Ancient Egyptian dna-Kraus et al

[MOESAN]

@Daniel
I'll be long:
You mention:
Two other populations fit as 2-way mixtures in Table S3.5: Neolithic Anatolians fit as ~86% Dzudzuana and ~14% Natufians. This does not disprove that Neolithic Anatolians are approximately a clade with Dzudzuana, since Natufians trace ~86-89% of their ancestry to Dzudzuana (Tables S3.2, 5), and thus Neolithic Anatolians trace >98% of their ancestry from Dzudzuana, also in agreement with the 2-way models of Table S3.2. This does not mean that there was gene flow from the Levant into western Anatolia, as the (unsampled) hunter-gatherer precursors of Neolithic Anatolians may not have been identical to Dzudzuana.
Me :
I wrote to quickly and confused myself, sorry for my hurrying; I did not remember the « Dzudzuana » was considered so high among Natufians, I believed the BE ‘s part was very higher in these last ones. In the graph the direct Dzudzupart is 73 % but yes the total ‘dzudzulike’ part is about 87/88 %. I was wrong, and Natufians were rather poorer in BE than Dzudzuana, what disproves some of my bets.
Concerning flow between Neolithic Anatolians and Levant, a study about AHG and their successors in Néolithic Anatolia estimates an introgression of AHG or AAF to form Levant Farmers (I suppose = PPNB). It does not speak of a flow in the opposite direction at these dates but mentions this South → North flow into ACF (Anatolian Ceramic Farmers).


You :
The paper I quoted had EEF at 66% Natufian and I believe the rest from the Caucasus but I find your take on EEF being half Natufian and half WHG interesting, especially since the consensus is that EEF originated with Basal Eurasians in the Near East.
Me :
In the same answer of your, it’s «Neolithic Anatolians fit as ~86% Dzudzuana and ~14% Natufians. » - some discrepancy here !?: nevertheless EEF is very close to Neolithic Anatolian !
Concerning my « take » : we have to distinguish between « X-like » components and true X origin or introgression. I think the statement would better be « EEF (in some survey, it can vary according to others) is halfway between WHG and a pop akin to Natufian ».


You mention:
Conclusions We summarize our main conclusions from this section:“Western” Near Eastern populations, including Dzudzuana from the Caucasus, belonged to a cline of decreasing Villabruna/increasing deep ancestry (I add : BE in this ‘deep ancestry’ ?): Villabruna→Dzudzuana/Anatolia_N→PPNB→Natufian→Taforalt “Eastern” Near Eastern populations, including Caucasus hunter-gatherers (CHG) and Neolithic Iranians (Iran_N) traced most of their ancestry from populations of this cline, but also had additional Ancient North Eurasian/Eastern non-African (ANE/ENA) admixture."
You :In this case, Dzudzuana and Natufian are basically the same. If I recall, their tools look similar too.
Me :
Dzudzuana and Natufians are on the same cline, and their principal component is Dzudzuana or Dzudzuana-like, so something close to Villabruna-like + BE, but Dzudzuana is closer to WHG & Villabruna, and lack the ANA input.
I found in I. Lazaridis paper :
[To better understand the relationship of Dzudzuana to other ancient West Eurasian populations, we performed symmetry testing using f-statistics(Extended Data Fig. 5). These analyses show that ESHG share more alleles with Dzudzuana than with PGNE populations, except Neolithic Anatolians who form a clade with Dzudzuana to the exclusion of ESHG (Extended Data Fig. 5a). Thus, our results prove that the European affinity of Neolithic Anatolians does not necessarily reflect any admixture into the Near East from Europe, as an Anatolian Neolithic-like population already existed in parts of the Near East by ~26kya.]
So, Dzudzuana forms a clade with Anatolian Farmers, not with Natufians, spite it seems the principal component in natufians. The fact the Villabruna-like is old in Anatolia does not mean Villabruna iself came recently from Near-East.


some bits of biblio :
[The Villabruna cluster has been modeled s contributing to both the ~30kya Věstonice and ~20kya El Mirón-cluster populations suggesting that it must have existed somewhere in relatively unmixed form long before the oldest genetic data we have from it at ~14kya. However, it is unlikely that the Villabruna cluster sojourned in mainland Europe, as members of the cluster have been attested there only by ~14kya, marking an increased affinity of these European populations of the time to Near Eastern ones.] BTW « increased affinity » is not « quasi-identity » !


