August 22, 2012

East Eurasian-like ancestry in Northern Europe (part 3)

(This is the third part of the series. See part 1 and part 2.)

In the first two parts of the series, I showed that northern European populations show hints of East Eurasian ancestry when compared against Sardinians. I used Dai, Han, and Karitiana as reference populations for East Eurasia. In the current post, I extend this analysis by using HGDP Papuans and the Onge (Reich et al. 2009) from the Andaman Islands.

The f4 statistics using Karitiana, Papuan, and Onge populations can be found in this spreadsheet.

Below, you can see that they are all near perfectly correlated with each other.

The visual appraisal is confirmed when we calculate the correlation coefficients:

The fact that all three populations track the same signal is strong evidence for the direction of gene flow: from Asia into northern Europe. If the signal was present in only one of the three populations, then it could conceivably be an artefact of gene flow in the opposite direction (from northern Europeans to the affected population). But, the fact that all three populations show the same pattern would require northern European-like admixture in the Andaman Islands, Papuan New Guinea and South America, which does not appear very parsimonious.

While the signals from the three populations are correlated, their intensity varies. The Z-scores provide a measure of this intensity. The mean Z-scores using a Karitiana, Papuan, and Onge reference across all populations are respectively -17.7, -8.0, and -6.0.

While I did not include the Han reference of part 1 in this analysis, inspection of the f4 statistics (which can be obtained at the bottom of that part), suggests that the Z-scores become more significant when using an Onge, Papuan, Han, and Karitiana reference in that order. For example, for the Finnish_D population, they are: -10.037, -13.2949, -23.9305, and -27.764 respectively.

It thus appears that the element contributing East Eurasian-like ancestry in northern Europeans was derived from the northern spectrum of East Eurasians; the Karitiana may live in South America today, but they trace their ancestors to northern Eurasia, having entered the Americas c. 15ka.

In my opinion, the signal has been formed by a superposition of a few factors:

  1. The fact that Y-haplogroup R, the main lineage in modern northern Europeans has a common origin (Y-haplogroup P) with haplogroup Q, the main lineage in modern Amerindians, and many Siberians. We can hypothesize that the population that brought R into Europe was intermediate genetically across the Caucasoid-Mongoloid spectrum. In West Eurasia, this population admixed with the Palaeo-West Eurasians (Y-haplogroups IJ, G, and possibly LT), and contributed their DNA primarily to the northern Europeoids.
  2. Other population movements of more regional impact, such as Y-haplogroup N, which affected mainly Uralic, Baltic, and East Slavic populations, as well as elements from the mixed West/East Eurasian mtDNA contact zone that ancient DNA analysis has revealed in Eastern Europe and Siberia.
The raw dumps of fourpop output for Papuan and Onge reference can be found here.


Hector said...

The following scenario, which I do not think is particularly parsimonious, is still plausible.

1 Very old West to Northern East Eurasian influence
2 Northen East Eurasian influence on the three populations.

Klyosov probably would advocate a variant of this.
1 for him would be represneted by Y haplogroup MNOPS.
with a caveat that Northern Eurasians were less admixed with previous populations perhaps represented by Y haplogroups C D.

But in that case 1 would be around or older than 40K and as I mentioned previously it is almost meaningless to talk about East and West Eurasians for populations that old. It reeks of political agenda than scientific.

I am not necessarily convinced by Dienekes conclusion but his approach is refreshing while not completely new. In particular he applied, to genetics, the popular method in linguistics of determining the direction of loan words.

It is not the first time that I see this in genetics but it almost ranks up as something original. Very impressed.

German Dziebel said...

You did a good job yielding support for my out-of-America theory. It all makes perfect sense. Karitiana is a New World population, hence in the point of fact the gene flow to Europe came from the New World. It doesn't need to have come from Amazonia, as any Amerindian population from North to South America would perform in the same way as Karitiana.

What's up with San? Can you calculate Z-scores for San, or the panel is ascertained in them? I presume they will be lower than Onge, but would love to see some numbers.