# Population Genetics > Autosomal Genetics >  Northern Route for Out of Africa based on Whole Genomes

## Angela

This is the link to the Pagani et al study:
http://www.cell.com/ajhg/fulltext/S0...2815%2900156-1

"The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt."

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## LeBrok

I didn't go through paper yet, but I'm confused why they measure relation of hapogorups and not autosomal DNA? Probably I'm missing something. Furthermore it would be great to broader the scope, and not only concentrate on two countries. There could have been quick migrations from SSA to far parts of the world. I'm sure some central Africans migrated to Australia, not leaving much of a trace in modern populations in Asia. They could have taken alternative route.

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## bicicleur

I don't understand how such study can pinpoint what happened before the last ice age.
During last ice age few people survived in small pockets. The Sahara came much further south. The small pockets were the Ethiopian highlands, the Upper Nile, the southern Levant and the now submerged Persian Gulf.
If you want to know more I suggest Jeffrey I Rose :

http://www.jstor.org/stable/10.1086/657397

He has written many more articles on the Nubian complex and the Arabian paleolithic which shows that people were in Arabia since 125 ka and expanded from there some 55 ka.
So there was no straight OOA as Pagani et al above claim.

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## Angela

The evidence of the Paleolithic in Arabia is certainly a problem with the dating.

Now that I've read the paper more carefully, there are also problems with the populations they chose and the assumptions they made about their ethnogenesis. 

It's the same flaw that was present in a lot of the analyses prior to the availability of ancient dna. How do we know that the people currently living in certain areas are representative of such ancient populations? The authors say that they have solved this problem by "masking" the "Eurasian" dna in Egyptians and Ethiopians, but I'm not convinced that's possible. 

None of this means they're wrong about the initial flow using the northern route, of course.

So, I don't think this is very persuasive. I wish Dienekes were still posting. He had a lot of say at one point about OOA dating back to 125,000 years ago and then having a long sojourn in Arabia.

http://dienekes.blogspot.com/2013/12...lithic-in.html

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## bicicleur

Dienekes link leads to another article of  Jeffrey I Rose 

https://www.academia.edu/5401210/Through_a_prism_of_paradigms_a_century_of_research _into_the_origins_of_the_Upper_Palaeolithic_in_the _Levant

he demonstrated that the expansion of stone blade technology some 50 ka in the Levant and soon after in Europe, central Asia and India originated in Arabia and not in Africa

only a double expansion from Arabia can explain how haplo D in SE Asia got seperated from his bortherclade E in Africa by their nephews C and F : 
all 4 were in Arabia, and D and E moved out of Arabia first maybe as early as 70 ka, then C and F expanded around 50 ka with the stone blade technology

what exactly happened in Arabia 125-50 ka and how the interaction with Neanderthals was is still a mistery, but in the end they developped stone blades which outcompeted the Neanderthal levallois flakes

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## Expredel

C likely left Africa shortly before D left Africa around 55K ago (through Arabia) because it inhabits more islands, they obviously left using boats. F left around 45K ago through Arabia. E left around 15K years ago through Egypt. It's probably this late migration they are observing. There's no proof of E1b1 being outside of Africa before the ice age.

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## LeBrok

> There's no proof of E1b1 being outside of Africa before the ice age.


 Do you mean LGM (Last Glacial Maximum around 20 kya)? Because last Ice Age started 120 kya and ended just 12 kya.

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## Angela

Maybe the masking _is_ effective. Here is what they say about it:

"This finding was robust to a wide range of potential artifacts stemming from uncertainties in the masking process (Figures S3, S4, and S6A; Table S4; note particularly the false-positive rate displayed in column 8) and was replicated in a South Asian population (GIH; Figure S6B). Furthermore, we showed with simulations that the error rate present in the masking process (Table S4) was unlikely to affect our findings (Figures S4 and S6). Even when we added a 10% misclassification error to the Ethiopians, Egyptians held as the African population showing the highest affinity to non-Africans."

So, if the masking was effective, then it would mean that the _African_ portion of the Egyptians has a higher affinity to non-Africans than the _African_ portion of the Ethiopians, which would be evidence that the migration was through Egypt rather than Arabia. That wouldn't mean that _all_ the African in Egyptians (20% of their total genome) remains from that time, but some of it does, yes?

