Saturday, June 04, 2016

R1a-M780 map in India and AIT

If I had failed to notice before, I notice now that this following paper, if its conclusions stand, places the genetic record completely at odds with the linguistic Aryan Immigration/Migration Theory.
European Journal of Human Genetics (2015) 23, 124–131; doi:10.1038/ejhg.2014.50; published online 26 March 2014
The phylogenetic and geographic structure of Y-chromosome haplogroup R1a,
Peter Underhill et. al.
A brief explanation of why I say so.
Figure 1 from the above publication:

Caption:
Haplogroup (hg) R1a-M420 topology, shown within the context of hg R-M207. Common names of the SNPs discussed in this study are shown along the branches, with those genotyped presented in color and those for which phylogenetic placement was previously unknown in orange. Hg labels are assigned according to YCC nomenclature principles with an asterisk (*) denoting a paragroup.63 Dashed lines indicate lineages not observed in our sample. The marker Z280 was not used as it maps to duplicated ampliconic tracts.


Notice the positions of M417 -- Z93 -- M780.  Also note:
Of the 1693 European R1a-M417/Page7 samples, more than 96% were assigned to R1a-Z282 (Figure 2), whereas 98.4% of the 490 Central and South Asian R1a lineages belonged to hg R1a-Z93 (Figure 3), consistent with the previously proposed trend.
Let us take the position that M417 (the common ancestor of Indians and Europeans with R1a) originated outside India and its descendants in India are a result of immigration.  This would be (so far) in accord with the Aryan immigration theory.

Here is Figure 3-d from the paper
Caption: Spatial frequency distributions of Z93 affiliated haplogroups. Maps were generated as described in Figure 2.



The M780 map above might make sense if M780 arose well after the Aryans supposedly arrived in India, perhaps just prior to the urbanizing period of the Gangetic plain, well into the Iron Age, i.e., ~500 BC.  But the paper places this at least two thousand years earlier!
The corresponding diversification {of R1a} in the Middle East and South Asia is more obscure. However, early urbanization within the Indus Valley also occurred at this time57 and the geographic distribution of R1a-M780 (Figure 3d) may reflect this.
(The "mature Harappan phase" is 2600-1900 BC.  Wiki says Early Harappan has two phases - 3300 BC- 2800 BC, and 2800 BC - 2600 BC.)

The paper does say:
The four subhaplogroups of Z93 (branches 9-M582, 10-M560, 12-Z2125, and 17-M780, L657) constitute a multifurcation unresolved by 10Mb of sequencing; it is likely that no further resolution of this part of the tree will be possible with current technology. Similarly, the shared European branch has just three SNPs.
If R1a-M780 was present at the early urbanization within the Indus Valley, then the "genetic Indo-Aryans" had arrived in India earlier than 2600 BC, well before the first spoke-wheeled chariots (Andronovo, ~2000 BC).  Traditional Aryan immigration theory has them arrive after 1900 BC (after the collapse of the Indus Valley cities) and before 1200 BC (start of the Iron Age in India); and typically around 1400 BC,  around or just after the Sanskritic words (supposedly pre-Sanskritic) that appear in the Mitanni written records.  

Comments (18)

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It looks to me like M780 is a sub-branch of A93. Z93 is widespread in South Asia, Z280 in Europe, and both are common in Central Asia. Since they share a common ancestor, one needs to explain why all the z93 wound up SA and the Z280's in Europe. One plausible explanation is that both split off from the common ancestor, probably in Central Asia.

Do you have a better idea?
1 reply · active 456 weeks ago
Well, the only way coming to mind right now is tiny founder effects. If the Z93, Z280 split occurred in Central Asia prior to the migrations, then they couldn't have neatly split the way they have. If a substantial precursor to (Z93, Z280) population, i.e., M417 moved east and a substantial precursor population of M417 moved West, and Z93, Z280 evolved along the way, then India should have M417 (non-Z93) and Europe should have M417 (non-Z280) populations which they don't seem to have.
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Same Guest · 456 weeks ago

It also seems highly suggestive that the M417 split (into z280 and z93) occurred more or less simultaneously with the Yamanya expansion.
2 replies · active 455 weeks ago
Well, if I remember correctly, the ancient DNA shows a replacement of R1b by R1a at the time of the Yamanya expansion.

