October 14, 2012

Differential relationship of ANI to Caucasus populations

The observation in Reich et al. (2009) that Ancestral North Indians (ANI) and CEU (HapMap White Utahns) form a clade to the exclusion of Adygei (a NW Caucasian HGDP population) has always puzzled me, because in my ADMIXTURE experiments, the dominant West Eurasian component in South Asia has always been one centered in the Caucasus rather than Europe, an observation also confirmed by Metspalu et al. (2011).

I have now used the qpDstat program of ADMIXTOOLS to calculate some D-statistics using a wide variety of West Asian populations that have appeared in the literature since 2009 (mainly Behar et al. 2010, and Yunusbayev et al. 2011), in addition to the Adygei. This analysis is based on 87,925 SNPs. I have kept SNPs included in the Rutgers map for Illumina chips, since most of the datasets merged with the Reich et al. (2009) dataset were genotyped on such chips, and applied a --geno 0.01 flag after merging the various datasets.

The following populations were considered:
North_Kannadi, Sindhi, Pathan, Kashmiri_Pandit, Brahmins_from_Uttar_Pradesh_M, Iyer_D, Iyengar_D, CEU30, Onge, Adygei, Lezgins, Georgians, Ukranians_Y, Abhkasians_Y, Chechens_Y, North_Ossetians_Y, Armenians_Y, Kurds_Y, Iranians_19, Romanians_14, Bulgarians_Y, Greek_D
I calculated D-statistics of the form:

D(CEU30, non-CEU West Eurasian; South Asian, Onge)

I report, for each South Asian population, the score for non-CEU West Eurasian being Adygei, and the most negative Z-score:


It is clear, that while CEU are more related to Indian cline populations than Adygei are, at least for the case of the Pathans, they are less related to them than Georgians are. The Georgian population is one of the modal populations of the West Asian autosomal component.

The full set of results can be found here. It appears that North Ossetians (who are also from the NW Caucasus) follow the Adygei pattern, while Abkhazians, Lezgins, and Armenians appear more related to ANI than CEU are, similar to the Georgian pattern.

Interestingly, D(CEU, Iranian; South Asian, Onge) appear positive, and this is probably not because CEU are more related to ANI than Iranians, but because Iranians also have ASI admixture.

Ukrainians do not appear more closely related to ANI than CEU are, rather the opposite. This is consistent with the recent f3-statistics analysis of South Indian Brahmins, in which the strongest signals of admixture involved populations from Western Europe, the Balkans, and West Asia, but not from eastern Europe.

All the available evidence suggests that ANI is most related to populations of the South and NE Caucasus, and not to those of the NW Caucasus like Adygei. To confirm this, I calculated some additional D-statistics (also included in the spreadsheet):


All in all, this seems to be very consistent with my working model of Eurasian prehistory. It is also in agreement with proposals for a genetic relationship between Indo-European and NE Caucasian/Hurrian and/or early contacts between it and Kartvelian. No such relationship, as far as I can tell, has been seriously advanced with respect to NW Caucasian languages.

A valuable lesson from this analysis is that now that multiple West Asian populations have been genotyped, caution must be exercised when using the HGDP Adygei, because they are clearly not representative of the different language families (NE/S Caucasian and Indo-European) present in West Asia. Surprises may lurk even at the sub-1000km scale in a region as diverse as the Caucasus.

16 comments:

Onur said...

It would be interesting to see Turks in this test and to learn which pattern they follow with regard to ANI affinity.

zardos said...

There were more than just one West Eurasian colonisation event for India. Among the first in North India were the people of the Indus valley civilisation. There is no proof of them being Indo-European, but there remains the possibility that they are related to Mesopotamian and Caucasian people.

How does your approach differentiate between different admixture events with any certainty?

Reading your comments on this, what you detected seems to be the earlier Neolithic, not the later Indo-European genflow.

Dienekes said...

Reading your comments on this, what you detected seems to be the earlier Neolithic, not the later Indo-European genflow.


I don't know what you mean, as I have detected no signals old enough to represent a Neolithic admixture event.

And, actually, if India is anything like Europe, migration was not followed immediately by admixture, since in Europe the Sardinian-like population seems to have been maintained until the Iron Age.

Grebmörts said...

DIYDodecad K12b shows the people on Europe's western fringe having more Gedrosia ancestry than Caucasus. Here are the European groups having %Gedrosia - %Caucasus greater than zero:
12.6 Argyll_1KG
12.0 Orcadian
11.8 Orkney_1KG
11.7 Irish_D
10.0 British_D
9.8 French_Basque
9.4 Cornwall_1KG
9.1 Pais_Vasco_1KG
8.1 Norwegian_D
7.5 English_D
7.3 British_Isles_D
7.3 CEU30
6.9 Kent_1KG
6.5 Swedish_D
5.1 Dutch_D
4.4 Mixed_Germanic_D
0.2 French_D

These were the people furthest from the neolithic revolution, so maybe they show more Palaeo-European ancestry. Did the Palaeo-Europeans have a common origin with Gedrosians/Ancestral North Indians?

Annie Mouse said...

CEU is a rotten proxy for anything other than folk from Utah. These folk are known to be admixed with all sorts.

If you are looking to find out what is happening in WEstern Europe, use an actual Western European proxy. CEU is too corrupted.

terryt said...

"I have now used the qpDstat program of ADMIXTOOLS to calculate some D-statistics using a wide variety of West Asian populations that have appeared in the literature since 2009"

Pity no-one has done anything for the New Guinea and Aboriginal Australian populations. They woould make a really interesting comparison to both ANI and ASI, not to mention SE Asian, East Asian and Native American populations.