However, it's been posited that some of the haplotype sharing between Egyptians and non-Africans stems from early back to Africa migrations. (Y dna "E" ususally) This is what they have to say about that...

"Alternative scenarios involving early back-to-Africa migrations27 as the source of haplotype sharing between Egyptian′ and non-African samples were considered as sources of the observed pattern. However, such confounding backflow would need to have taken place prior to the split between East Asians and Europeans (ca. ∼40,000 years ago) and, if this genetic component originated from the main OOA founding event, is likely to have been removed by the non-African masking procedure, which was designed for this purpose."

This would also take care of the Neanderthal admixture problem, as we know there were Neanderthals in the Levant, so that would explain how all OOA populations have it.

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## LeBrok

> Maybe the masking _is_ effective. Here is what they say about it:
> 
> "This finding was robust to a wide range of potential artifacts stemming from uncertainties in the masking process (Figures S3, S4, and S6A; Table S4; note particularly the false-positive rate displayed in column 8) and was replicated in a South Asian population (GIH; Figure S6B). Furthermore, we showed with simulations that the error rate present in the masking process (Table S4) was unlikely to affect our findings (Figures S4 and S6). Even when we added a 10% misclassification error to the Ethiopians, Egyptians held as the African population showing the highest affinity to non-Africans."
> 
> So, if the masking was effective, then it would mean that the _African_ portion of the Egyptians has a higher affinity to non-Africans than the _African_ portion of the Ethiopians, which would be evidence that the migration was through Egypt rather than Arabia. That wouldn't mean that _all_ the African in Egyptians (20% of their total genome) remains from that time, but some of it does, yes?
> 
> However, it's been posited that some of the haplotype sharing between Egyptians and non-Africans stems from early back to Africa migrations. (Y dna "E" ususally) This is what they have to say about that...
> 
> "Alternative scenarios involving early back-to-Africa migrations27 as the source of haplotype sharing between Egyptian′ and non-African samples were considered as sources of the observed pattern. However, such confounding backflow would need to have taken place prior to the split between East Asians and Europeans (ca. ∼40,000 years ago) and, if this genetic component originated from the main OOA founding event, is likely to have been removed by the non-African masking procedure, which was designed for this purpose."
> ...


23andme reports 0.3% Neanderthal in Nigerians. There might have been some substantial back flow.

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## Sile

I do not recall any Pharaohs being of sub-Saharan lineage, their genetics are Eurasian ...............if someone has other info, please advise.

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## bicicleur

> Maybe the masking _is_ effective. Here is what they say about it:
> 
> "This finding was robust to a wide range of potential artifacts stemming from uncertainties in the masking process (Figures S3, S4, and S6A; Table S4; note particularly the false-positive rate displayed in column 8) and was replicated in a South Asian population (GIH; Figure S6B). Furthermore, we showed with simulations that the error rate present in the masking process (Table S4) was unlikely to affect our findings (Figures S4 and S6). Even when we added a 10% misclassification error to the Ethiopians, Egyptians held as the African population showing the highest affinity to non-Africans."
> 
> So, if the masking was effective, then it would mean that the _African_ portion of the Egyptians has a higher affinity to non-Africans than the _African_ portion of the Ethiopians, which would be evidence that the migration was through Egypt rather than Arabia. That wouldn't mean that _all_ the African in Egyptians (20% of their total genome) remains from that time, but some of it does, yes?
> 
> However, it's been posited that some of the haplotype sharing between Egyptians and non-Africans stems from early back to Africa migrations. (Y dna "E" ususally) This is what they have to say about that...
> 
> "Alternative scenarios involving early back-to-Africa migrations27 as the source of haplotype sharing between Egyptian′ and non-African samples were considered as sources of the observed pattern. However, such confounding backflow would need to have taken place prior to the split between East Asians and Europeans (ca. ∼40,000 years ago) and, if this genetic component originated from the main OOA founding event, is likely to have been removed by the non-African masking procedure, which was designed for this purpose."
> ...