[Post-glacial Near Easterners and North Africans (PGNE) (CHG, Natufians, TaforaltIbero-Maurusians from North Africa, and early Neolithic farmers from Anatolia, Iran, the Levant and the Maghreb) are strongly differentiated from all European and Siberian hunter-gatherers (ESHG) (FST= 0.078−0.267). By contrast, Dzudzuana is genetically closer to both contemporaneous Gravettians from Europe (0.051±0.012) and also to the much later Neolithic Anatolian farmers (0.039±0.005) who are genetically closest to them according to this measure. Genetic drift inflates FSTover time, so the affinity to the Gravettians may partly be due to the great age of these samples. However, age cannot explain the affinity to much later Neolithic Anatolians of ~8kya, a population closer to Dzudzuana than any other PGNE European hunter-gatherers in our analysis form a cline with Villabruna/WHG samples on one end and ANE on the other. None of the PGNE populations other than the Neolithic Anatolians cluster with the Ice Age Caucasus population from Dzudzuana. As reported previously, present-day West Eurasians are much more homogeneous than ancient ones, reflecting extensive post-Neolithic admixture.]


Rather, ancestry deeply related to the Villabruna cluster was present not only in Gravettian and Magdalenian-era Europeans but also in the populations of the Caucasus, by ~26kya. Neolithic Anatolians, while forming a clade with Dzudzuana with respect to ESHG , share more alleles with all other PGNE suggesting that PGNE share at least partially common descent to the exclusion of the much older samples from Dzudzuana.


Western PGNE populations, including Neolithic Anatolians, pre-pottery Neolithic farmers from the Levant (PPNB), Natufians, and Taforalt, can all be modeled as a mixture of Dzudzuana and additional ‘Deep’ ancestry that may represent an even earlier split than the Basal Eurasians.]
& : just to say things are not always very simple in anDNA !


I ‘ll try to put order in my head on this matter :
Villabruna and certainly the ‘villabruna-like’ in Dzudzuana are old heritages of Common West Eurasian ;
the BE (and perhaps their ‘deep’ ancestry) present in Near-East, seems absent in ancient European HG’s, even in the Villabruna cluster, and, more interesting, almost absent later in Balkans HG’s ; this seems exclude that the most of Balkans HG’s came from Near-East. Or it would ask for a very strong drift.
Nothing proves us with certainty that this ‘villabruna-like’ ancestry in Near-East came lately from Europe into Near-East, nor the contrary.
As BE and ANA present among Natufians, are absent from European HG’s, I can exclude that some ‘natufian-like’ or even ‘dzudzuana-like’ pop colonised Europe before the Agriculture.
Let alone the supposed percentages of components in the diverse pops, varying according to surveys, we see the big global distances between European HG’s or every time and the Near-East ones, even before the perceptible CHG or Iran inputs and even if the SE Europe HG’s And Villabruna cluster are a bit less far.
To conclude, it’s uneasy to localise the Common West Eurasian part ancestral to Dzudzuana and to others, I see it around Black Sea or Caucasus, or not too far at some very ancient stage of history, a central position between West and Central-East Eurasia, close to possible glacial refuges.

 

[Daniel]

I prefer the other scheme (the Dzudzu's paper one) - but in the one you produce, we see interactions between Villabruna and Levant, and then between Villabruna and Anatolia. In fact, rather a 'villabrunalike' from Dzudzuana?
we have to put apart hypothetical ancestral populations concerning auDNA and true historical populations, well dated;
the BE part of Natufians ancestors branched off the ancestors of Villabruna long ago in this scheme, and only later mixed with descendants of this late one.
the admixture %s calculated (more or less accutely) are not sufficient, we have to see the auDNA distances, and then, spite the late strictly speaking Villabruna people were living roughly at the same time than the Natufians, they were very distant one from another, by different partial new admixtures but also by drift, and drift requires time of separation. So for me, no, Natufian cannot be ancestor to Villanova, even in the sensu stricto Villabruna. I could use the argument of chronology: at least historical true Natufians are not old enough to be ancestors of any kind of 'villabruna'.

Image from Dzudzuana paper and Ancient human genomes suggest three ancestral populations for present-day Europeans

Dzudzuana is dated twice as old as Villabruna and as seen in the tree, Lazaridis has Basal Eurasian ancestry that dates much earlier than WHG's West Eurasian ancestry.

In the Dzudzuana paper, Lazardis states: "The earliest ancient DNA data of modern humans from Europe dates to ∼40 thousand years ago^1-4, but that from the Caucasus and the Near East to only ∼14 thousand years ago5,6, from populations who lived long after the Last Glacial Maximum (LGM) ∼26.5-19 thousand years ago7."