Kurti said...

@Zardos

If the ANU admixture found in Indians was Neolithic it should have been more "Mediterranean" like than "West Asian".

Davidski said...

"I don't know what you mean, as I have detected no signals old enough to represent a Neolithic admixture event.

And, actually, if India is anything like Europe, migration was not followed immediately by admixture, since in Europe the Sardinian-like population seems to have been maintained until the Iron Age."

Exactly, so the signals you're picking up represent in large part Neolithic migrations, and then slow mixing.

That's the case both in India and Europe.

Bronze Age...lol.

Dienekes said...

Exactly, so the signals you're picking up represent in large part Neolithic migrations, and then slow mixing.

The only problem with that little theory of yours is that the West Asian component not only did not mix with with the others until late in prehistory, but was also ABSENT, as far as we can tell from the available DNA evidence until late in prehistory.

Until 5ka, we have evidence in Europe for a Sardinian-like farmer population and an ultra-North European-like hunter-gatherer population that is outside current variation, but no evidence for the West Asian influence.

That influence may have made its appearance at the eastern outskirts of Europe (e.g., the Balkans or the eastern European plain), but certainly did not become ubiquitous across Europe until Bronze Age.

zardos said...

Dienekes, I think the best thing to do is to test Harrapans before coming to any such conclusions concerning chronology of the admixture events. I see no reason why this shouldn't be done in the near future.

What's the signal of the earlier Neolithic Indians with obvious West Eurasians affiliations, if it is not the West Asian? ANI is surely not the result of just one event and even less so from a later than Neolithic event alone.


@Kurti
There is no reason to think of the Neolithic culture bearers as being Mediterranean in India. Older Neolithic cultures with West Eurasian connections were present in India and those can be different from the ones in Europe.

andrew said...

"There were more than just one West Eurasian colonisation event for India. Among the first in North India were the people of the Indus valley civilisation."

The point that ANI has multiple layers of West Eurasian colonization is a very solid one. While Indo-Aryan very likely reached India via Central Asia (a likely source of CEU similarity), the Indus River Valley civilization probably arrived via Iran, and Georgians on the boundary between Iran and more definitively West Eurasian Anatolia would have a blend of both and hence have some similarity via a first wave ANI Indus River Valley layer and some via a second wave Indo-Aryan invasion layer. So, even though Georgians are closer to ANI, they may not be closer to the Indo-Aryans who may be closer to CEU.

"CEU is a rotten proxy for anything other than folk from Utah."

I used to think this, but have since been quite convinced otherwise, both by the decent fit of CEU to Western European Caucasian and because I know more about the demographic history of Utah Whites who were within the sample.

The founding Mormon population of Utah was overwhelmingly from New England and migrated away prior to absorbing the waves of Roman Catholic European migration that was beginning around the time of their ethnogenesis (this coincided with both the disestablishment of the Puritan successor Congregational Church and the influx due to push factors of European immigrants). They didn't pick up many people along the way to Utah (they were despised and terrorized by the locals all the way from New England to Missouri), and their missionary efforts which brought outsiders in didn't really take off until they were settled in Utah, and transportation with the outside world had improved. The ancestry screen in the sample kept out most subsequent admixture.

Moreover, New England prior to Mormon ethnogenesis, from the arrival of the Puritans from England (who migrated before Britain's international empire had brought in admixture from around the globe to Puritan areas) were very effective at using there more or less theocratic regime to keep out outsiders who were not from the same source as the original Puritans and the Puritans had the highest rate of natural increase as opposed to population growth from immigration of any of the founding populations of the United States (about three more surviving children per woman per lifetime than the least prolific colonies, although with fairly long generations compared to the South and Appalachia, so there wasn't much admixture derived from imported indentured servants either (there were far more white indentured servants in the Mid-Atlantic region.

CEU is about as close as you can get to a population genetic time capsule of Eastern England of the 1600s anywhere in the world. And, that region's last real population genetic upheaval was probably the Norman Invasion of 1066, so CEU is pretty close to what Eastern England looked like genetically about 900 years ago.

Amanda S said...

Andrew, analysis of the CEU sample does not support your claims. Look at the analysis on the Eurogenes website for example (http://bga101.blogspot.com.au/2012/02/genetic-substructures-within-hapmap-ceu.html). [Dienekes, I'm sorry if you've also done this analysis but I found this one first by googling.]

Colonial British America included individuals from a number of different European countries apart from England including Holland, Germany and Sweden so it's not surprising that the CEU sample is more diverse than an ancestrally focused English one would be.

Jim said...

"The founding Mormon population of Utah was overwhelmingly from New England and migrated away prior to absorbing the waves of Roman Catholic European migration that was beginning around the time of their ethnogenesis"

Yes, Andrew, and even when others did join the colony the majority were from Britain, still pre-immigration - out of British Isrealite groups and other similar sects. The Romneys were part of that migration.

Nirjhar007 said...

''And, actually, if India is anything like Europe, migration was not followed immediately by admixture, since in Europe the Sardinian-like population seems to have been maintained until the Iron Age.''
Actually aDNA is trustable not these indirectmethods to get atleast the a true age for any kind of genetic trait but we can expect something from farmana and yes archaeology does speak of 2 intrusions to south asia at neolithic period.

Annie Mouse said...

Nice Amanda

Andrew also note the traces of African and East Asian.

SimonW said...

@Grebmörts

The evidence we've got from western European hunter-gatherers does not support your speculations. Mesolithic Iberians from northwest Spain (La Brana-Arintero) in K12b are mostly a mix of Atlantic_Med and North_European, with 0% Gedrosia.