I am skeptical too about this masking. How do you know what should be masked and what not? You need to make some assumptions that are not 100 % sure.
And as I explained above there was an early back-to-Africa migration.
Haplogroup E came back to NE Africa.
I'm not sure, did haplo E also have Neanderthal admixture ? 
Haplogrupo_E-ADN-Y jpg.jpg
Considering that there is no subsaharan Neanderthal admixture and judging by the present distribution of E, I would thnik not.
So the backmigration would have been before the Neanderthal admixture.
There were not only Neanderthals in the Levant, but also in the Zagros Mts, while there were modern humans in the Persian Gulf. This is also a possible admixture area.

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## bicicleur

> 23andme reports 0.3% Neanderthal in Nigerians. There might have been some substantial back flow.


that is less than the 2% in Eurasians
it might have been brought by the cattle herders R1-V88 or T from Anatolia or by Islamic Arabs J1-P58

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## bicicleur

> I do not recall any Pharaohs being of sub-Saharan lineage, their genetics are Eurasian ...............if someone has other info, please advise.


IMO anciant Egyptians were mainly indogenous Nile Valley E1b1b mixed with some E1b1a and some farmers form SW Asia, J and T
sub-Saharans would at that time have been haplo A or B

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## Maleth

> I do not recall any Pharaohs being of sub-Saharan lineage, their genetics are Eurasian ...............if someone has other info, please advise.


According to a genetic study in December 2012, Ramesses III belonged to Y-DNA haplogroup E1b1a. The E Y-DNA haplogroups predominate in most Sub-Saharan Africans.[29]

http://en.wikipedia.org/wiki/Ramesses_III

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## Angela

> According to a genetic study in December 2012, Ramesses III belonged to Y-DNA haplogroup E1b1a. The E Y-DNA haplogroups predominate in most Sub-Saharan Africans.[29]
> 
> http://en.wikipedia.org/wiki/Ramesses_III


That's true. I guess it depends what yDna is labelled "SSA", or better yet "Basal African"? I think Bicicleur may be correct. Perhaps "SSA" men, or "Basal Africans", were the "A" and "B" carriers, and _all_ the E lines are products of a back migration. Certainly, though, certain "E" lines are "SSA" today, and the Emperor Rameses' line is one of them, yes?

There are also the Nubian dynasties whose Pharaohs would likely have carried the same lineages. 

As I said before, I just don't understand precisely what is being "masked". Is the autosomal input brought by the back migration of the "E" lineages included in the "Eurasian" that is masked or in the "African" that is left and is being analyzed? Or, as it sounds from the paper, do they not believe that the "E" lineages back migrated and instead believe they stayed in Africa until maybe 15,000 years ago?

Today, the Egyptians seem to be 80% "Middle East", or Eurasian. I'm sure part of that is from the Islamic migrations, but much of it also has to have come from the Neolithic. We just don't know the percentages at the different time periods. 

As to the 20% "SSA" that is left over, I'm not sure if they did, or would even be able to sub-divide it into the "SSA" that has been there since OOA from the "SSA" that came over the millennia. We certainly know that some of it came with the Arab slave trade. Anwar Sadat was a prime example of a recent mating between Egyptians and SSA women.

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## Expredel

> I do not recall any Pharaohs being of sub-Saharan lineage, their genetics are Eurasian ...............if someone has other info, please advise.


Tutankhamun was R1b M269 so the initial Egyptian civilization likely had a Eurasian origin. It appears Egyptian officials forbid the publishing of Tut's haplogroup and it leaked accidentally, so this casts doubts regarding the reliability of all data coming out of Egypt.

The idea of a backmigration of E1b has me confused, it appears Y haplogroup research is quickly becoming political with people having an emotional investment in a certain outcome.

European Neanderthal ancestry averages at 2.6% according to 23andme so 0.3% admixture suggests 15% Eurasian admixture in Nigeria, of which the most likely source is the R1b-V88 migration which peaks near the north-east border of Nigeria.

High resolution Neanderthal admixture maps would be very interesting. The similar distribution might be explained by genetic incompatibility, so while there could have been several admixture events the DNA would be selected against until very little of it remained.