"A discontinuity between earlier and later steppe populations is also suggested by the shift from an R1b Y-chromosome gene pool into an R1a-dominated one in the Srubnaya (Supplementary Data Table 1). We caution that this does not mean that new populations migrated into the steppe as R1a was also detected in Eneolithic Samara and an outlier Poltavka individual (Supplementary Data Table 1); it is possible that R1a males continued to abide in the Samara region but were not included in the rich burials associated with the Yamnaya and Poltavka elites in the intervening period." (from http://www.biorxiv.org/content/biorxiv/early/2015... )

---
IMO, either R1a were always there at Srubnaya but were not elite and overthrew the R1b just in time to gallop off towards India per Aryan Invasion Theory, or else, R1a arrived there (from where? from the east?)
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Same Guest · 455 weeks ago

Your author (Underhill) thinks R1a originated in Iran, with a divergence time of about 25 kyr ago. That would be long before the development of agriculture and consequent elites.
Not sure if you are following ancient DNA results, that are giving new insights into arrival of steppe ancestry and Iranian neolithic ancestry to India, resulting in what was called "ANI" by Reich et al 2009.
http://biorxiv.org/content/early/2016/06/16/05931...

"We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe; all sampled South Asian groups are inferred to have significant amounts of both ancestral types. The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘Indian Cline’ of such ancestry 35,36 is inferred to have ~18% steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~50%, similar to present-day northern Europeans"

I'm not sure how long will denial of Aryan migration continue.
2 replies · active 454 weeks ago
Thanks for the paper. The problem is that relatedness does not show direction. Further, remember the theory that I disagree with - that the Aryans entered India around 1400 BC, perhaps earlier but certainly after 1900 BC. I have been very specific about the theory that I disagree with.

PS:

"... farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia."

One could also say, farmers and pastoralists from India spread out into Iran, and into the Steppes.
The burst of R1a-Z93 is understood to have happened 4-4.5kya, so that fits with the ~1900 BC date for arrival of Aryans in India you mention. See "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences", Poznik, 2016.

On the issue of directionality, If out of India was the direction, then Iranian neolithic farmers would not magically lose the Onge component. The Onge component is missing in admixture analysis of Iranian, Caucasian or even Steppe neolithic as well as bronze age genes. In the Laziridis paper, see Fig 4b for Admix analysis of Neolithic and Bronze Age populations of Iran, Caucasus and Steppe. Compare with extended data figure 4e for Admix analysis of Indian populations.
Also, think about it. India has always had a significant fraction of the world's population, at least a few millenia after the Toba eruption around 70000 BC (though the Paleolithic evidence is mixed - Indian populations may not have been badly affected by the Toba eruption). Archaeology attests to farming in South Asia to at least 6500 BC (Mehrgarh), that would have produced the post-hunter-gatherer/pastoralist population explosion. The number of steppes people who would have had to enter India to be a primary source of genes would be quite enormous.
But what is the origin of Mehrgarh farming ?

"The Near-Eastern Roots of the Neolithic in South Asia", K. Gangal et al, 2014
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC40129...
1 reply · active 454 weeks ago
I guess you do not grasp the significant difference between a demic diffusion 9000 years ago with the advent of farming and an invasion or major migration 3500 years ago with the advent of the chariot. If you don't, is there any point in continuing?
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Same Guest · 454 weeks ago

Try asking yourself this question, Arun: are your objections based on science or politics/nationalism? If so, why bother even thinking about the facts?

Not that I can imagine why it should matter which of your ancestors came from where thousands of years ago.
1 reply · active 454 weeks ago
Sorry, I find that to be a stupid question. For instance, if I.E. spread through agriculture - Renfrew's original demic diffusion theory, not its later versions - then one should seek to decipher the Indus Valley script in one way; otherwise another.

Secondly, you're ignoring very recent European history. The idea of the "Aryan race" that was a global bearer of civilization was a factor in World War II and genocide. So European politics and culture made it matter.
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Same Guest · 454 weeks ago

The fact that racist nutjobs constructed a ridiculous theory of an "Aryan race" as a bearer of civilization shouldn't blind us to the facts. Most of those racist ideas have been firmly discredited, but the notion of an Indo-European expansion has never been dented. Their have been many human migrations, driven either by climate or technology. If the IE expansion was driven by agriculture (Renfrew) it came from the Middle East, Anatolia, or Iran. If, as seems more likely, it was driven by the horse, it came from central Asia. Either way it didn't come from Europe, India, or East Asia.

In the latter case, it was hardly the bearer of civilization, which had already existed in the Middle East and India.
1 reply · active 454 weeks ago
As I have written repeatedly, there is specifically one version of the IE migration theory that I disagree with. The facts are that the literary evidence points to something before 1900 BC. If that turns out to be true, then quite some other history has to be written.

It is a mistake to lump together the (undeniable) farming expansion and the much less well established horse/chariot expansion to the east as facets of the same theory. If I.E. spread with agriculture, then a whole lot of historical linguistics theory is simply wrong, and have to be reworked.

