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Angela
27-01-16, 17:21
See:
Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structurehttp://www.pnas.org/content/early/2016/01/20/1513197113

"India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform."

Razib Khan has written a perceptive critique of the paper, in my opinion.
http://www.unz.com/gnxp/south-asians-are-not-descended-from-four-populations/

Even for those with a minimal interest in South Asian genetics, the critique is an important read for highlighting the limitations of Admixture programs. If more people understood this we wouldn't get the absurdity of a recent thread at Anthrogenica which purported to find the most "European" ethnic groups based on Admixture results for things like "West Mediterranean" versus "East Mediterranean" and other nonsense. One would think that all the papers of the last few years had never appeared.

Anyway, here are some pertinent quotes:
"Long-time readers will see the immediate problem: you can’t use ADMIXTURE like this! There is no guarantee that a group that is 100% x actually is in a situation where x corresponds to a genuine discrete ancestral population that existed in reality. That is, these sorts of models push a certain number of ancestral populations, and force individuals into being combinations of those. The model is constrained by the data you are putting into it to generate the results. For example, if I took Uygurs and Europeans, and did a K = 2, the Uygurs may form one cluster, and the Europeans another, at 100% levels. But we know from history and other methodologies that the Uygurs are a recently mixed group (within the last 2,000 years). Nevertheless if you tell the package to assume K = 2 with Uygurs and Northern Europeans, then it will place these into two distinct groups. And in fact, the result tells you something real and significant about the relatedness of the individuals in the data…but it doesn’t tell you necessarily anything about the real population history."

"To repeat, ADMIXTURE does not necessarily give you real population combinations!!! In fact, populations are to some extent a social construct, insofar as they’re just really collapsing the genetic variation which is the result of a particular demographic and pedigree history. "

"Instead of relying on ADMIXTURE so much, they should have also utilized D-stats and f-stats (not as sensitive to drift), as well as TreeMix. I think that would have quickly shown that some of these “pure” groups were mixed. Second, there is the issue of time-since-admixture. They obtained lower values than the 2013 paper. Why? Because they use source populations (and probably the methodology) which are somewhat different from that earlier work. Honestly if some of these populations are compounds, then it doesn’t make sense to necessarily use them as idealized donors in an admixture event."

LeBrok
28-01-16, 06:47
A great example of admixture problem, Angela. As I mentioned many times before, I'm so looking forward to admixtures build on ancient DNA source. It takes sooo looong. At this point I expected most of archeologists and anthropologists jumping on genetic bandwagon testing every known bone.

Tomenable
29-01-16, 20:47
At this point I expected most of archeologists and anthropologists jumping on genetic bandwagon testing every known bone.

There is still a lot of resistance by archeologists & historians (and maybe anthropologists) to making use of genetics in their research.

For various reasons.

Namu
02-03-16, 11:48
So Andaman Islands are ancestral component to indian populations. Anyone think it plausible it would show up in Romani descendants ? I've confirmed ancestry from Sinti nomads to the Balkans, and show up consistent but trace amount of Far East (near Indonesia) / Andaman Island admixture in addition to the expected ASI.

Maciamo
02-03-16, 12:29
I suppose that when they say 'five ancestral components', they mean five migrations of people into the Indian subcontinent ? But they do not take into account the fact that these migrants were already made up of different ancestral populations. The Neolithic farmers were essentially G2a, but they absorbed native 'Gedrosian' people belonging to Y-haplogroup J2 along the way during their migration eastward to India. The Indo-Aryans were first admixed in the Steppe (Yamna R1b introgression into East European I2a and R1a populations), then a second time in Central Asia (Andronovo and BMAC) with J2a, and to a lesser extent G1, Q and R1b1a (M73). Pre-IE inhabitants of Central Asia were, in turn, were already the result of several populations converging with one another.

So saying that there are only five ancestral components in India is like saying that spaghetti bolognese is made of three components: pasta, sauce and cheese, without considering that the sauce was itself made with many ingredients. That's one way of looking at it, but that seems to push the oversimplification a bit too far for a serious scientific paper.

Admixtures are very tricky to use because they use Zombie populations which, as Razib Khan said, may not correspond to a discrete ancestral population that existed in reality. This is why I have concentrated my efforts on Y-DNA and mtDNA even after the development of autosomal admixture tools about six years ago. It's much easier and far more reliable to trace back migrations and historical populations with distinct Y-DNA lines than with hotchpotch admixtures.

It's always a good idea to try to model admixture on historical population defined by Y-DNA haplogroups rather than the opposite. The best attempts have been to recreate the admixtures of the original Mesolithic Europeans (WHG and EHG) and Caucasians (CHG), G2a Neolithic farmers (ENF and EEF), R1b PIE (Yamna) and R1a PIE (Corded Ware, Sintashta). But even those real ancient individuals aren't completely homogeneous and frequently intermingled with neighbouring populations. The drawback of Y-DNA is that it requires enough samples (hundreds if possible) to get a good idea of just how admixed a population was. That's when admixtures can help. But using only admixtures to infer the ancient sources of a modern population, like the Basu et al. paper attempts, is very perilous indeed.

Namu
02-03-16, 12:33
You might still be able to trace specific sauces though, and not only the ingredients used in them... e.g. years of college cooking taught me to identify the Buitoni mushroom-bolognese sauce with great accuracy.

Goga
02-03-16, 15:09
I suppose that when they say 'five ancestral components', they mean five migrations of people into the Indian subcontinent ? But they do not take into account the fact that these migrants were already made up of different ancestral populations. The Neolithic farmers were essentially G2a, but they absorbed native 'Gedrosian' people belonging to Y-haplogroup J2 along the way during their migration eastward to India. The Indo-Aryans were first admixed in the Steppe (Yamna R1b introgression into East European I2a and R1a populations), then a second time in Central Asia (Andronovo and BMAC) with J2a, and to a lesser extent G1, Q and R1b1a (M73). Pre-IE inhabitants of Central Asia were, in turn, were already the result of several populations converging with one another.

