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Things are not that clear for other Caucasoid populations, e.g., southern
Europeans or northwestern Europeans. The authors assume that the different
position of these two groups on the San-Chinese axis is due only to
Sub-Saharan admixture in southern Europeans. This implicit assumption is
the Achilles' heel of the paper.
Because of genetic drift, two populations that diverged from a common ancestor
will have different allele frequencies. However, imagine if we looked at these
allele differences and saw that a population A not only had different frequencies
than B, but also the difference in frequencies tended to be in the direction of a
Sub-Saharan population. For example, at some locus f(A)=0.4, f(B)=0.3, and
f(Sub-Saharan)=0.1. You can see that B's frequency deviates from A's in the
direction of Sub-Saharans. This may occur due to random drift for one particular
marker, but if it occurs systematically across the genome, then admixture is a
likely explanation. This is the basis of the 3-population test used by the authors.
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Note that because of symmetry, a highly negative value in their 4-population test
(x, CEU, Papuan, YRI) indicates Sub-Saharan admixture, while a highly
positive one would indicate "Papuan" admixture! The authors do observe
positive values, suggesting that some northern European populations are
Papuan-shifted even with respect to CEU, most notably Russia with a Z-score of
11.4. Thankfully, we are spared a paper on Papuan admixture in Russia.
These tests are an important statistical tool, and many of this paper's authors
have used them before to study the Indian Cline of populations. However, the
In their study of the Indian Cline, Reich et al. (2009) excluded groups that
were shifted towards CHB, thus ensuring that they were left with groups that
could be modeled as a simple mix of two ancestral population elements.
Moreover, they used the Onge a relatively isolated population from the Indian
Ocean as a control group that could be said to form a clade with Ancestral South
Indians at the exclusion of West Eurasians. In the current paper it is simply
assumed that northern Europeans have no African admixture.
Application of the test to each West Eurasian population (using A =
YRI and B= CEU) finds little or no evidence of mixture in North
Europeans but highly significant evidence in many Southern
European, Levantine and Jewish groups (Table 1).
In other words: taking CEU (a northern European population) as the
standard, northern Europeans have no evidence of African admixture.
Sardinians are an important test case for the authors' model. Their 3-population
test shows no evidence of admixture, while the 4-population test does. Moreover,
their STRUCTURE analysis shows a trivial 0.2%, whereas the authors estimate
their Sub-Saharan admixture as 2.9%.
Let's begin by performing a PCA analysis of Sardinians, CHB, and CEU, which
is shown below.
CEU is shifted towards CHB relative to Sardinian. This is made more visually
obvious if we blow up the CEU/CHB portion of the above plot:
CEU is shifted towards CHB by 2.4% relative to Sardinians. This is quite close
to the 2.5% East/South Asian K=3 admixture for Britons in my most recent
analysis, done with a different East Asian reference and a different method
(ADMIXTURE); the CEU sample of White Utahns has been repeatedly shown
to be most similar to people from the British Isles or Northwestern Europe.
and a blowup:
Sardinians are shifted 1.1% relative to CEU towards YRI. Again, this is close to
the 0.9% K=3 Sub-Saharan ADMIXTURE result I recently obtained.
So, where does the 2.9% Sub-Saharan admixture in Sardinians come from?
Moorjani et al. estimate this percentage under the assumption that Northern
Europeans are not shifted towards Chinese, i.e., that East Eurasians are
irrelevant. Clearly, as we have seen, this is wrong. As we shall see, this
erroneous assumption leads to the erroneous admixture estimate.
Now, I will demonstrate how the spurious 2.9% result can be obtained. By
doing so, it will become obvious why Moorjani et al. obtained this result as a
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result of ignoring the eastern Asian shift of their northern European sample in
their analysis.
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When we run all four populations together, Sardinians are shifted towards YRI
along Dimension 1, and CEU are shifted towards CHB along Dimension 2.
Given that the eigenvalue for PC1 is approximately twice (50.15) that for PC2
(25.31), and doing a little high school geometry on the triangle (Sardinian, CEU,
YRI), we project Sardinian onto the CEU-YRI line, intersecting at point X. We
thus obtain the estimated "CEU" admixture as:
[distance(YRI,X)-distance(X,CEU)]/[distance(YRI,X)+distance(X,CEU)]
=
[distance(YRI,
Sardinian)^2-distance(CEU,Sardinian)^2]
distance(CEU,YRI)^2
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Ashkenazi Jews
The example of the Sardinians showed how lack of controling for East Eurasian
shift tended to overestimate the degree of Sub-Saharan admixture. Another test
case is that of Ashkenazi Jews. The authors find no evidence of admixture with
their 3-population test, but do find such evidence with their 4-population test, as
well as with STRUCTURE.
On a PCA plot of CHB, Ashkenazi (Behar et al. 2011), and CEU, the Ashkenazi
are shifted 3.3% towards CHB along eigenvector 1.
On a PCA plot of YRI, CEU, and Ashkenazi, the Ashkenazi are shifted by 5.3%
towards YRI.
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In the case of the Sardinians, their African-shift together with CEU's Asian-shift
caused Sardinians/CEU to diverge on the African-Asian axis, and Moorjani et al.
took the entirety of this divergence to represent African admixture in Sardinians.
In this case Ashkenazi are both Asian- and African-shifted relative to CEU. The
two shifts partially cancel each other out: Ashkenazi are pulled towards Africans
on the YRI-CHB axis because of their YRI-shift, and away from them because
of their CHB-shift. Failing to account for these processes, the authors assume
that only Sub-Saharan admixture in Ashkenazi can accont for the different
position of CEU and Ashkenazi on the Asian-African axis, coming up with a
2.8-3.2% "Sub-Saharan admixture" in two different samples.
And, here is a second way of seeing how this spurious admixture estimate
follows from the phenomenon I am describing. CEU are (in terms of Fst) 0.76
times distant from CHB as they are from YRI (Fst=0.17 and 0.129). In other
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Papuans
I have also carried an experiment with Sardinians, Ashkenazi Jews, CEU, and
Papuans, instead of CHB, as Papuans are also used in the paper as an outgroup
population.
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It is clear that the populations show differential shift towards Papuans that is
concordant with their above-described shift towards the Chinese.
Henn et al. (2011) contains Tuscan, Yoruba, Maasai, Bulala samples, so I ran
the Tuscans as test data in a supervised ADMIXTURE 1.1 analysis together
with these African groups, HGDP-CEPH North_Italian, and HapMap3 CEU.
That is, I'm playing along -for the sake of argument- with the idea that East
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The inclusion in the paper of HapMap3 Luhya Bantu but not of HapMap3
Luhya Maasai is puzzling, and the choice of one group over the other is passed
in silence.
Much more can be said, but let's summarize: the model of Moorjani et al. (2011)
fails because:
1. It does not account for the West-East Eurasian axis, folding everything
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