There are other concerns which exercise other people a lot more than they bother me. This is just FYI for you, so you don't repeat this "firmly discredited" nonsense. Among the political facts are that "racist ideas have been firmly discredited" is about as true as saying that desegregation of schools in the USA ended racism. The fact is that modern day Tamil Nadu politics is founded upon the "Dravidian/Aryan" divide. The fact is that various evangelists use "Aryan/Dravidian" theory in India as a means to proselytize. The Sri Lankan civil war had some echo of that as well (the "Aryan Sinhalese v. the Dravidian Tamils). The very modern day Columbia University Professor Sheldon Pollock wants Sanskrit to be taught only in some specific ways because his theory is that it is the malevolent influence of Sanskrit that turned German intellectuals into Nazis. And so on.
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Same Guest · 454 weeks ago

Racism clearly survives all over the place, but I was referring specifically to the notion that "Aryans" were Northern Europeans. The ancient DNA genetic data is pretty clear about the path of IE from Central Asia into Europe. There does not (yet, anyway) exist comparable ancient genome data from South or East Asia, but there is highly suggestive archaeology.

If IVC people turn out to be closely related to those who brought IE into Europe, Renfrew is going to look a lot more credible. If they turn out to be ASI or some mixture of ASI and Middle Eastern, then AIT is back in charge.
1 reply · active 454 weeks ago
I would say that the modern population genetic data and the archaeological data are consistent with a Yamnaya incursion into Europe. The ancient DNA data is also consistent. There is no literary record, and neither genes nor archaeology inform us about language, but presumably the Yamnaya incursion is a candidate to which to tie IE expansion into Europe. The problem is that the earlier farmers are also a candidate for I.E. introduction into Europe. Neither genes nor archaeology can help us decide between the two. Most historical linguists like the shorter time depth and favor the Yamnaya theory. But their tools, e.g., "glottochronology" are riddled with flaws.

The archaeological record for India does not show a Yamnaya incursion or Andronovo incursion or any other significant incursion in the 1900 BC - 1200 BC timeframe. Language-wise - the Rg Veda is the oldest attested I.E. example but is known via oral tradition; and the Mitanni records with a few Vedic deities and I.E. words as its closest competitor; but the Indian archaeological record does not provide any evidence of language. (Re: Hittite, see below) India does not yet have any ancient DNA. Genetics of the modern population so far rules out any significant incursion into India 4000-2500 years ago - but India remains a grossly undersampled population.

The Saraswati River mentioned in the Rg Veda is named with other rivers; in the hymn, these other rivers are in the correct geographic sequence of rivers of the Indus and Gangetic systems. If we thus place the Saraswati, it was a mighty river then, it now corresponds to the seasonal Ghagghar-Hakra; the channel along of which the majority of Harappan civilization sites are found; it corresponds to the Saraswati, already dried up by the time of the Mahabharata. If we accept this identification it places the Rg Veda to before 2000 BC. Since Hittite is attested to 1600-1300 BC in written records (only), the Rg Veda would be the oldest attested I.E.

We need not accept this identification of the Saraswati, linguists such as Harvard's Sanskritist M. Witzel have theorized that some other river in Afghanistan was the original Saraswati, and for some reason the Rg Vedic people transferred the name to the already-dried up river bed that they found when they entered India.

The Rg Veda was composed in India, of that there can be little doubt. But the Saraswati timeline throws the historical linguists' 1900 BC - 1200 BC time line into confusion, so they hypothesize that the hymns are sometimes a memory of some other place where the "original" Saraswati was. They also dismiss the Rg Vedic mention of the sea and of hundred-oared boats, which are not there in the deep inland Afghan location that they want to place the "original" Saraswati, by saying that the composers were incorrigible boasters and exaggerators. Then, by their estimates, these memories were transformed into Rg Vedic hymns around 1400 BC. Then Hittite becomes the oldest attested IE language.
FACT NO 1: RIVER SARASWATI WAS PERENNIAL FROM ABOUT 7000 BCE TO 2500 BCE (Chatterjee, A., Ray, J.S., Shukla, A.D. et al. On the existence of a perennial river in the Harappan heartland. Sci Rep 9, 17221 (2019))
FACT NO 2: EVIDENCE FROM RIG VEDA ON A STRONG RIVER SARASWATI FLOWING FROM THE MOUNTAINS TO THE OCEAN BETWEEN YAMUNA AND SUTLEJ WITH PURUS RESIDING ON BOTH SIDES OF THE RIVER
LOGIC : Vedic Aryas (Not necessarily Indo-European) were there around river Sarasati at some time between 7000 BCE to 4000 BCE. Thus theuy were part of pre-harappan or pre-Indus Valley settlements around the river. Bhirana earliest layer is dated 7000 BCE,. In India R1a M417 was autochtonous (Several ancient tribes like the Dravidian Chenchu, or MP Gonds were found to have R1a subclades). M780 also seems to be autochtonous. There is no proof therefore that a wave of migrants came to India between 1500 BCE to 1000 BCE. However Scythiand (Sakas) and Kushans from the BMAC and north area did invade and rule North western India for a few centures and the brought some Z2125.

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