Five years earlier he used the exact same tree but had Near Eastern ancestry as vastly older: “WHG/Eastern non-African split must have occurred >40,000 years ago (as it must predate the Tianyuan²² individual from China which clusters with Asians to the exclusion of Europeans). The Basal Eurasian split must be even older, and might be related to early settlement of the Levant²³ or Arabia^24,25 prior to the diversification of most Eurasians, or more recent gene flow from Africa²⁶. Ancient human genomes suggest three ancestral populations for present-day Europeans. His Bar Josef reference 23 states: “In sum, it appears that in spite of the chronological ambiguities, archaic human types related to Modern humans who migrated out of Africa at an unknown age —sometime between 300-100 Ka— formed the early population of the Levant.”

 

[Daniel]

Im thinking Dzudzuana ancestral to Villabruna is possible?

Wait, where are you seeing that Dzudzuana has more BE than Natufian?

 

[MOESAN]

View attachment 12459Image from Dzudzuana paper and Ancient human genomes suggest three ancestral populations for present-day Europeans

Dzudzuana is dated twice as old as Villabruna and as seen in the tree, Lazaridis has Basal Eurasian ancestry that dates much earlier than WHG's West Eurasian ancestry.

In the Dzudzuana paper, Lazardis states: "The earliest ancient DNA data of modern humans from Europe dates to ∼40 thousand years ago^1-4, but that from the Caucasus and the Near East to only ∼14 thousand years ago5,6, from populations who lived long after the Last Glacial Maximum (LGM) ∼26.5-19 thousand years ago7."

Five years earlier he used the exact same tree but had Near Eastern ancestry as vastly older: “WHG/Eastern non-African split must have occurred >40,000 years ago (as it must predate the Tianyuan²² individual from China which clusters with Asians to the exclusion of Europeans). The Basal Eurasian split must be even older, and might be related to early settlement of the Levant²³ or Arabia^24,25 prior to the diversification of most Eurasians, or more recent gene flow from Africa²⁶. Ancient human genomes suggest three ancestral populations for present-day Europeans. His Bar Josef reference 23 states: “In sum, it appears that in spite of the chronological ambiguities, archaic human types related to Modern humans who migrated out of Africa at an unknown age —sometime between 300-100 Ka— formed the early population of the Levant.”

Please, don't confuse population-like component (kind of plausible ghost) with historical true populations.
'Basal Eurasian' (a component, not an historical pop) splitted long ago from the most of European HG's of any time;
But Dzudzuana, absent here on your old graph, IS NOT 'Basal Eurasian', and Natufian iIS NOT 'Basal Eurasian'; they are apparently mixes of a 'Common Western Eurasian' or here only 'West Eurasian' with 'Basal Eurasian', and in the case of Natufian (absent too on your graph), an addition of 'Ancient or Ancestral North African', itself an old mix with partly some common stuff.
Look at the dates written on your own graph:* specific 'Villabruna' and 'Natufian' are of same period spite their ancestral components are evidently older. But the real 'Natufian' pop CANNOT have given birth either to real 'Villabruna' or (evidently) to older 'Villabruna cluster', because whatever the ‘Natufian’s date of birth, they have components which lack among ‘Villabruna’ of any sort.
I don't see how to tell you differently.


* : do’nt take the vertical position of the pops on the graph for a true value of their respective age. Do read the dates, one time again

 

[MOESAN]

Im thinking Dzudzuana ancestral to Villabruna is possible?

Wait, where are you seeing that Dzudzuana has more BE than Natufian?

BE : it’s not God’s words, but my understanding, only :
If I understood well the graph in Dzudzuana paper, ‘Dzudzulike’ has ~28 % of ‘BE-like’ and Taforalt has ~28 % * 65 % of ‘BE-like’, it’s to say 18,2 % of it -
Natufian has 73 % of ‘Dzudzulike’ (so 28 % * 73 % = 20,4 % of ‘BE-like’) and 27 % of ‘Taforaltlike’ (so 18,2 % * 27 % = 4,9 % of ‘BE-like’) ; all in all it would be 25,3 % of ‘BE-like’ in Natufian ; it’s rough calculations based on the graph, but it seems showing that Natufians would have been a little less than Dzudzuana people. Maybe I’m wrong ? It's true I believed there was more BE among Natufians...

