Was Dienekess unto this before me - Africa-Europe Connection

[djoser-xyyman]

Running down TreeMix I came across this from Dienekes.

Was way ahead of his time. This was written in 2012.

dienekes.blogspot.com/2012/03/treemix-analysis-of-north-eurasians-and.html

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Complaint by a customer to the Creators of the program TreeMix about the results being obtained. He does not like Europeans carrying greater than 50% African ancestry. He thinks something is wrong with the program and is complaining. Basal Eurasian? he! HE! was around since 2012. He! He!

code.google.com/archive/p/treemix/issues/1

Posted on Mar 16, 2012 by Helpful Hippo

Well known anthropology blogger Dienekes Pontikos has been using Treemix and eventually, when analyzing Eurasians with YRI as outgroup, produced for m=1-10 a 68% weight apparent migration from a point between Basques and Sardinians to YRI (HapMap Yoruba from Nigeria).

vide: www.dienekes.blogspot.com.es/2012/03/treemix-analysis-of-north-eurasians-and.html

It makes absolutely no sense. Although Dienekes is persuaded that it fits some odd hypothesis of his own in which Eurasian males with Y-DNA E massively conquered Africa in some unknown prehistoric episode - something I don't agree with, it should not show up that way in any case.

I believe that it must be a bug and that the developers want to know about this problem. Even if it ends up not being a bug (what would really surprise me) you certainly want to know what your program makes that is so extremely unexpected, right?





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64% from (Sardinians/Basques) to Yoruba; this is difficult to interpret, but there has been evidence in the past that Africans and West Eurasians share more ancestry than Africans and East Asians do. In the linked post, I proposed a major episode of back-migration into Africa, and it is perhaps this that is being captured by this migration edge: Sardinians/Basques are the only two South-West Eurasian populations included, and any back-migration into Africa must have originated in the southern parts of West Eurasia.

Such a high level of back-migration may in fact be plausible, since Yoruba are a predominantly Y-haplogroup E bearing population, and the origin of the DE clade of the human Y-chromosome phylogeny is up in the air with both an African and Eurasian case having been advanced. Personally, I favor the Eurasian case, since within the CT clade, we have two subclades: CF (Eurasian) and DE (Eurasian/African).

Interestingly, John Hawks has recently discovered an unanticipated excess of "Neandertal ancestry" in Yoruba. This may also point to a back-migration into Africa and/or admixture of a group of Africans related to Eurasians (whom I've called Afrasians), with groups of Africans (Palaeoafricans) that split before the H. sapiens/H. neandertalensis common ancestor.

There is, however, another detail in the figure that may have escaped your notice: there is now about 0.5 worth of drift in the figure (left-to-right) as opposed to only 0.12 in the tree without migration edges. So, perhaps what we are seeing is indeed the first sign of admixture between modern and archaic humans in Africa, which has been made more likely by recent anthropological discoveries.

It's not clear to me whether TreeMix has stumbled onto something important or not, but it is certainly worth keeping in mind that the above model fits the data better than the simple tree model. Moreover, TreeMix attempts to reverse the polarity of migration edges, and -apparently- the (Sardinian, French_Basque)-to-Yoruba edge is preferable to the reverse.

So, we should keep our minds open to the possibility that the greater similarity of West Eurasians to Africans is not the result of multiple Out-of-Africa waves, one of which affected only West Eurasians, but of an Into-Africa back-migration from West Eurasia.

So far, tree-based models have focused on how diverse African groups are, and hence, the reduced diversity of Eurasians has been interpreted as an Out-of-Africa bottleneck that carried a subset of African variation into Eurasia.

But, there is an alternative interpretation of the evidence, namely that African groups are diverse because they carry a superset of ancient Into-Africa variation, with the African-specific part of their variation being the result of admixture with pre-existing African hominins. Such a scenario cannot be captured by tree models, but is apparently considered and not rejected by TreeMix which allows for lateral gene flow. Let's wait and see what new things come from full genome sequencing.