So saying that there are only five ancestral components in India is like saying that spaghetti bolognese is made of three components: pasta, sauce and cheese, without considering that the sauce was itself made with many ingredients. That's one way of looking at it, but that seems to push the oversimplification a bit too far for a serious scientific paper.

Admixtures are very tricky to use because they use Zombie populations which, as Razib Khan said, may not correspond to a discrete ancestral population that existed in reality. This is why I have concentrated my efforts on Y-DNA and mtDNA even after the development of autosomal admixture tools about six years ago. It's much easier and far more reliable to trace back migrations and historical populations with distinct Y-DNA lines than with hotchpotch admixtures.

It's always a good idea to try to model admixture on historical population defined by Y-DNA haplogroups rather than the opposite. The best attempts have been to recreate the admixtures of the original Mesolithic Europeans (WHG and EHG) and Caucasians (CHG), G2a Neolithic farmers (ENF and EEF), R1b PIE (Yamna) and R1a PIE (Corded Ware, Sintashta). But even those real ancient individuals aren't completely homogeneous and frequently intermingled with neighbouring populations. The drawback of Y-DNA is that it requires enough samples (hundreds if possible) to get a good idea of just how admixed a population was. That's when admixtures can help. But using only admixtures to infer the ancient sources of a modern population, like the Basu et al. paper attempts, is very perilous indeed.
Hmm, not really. Indic came from the same source as the original IE in Yamnaya. That means from Maykop/Leyla Tepe. PIE migrated into 2 directions. One went into Yamnaya (R1b & J2a) and second went to SouthCentral Asia (Northern part of the Iranian Plateau) (R1a & J2a). IEan speakers in the Yamnaya Horizon mixed with the Western Steppes folks, while IEan speakers in SouthCentral Asia mixed with the Eastern Steppes folks.

Those first IEan speakers who migrated into the Yamnaya and South Central Asia were mostly CHG / Gedrosia folks. PIE evolved within this people. Proto-proto-PIE was part of the Gedrosia folks...

Goga
02-03-16, 16:09
Why is proto-proto-Indic not from the Eastern Steppes? Very simple, because Indic is closer to Greco-Anatolian (Greek, Hittite etc.), Armenian, West Iranic (Aryan), East Iranic etc..

Or are deranged people claiming that Greek, Hittite and Armenian are also from the Eastern Steppes?

Most Indic languages have also an ergativity construction, which mean that they have to be from West Asia.

Maciamo
02-03-16, 16:34
You might still be able to trace specific sauces though, and not only the ingredients used in them... e.g. years of college cooking taught me to identify the Buitoni mushroom-bolognese sauce with great accuracy.

That's not my point. A good cook could probably identify all the ingredients in a sauce and work the recipe backward (approximately). It's possible to some extent with autosomal admixtures too, but much harder than with Y-DNA lineages. The more ingredients in the mix, the harder it is to get all components right.

Maciamo
02-03-16, 16:40
Why is proto-proto-Indic not from the Eastern Steppes? Very simple, because Indic is closer to Greco-Anatolian (Greek, Hittite etc.), Armenian, West Iranic (Aryan), East Iranic etc..

Or are deranged people claiming that Greek, Hittite and Armenian are also from the Eastern Steppes?

Most Indic languages have also an ergativity construction, which mean that they have to be from West Asia.

Greek, Hittite and Armenian all derive from a Steppe migrations to the Balkans. The first migration (from 4200 BCE) brought R1b-L23, from which could be derived Anatolian languages (Luwian, Hittite). But a much later migration, possibly from the Seima-Turbino culture (c. 1900-1600 BCE) in the northern steppe, brought R1a to the same region. The merger of the two IE languages gave rise to Mycenaean Greek and Proto-Armenian. These are therefore hybrid R1a-R1b, like the Germanic, Albanian, Thracian and Dacian branches of IE.

Goga
02-03-16, 16:51
Greek, Hittite and Armenian all derive from a Steppe migrations to the Balkans.
This is not true. There is absolutely no evidenced for such a claim. I believe that Greek language migrated right from the Eatern Anatolia. Think only about the GRECO-ARYAN connection. Greek is MUCH closer to Iranic (Aryan) languages than to Balto-Slavic or Germanic languages. A PIE language migrated (with hg. R1b & J2a) from the Iranian Plateau (Leyla-Tepe) into Greece/Western Anatolia and gave birth to Greek, Hittite, Armenian etc. (Greco-Anatolian languages).

The point is that Greek has NEVER been in the Eastern Steppes (Central Asia). Some folks say that Indic is from the Eastern Steppes (Central Asia). This is 100% wrong! If Indic was from the Eastern Steppes (Central Asia) it would be closer to Balto-Slavic languages than to Greek or Armenian. While the fact is that Indic languages are closer to Armenian, Greek, Iranic (Aryan) languages than to Balto-Slavic languages.


http://s27.postimg.org/8vl9wsj8j/Anatolian_hypothesis.jpg



Indic has also an ergative construction. Balto-Slavic languages don't have any ergative construction at all, while pure Aryan languages like Kurdish have also an ergative construction.

Ergative construction is from West Asia and not from the Eastern Steppes (Central Asia), period…


"The ergative construction in modern Indo-Aryan": http://www.sciencedirect.com/science/article/pii/0024384152900375

"The ergative construction in Kurdish": http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=4047700