 

[Daniel]

Please, don't confuse population-like component (kind of plausible ghost) with historical true populations.
'Basal Eurasian' (a component, not an historical pop) splitted long ago from the most of European HG's of any time;
But Dzudzuana, absent here on your old graph, IS NOT 'Basal Eurasian', and Natufian iIS NOT 'Basal Eurasian'; they are apparently mixes of a 'Common Western Eurasian' or here only 'West Eurasian' with 'Basal Eurasian', and in the case of Natufian (absent too on your graph), an addition of 'Ancient or Ancestral North African', itself an old mix with partly some common stuff.
Look at the dates written on your own graph:* specific 'Villabruna' and 'Natufian' are of same period spite their ancestral components are evidently older. But the real 'Natufian' pop CANNOT have given birth either to real 'Villabruna' or (evidently) to older 'Villabruna cluster', because whatever the ‘Natufian’s date of birth, they have components which lack among ‘Villabruna’ of any sort.
I don't see how to tell you differently.


* : do’nt take the vertical position of the pops on the graph for a true value of their respective age. Do read the dates, one time again

Ghost populations are real and in this case ive been trying to show you who they are. For some reason probably biased, Lazaridis et al. has totally abandoned his earlier recognition that Levantine Cro-magnons are the original Basal Eurasians--first to branch off from the Oceanic-like non-Africans.

Not only that, Lazaridis et al. then rests his whole opening line upon Europe's Oase being 40,000 years old. I guess it could be due with Oase having lots of Neanderthal and Lazaridis' presumption that Basal Eurasians have none but I say that these Oceanics have always had relatively lots of Neanderthal.

You totally ignored my bringing up Lazaridis et al's earlier Levantine Cro-Magnon report but answered with talk of liking the Dzudzuana tree better and that Natufian Basal Eurasian branched off of Villabruna. So now I post the Dzudzuana tree and show you that neither of Lazaridis’ trees show his conclusion of Natufian's Basal Eurasian descending from Western Hunter Gatherers but you keep ignoring that too. Not only that but you now seem to want to totally abandon BE and or pretend that its vertical position on the tree is not like it shows. You also now refer me back to the newer tree because you feel it shows the 14kya dated Natufian being to young to be ancestral to 15kya Villabruna

That said, its likewise negative evidence to insinuate that 27kya Dsudzuana is the earliest line of Basal Eurasian simply because he has some Basal Eurasian. In fact, contrary to your earlier statement, Natufians are estimated to be around 64% Basal Eurasian while Dzudzuana is only 28% Basal Eurasian, which favors my point of their lineage being ancestral to West Eurasians such as WHGs.

I could be missing something because Ive had a really bad cold (hopefully not you know what) but I'm sure I'm on to something here

 

[MOESAN]

concerning BE I can referr myself to Lazaridis' diverse graphs: they have no big contradiction between them ATW. Personally I have not the scientific skils to discuss seriously Lazaridis; seemingly you have!
Cro-magnon has nothing to do recently with Natufians nor more ancient known Palestine remnants, besides their common human heritage and surely OOA.
for the other points, I think you don't understand anything in diverse works and in my posts.
The end.

 

[Daniel]

concerning BE I can referr myself to Lazaridis' diverse graphs: they have no big contradiction between them ATW. Personally I have not the scientific skils to discuss seriously Lazaridis; seemingly you have!
Cro-magnon has nothing to do recently with Natufians nor more ancient known Palestine remnants, besides their common human heritage and surely OOA.
for the other points, I think you don't understand anything in diverse works and in my posts.
The end.

Again, you are totally dismissing Lazaridis' et al prior 2015 conclusion of "Levantine Cro-Magnons" representing Basal Eurasians, which later Natufians are estimated to have carried 64%

but then Lazaridis et al seem to ignore their earlier conclusion as well but they do write this with capitals: "Europeans are differentiated by an excess of up to ~20% Villabruna-related ancestry relative to non-European populations AND ALSO BY A RELATIVE **LACK OF **EXTRA ‘DEEP’ ANCESTRY **COMPARED**TO THE NEAR EAST AND NORTH AFRICA , a type of ancestry that may only partially be explained by the Basal Eurasian ancestry of ancient West Eurasian populations and MUST ALSO TRACE TO AFRICA"

Well your right, they should make this stuff easier to read. Im not sure how they come to this conclusion when EFF are estimated to contain 66% Natufian. Unless modern Europeans are closer to Villabruna than they are to EFF and could that actually have to do with the R1b line. Nah, Villabuna's R1b is V88 which is Levantine and African. Maybe his WHG I2a who remained elite among the Yamnaya