[zarahan]

His spiel has several glaring weaknesses. He claims-quote:

But, there is an alternative interpretation of the evidence, namely that African groups are diverse because they carry a superset of ancient Into-Africa variation, with the African-specific part of their variation being the result of admixture with pre-existing African hominins. Such a scenario cannot be captured by tree models, but is apparently considered and not rejected by TreeMix which allows for lateral gene flow. Let's wait and see what new things come from full genome sequencing.

1--Intra-African variation may indeed add to African diversity, but this itself calls certain aspects of his "backflow"
claims into question, in that claimed "EUrasian" variants may simply be a slice of the variation flowing out of
Africa, being originally IN, AND FROM AFRICA. Indeed some scholars hold that certain "root types" of DNA developed
in Africa FIRST, on the principle that gene divergence precedes population divergence.




2--His claim about -quote:
"the African-specific part of their variation being the result of admixture with pre-existing African hominins..

^^Sounds like ad hoc nonsense, and he offers no evidence in support. In fact there is no "African specific" variation.
If all the variants are coming from Africa- ALL are African, not 20% "EUrasian" and 80% African before they have even left
the continent. How can there be "EUrasian" variants when the migrants have not even entered "Eurasia" yet foo? lol

And who says the so-called "Africa specific" variation is due to admixture with "pre-existing African hominins"?
Baloney- and of course, he offers no credible evidence of this fantasy either. In fact, gene variants have
developed among recent Africans without needing any ancient "pre-existing hominins" to explain why. M1a and other
African variants did not need any "pre-existing hominins" shuffling around to make them happen.




3--Few knowledgeable people deny that depending on the era, at some level, there was movement from outside Africa, but
assorted "backflowees" in many cases looked like some tropical Africans, or those labeled in social construct terms "black."
This puts a spike in much beloved "biodiversity" claims of "wandering Caucasoid" waves swamping the shores of Africa.
Different DNA labels for different people still founder on the rock of this phenotypic reality, and the fact that phenotypically
tropical Africans are the most diverse in he world. Narrow noses for example are part of INDIGENOUS African diversity,
there being plenty of scope for them to develop not only through native genetic variation over time, but also based
on climatic variables. Cold high mountain zones, or deserts for example, both within the tropics of Africa, have produced
narrower noses without any need for "incoming Causacoids."

Note- this is not a "denial" of so-called "back migration" just recognition that the diversity of Africa, both as to
(a) built-in native genetically, and (b) based on climatic/enviro variables, does not fundamentally require any
outside influences to explain it. This caveat added because some afro-"enthusiasts," failing to read the data in context,
and failing to qualify sweeping statements, seem to think that there was no outside movement into Africa at all until assorted
folk like Assyrians, Hyskos, Arabs or Greeks showed up. Such absolutist claims, (failing to properly qualify), are shaky and
only allow opponents to score easy debunking points.


^Note- this does not mean that everybody "looked West African.." - variation occurs across widely spaced time and groups..


4--He says tree models do not support his fantasy scenario, and Treemix does not confirm. He then sys lets wait
and see if full genome sequencing will give us the answer. But given the dubious nature of these claims
no amount of "sequencing" will support them.


Dienekes is persuaded that it fits some odd hypothesis of his own in which Eurasian males with Y-DNA E massively conquered Africa in some unknown prehistoric episode -

The only problem with this claim, is that it is bullshiit..

[zarahan]

Was way ahead of his time. This was written in 2012.

^^SO he claims but another theory could be that African migration INTO EUrope, is responsible
for the genetic variation, or vice versa, as African returnees to the continent brought back
Eurasian spouses, servants, etc etc.. They are always pushing the incoming Caucasoids line. OK, well
what about the incoming Africans line into EUrope? Even, steven.

[djoser-xyyman]

They know deep down in their psyche there was never anything like back-migration Africa. It was always a one-directional trek until the ottoman Turks But they need to come up with an explanation for Basal Eurasia and the connectionto YRI. Lazaridis made it clear he could NOT disentangle BE with YRI. Lazaridis 2014.