratas as well.

Anyway, there tends to be a big difference between the percentages of the diverse haplogroups in the diverse social stratas (R1a1a for instance, has its highest percentage in the higher classes, particularly the Bhramins) - and the tribes, so it seems clear we're in presence of quite different processes, and that Indian haplogroups do have different independent histories with different original roles (and different geographical locations of origin - and it does seem clear to me that neolithic and subsequent times were crucial in these processes) allowing for an "Indo-aryan invasion" theory to exist, even if with blurry outlines as of now.

Little remark: The fact that J2-M172 can be found up to 15.87 and even 28.57 % among the lineages of the south Tribe foragers (much more than the tiny % of R1a1a (0% in most cases though) among these peoples) could possibly indicate that this basic J2-M172 lineage pre-dates neolithic in India, I guess.
Interestingly, J2a3 (this one has to be neolithic!) is not found at all in the higher castes of this study and the highest percentage of J2-M172 is actually among the schedule castes.
Anyway, all this seems to show that R1a1a and J2 as a whole, had largely a separate spreading in this region.

wagg said...

south central haplo:
"Wagg and BMDriver are the two sides of a coin"

Please, be kind enough to not compare me to an individual that tell us that there is a several centuries old western world plot, still at work today, to hide/change the true history of India, by people motivated by religious fanaticism ** and racial hatred towards Indians.

** (Alluding that all the western scientists are part of an "abrahamic" plot to hide the truth (if I understand correctly, but I'm not sure I do) is particularly funny as I'm pretty sure that a clear _majority_ of the scientists in most of the western world are agnostic or atheists and generally rather "left-leaning", politically, taken as a whole)


Nirjhar007 : "from the archaeological data of south asia it is confirmed that the subcontinent enjoyed almost a 5000 years of archaeological continuity"

It depends on who you ask to. Some archeological cultures have been associated with movements from bronze age central Asia (among the first one, the "Swat culture" (a.k.a. the "gandhara grave culture", around 1,700 BCE) fit the requirements for such a thing - then subsequent cultures in current India, per se, are considered as possible marks of an "Indo-aryan" advance).

Nirjhar007 said...

''it depends on who you ask to. Some archeological cultures have been associated with movements from bronze age central Asia (among the first one, the "Swat culture" (a.k.a. the "gandhara grave culture", around 1,700 BCE) fit the requirements for such a thing - then subsequent cultures in current India, per se, are considered as possible marks of an "Indo-aryan" advance).''
Many thanks for your thoughts but about cultures like gandhara grave i urge you to first take a good look at this vast analysis by a veteran archaeologist here-
http://www.archaeologyonline.net/artifacts/19th-century-paradigms.html
No the problem is not the attitude that a scholar follows but not giving the place of contrary thoughts which has same fidelity and magnitude compared to which he supports with not giving the credit to the contrary one deserves , the problem has a sentence also ''seeing what you want to see''.The very problem that the field of indology and indo-european studies have suffered for over 200 years,luckily that problem is getting a solution with some new academics like here-
http://new-indology.blogspot.in/
and with new researches from the the linguistic grounds also-
http://www.omilosmeleton.gr/pdf/en/indology/Vedic_and_Avestan.pdf
stay well.