September 16, 2012

Greeks on the crossroads of Eurasia

I used the qp3Pop program of ADMIXTOOLS which implements a 3-population test of admixture (Patterson et al. 2012), using Greek_D as a target population and any pair of other populations as possible parental populations. My dataset is similar to that used for the K7b/K12b, but includes all the new data that has accumulated since those tools were released. The number of SNPs is 186,241, and I have also limited the analysis to 115 populations with 10+ individuals.

For more details on the f3 statistic, you should really read the linked paper. Briefly, you should remember the following:

  1. Significant negative f3 statistics indicate that the target population and the two parentals do not form a simple tree, but are related in a complex way
  2. Positive f3 statistics are consistent with either a simple tree or a history of admixture followed by genetic drift
  3. It is not necessary for the parental populations to be themselves unadmixed
The full set of results can be seen in the spreadsheet.

Below you can see the 30 most negative f3 statistics.


The first thing that immediately jumps out is that Sardinians participate in most of these comparisons. And, given the mounting evidence for a Sardinian-like population in prehistoric Europe, including the Balkans, it does appear likely that a Sardinian-like element in the ancestry of Greeks is quite possible.

A different element that is paired up with Sardinians in the most negative f3 statistics consists of a variety of South Asian populations; these comparisons appear stronger than the Sardinian+East Asian ones. This dataset does not include Amerindian populations, for which the effect was strongest in the Patterson et al. paper. I suspect that South Asian populations give out stronger f3 statistics than East Asian ones, because South Asians are composed of a West Asian-like element and an Ancestral South Indian element which is related to East Eurasians. So, South Asians appear as a parental population on account of both the East Eurasian-shift effect observed by Patterson et al., as well as the West Asian-shift effect I've described in a few posts such as this.

A third set of significant comparisons involve Northern Europeans vs. Near Eastern populations, with extrema in the Baltic area and Arabia, which seems to correspond quite well with what I've called the "West Eurasian cline", with populations of northeastern Europe likely possessing a higher degree of continuity with the Mesolithic hunter-gatherers.

Overall, this exercise has convinced me that 2-way admixture models do not capture the complexity of Eurasian prehistory. The Greek population appears intermediate on a number of different clines, the two most important ones being between Sardinia and far Asia and between the Baltic and the Near East.

I will probably repeat this experiment with other populations from this set. I will also probably try to get some admixture dates using as many SNPs as possible, although rolloff appears to have fairly long running times, so I am not sure how practical that will be.

8 comments:

jackson_montgomery_devoni said...

Dienekes,

Do you believe it is safe now to assume this about the two main European components in your K12b analysis?

North European: An admixed component composed of both indigenous Mesolithic hunter-gatherer alleles and migrant Neolithic farmer alleles from Southern Europe

Mediterranean: The original Neolithic Southern European component with ultimate origins in the Middle East


Would that make sense?


Matt said...

I'm sure it would be computationally horrible and impractical, but this does make me wonder what the result of carrying out and exercise like http://dienekes.blogspot.co.uk/2012/09/inter-relationships-between-dodecad-k7b.html, where you "count the number of times it appears before the semi-colon, and subtract the number of times it appears after the semi-colon" would be repeated for your set of populations.

Ponto said...

This is my hypothesis: When a clearer and less unbiased picture comes in from the results of ancient dna that the Mediterranean element in Europe will be confined totally to the circum Mediterranean and the Near East, and that the North European element will be native to Eurasia spread from the borders of Europe all the way to the borders of Mongolia. Unfortunately, the results are biased towards Europe excluding other regions, and from a young age, the border of the start of agriculture in the western and northern parts of Europe. Too biased.

It is amusing that one other amateur wanted to exclude Sardinians, and Basques from Admixture runs because they skewed Northern and Central European results. My protest was that the Sardinians in particular showed the strongest affinity to me, the Tuscans also to a lesser degree. Excluding Sardinians just gave false results for circum Mediterranean peoples. Ascertainment bias producing calculator bias. Anyway, these things will be ironed out in the long run.

Michael Russell said...

I couldn't open your spreadsheet. The .out was unexpected, I was expecting .xls

What I was going to look at and think about were the significant positive f3 statistics (were there any?). Can you explain why these were not helpful in drawing noteworthy conclusions?

Dienekes said...

It's not a spreadsheet, open with a text editor.

@Matt

There are 760380 possible f3(A; B,C) choices so this would take weeks to compute.

eurologist said...

"the North European element will be native to Eurasia spread from the borders of Europe all the way to the borders of Mongolia...

Ponto,

I think admixture stretches back to and from the first European settlement until the Bronze Age and beyond. But I don't believe in endless unidirectional flows to the West.

The Gravettian already had a very strong eastern component, and I tend to believe that the Franco-Cantabrian refugium had a stratified structure, with more NE people at the NE margin, who then would dominate post LGM NE expansion (NE Magdalanian), in addition to the existence of Eastern refugia (Moravia, Balkans, Crimea, Caucasus, Kazakhstan, Altai, etc.). To me, the Ahrensburg and Hamburg cultures also show Eastern influences - although only some of this means connection to Central or Eastern Asia (e.g., Western Kazakhstan is part of Europe...).

Even without concrete flows of specific Eastern populations into Europe (but rather a 40,000 years shared heritage), it should be possible to disentangle this with better sampling in the respective regions, and future ancient DNA that should be expected from some of these colder and dryer regions.

Grey said...

"the Mediterranean element in Europe will be confined totally to the circum Mediterranean and the Near East"

I think it will spread up the Atlantic coast as well but in a different proportion.

Kurti said...

@ jackson_montgomery_devoni

Yes it does make sense and I assume that it ultimately originated in the Levant/Mesopotamia and moved first into Sardinian trough a sea root and from there moved further forward into Iberia (also trough sea) and later spread across Europe.