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## Angela

> Tutankhamun was R1b M269 so the initial Egyptian civilization likely had a Eurasian origin. It appears Egyptian officials forbid the publishing of Tut's haplogroup and it leaked accidentally, so this casts doubts regarding the reliability of all data coming out of Egypt.
> 
> The idea of a backmigration of E1b has me confused, it appears Y haplogroup research is quickly becoming political with people having an emotional investment in a certain outcome.
> 
> European Neanderthal ancestry averages at 2.6% according to 23andme so 0.3% admixture suggests 15% Eurasian admixture in Nigeria, of which the most likely source is the R1b-V88 migration which peaks near the north-east border of Nigeria.
> 
> High resolution Neanderthal admixture maps would be very interesting. The similar distribution might be explained by genetic incompatibility, so while there could have been several admixture events the DNA would be selected against until very little of it remained.


Tutankhamen was a Pharaoh of the _18th_ Egyptian dynasty.We have no way of knowing what yDna lineages the previous *17* dynasties carried. They all could have carried one form or another of yDna "E" for all we know. If Tutankhamen was R1b 269, which I tend to doubt, he might just as well have been descended from a Hyksos warrior who got lucky, even though the dynasty was devoted to expelling the Hyksos...sort of like Somerled turning out to be R1a. 

Regardless, it has nothing to do with "racial" classification if that is your interest. Lots of R1b black Africans all the way in Cameroon and other places in West Africa...you don't have to stay in Egypt. More likely, as the reconstructions show, Tutankhamen was probably a mixture of "Eurasian" and "African". A Pharaoh from a much earlier time, like Djoser, might have been even more autosomally African.

https://news.artnet.com/wp-content/n...-real-face.jpg



http://www.nemo.nu/ibisportal/0egypt...joserhelio.jpg


The scientists who propose that there might have been a back migration of y dna "E" into Africa are not African or even Near Eastern. Your conspiracy theories are baseless.

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## Sile

> IMO anciant Egyptians were mainly indogenous Nile Valley E1b1b mixed with some E1b1a and some farmers form SW Asia, J and T
> sub-Saharans would at that time have been haplo A or B


R1 haplogroup entered Africa centuries before J or T ever did. 
This points to Pharaohs or ancient Egyptians as being either E or R1 people in majority.

The isotope of Pharohs tested reveals no Sub-Saharan or Nubian.

Maybe the Bedouins of the Negev played a huge part in this society as well as Levantine peoples.

http://www.academia.edu/3642572/Unra...Neolithisation

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## Maleth

> Tutankhamun was R1b M269 so the initial Egyptian civilization likely had a Eurasian origin. It appears Egyptian officials forbid the publishing of Tut's haplogroup and it leaked accidentally, so this casts doubts regarding the reliability of all data coming out of Egypt.


Here is an interesting article

http://www.livescience.com/15388-dis...hamen-dna.html


Logically I find it difficult to believe that early Pharaohs can fall in the R1b category, its a little bit like saying that the Danish royal line is subsaharn e1b1a considering a logic historical path and geographical proximities and haplogroups migrations of the time. I am more inclined to believe that it could have been more probable with much later Pharaonic dynasties

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## Maleth

> Tutankhamen was a Pharaoh of the _18th_ Egyptian dynasty.We have no way of knowing what yDna lineages the previous *17* dynasties carried. They all could have carried one form or another of yDna "E" for all we know.


Why is that Angela? Just out of curiosity the dna analises of Ramses is not conclusive?




> Lots of R1b black Africans all the way in Cameroon and other places in West Africa...you don't have to stay in Egypt.


Thats correct but that would be the V88 type. Do we have a time when R1b migrated back to Africa? If not mistaken the re migration took place through Iberia. Would it have spread back to North Africa by that time?. I know some of the R1b V88 is present in North Africa in current populations

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## Angela

> Why is that Angela? Just out of curiosity the dna analises of Ramses is not conclusive?
> 
> 
> 
> Thats correct but that would be the V88 type. Do we have a time when R1b migrated back to Africa? If not mistaken the re migration took place through Iberia. Would it have spread back to North Africa by that time?. I know some of the R1b V88 is present in North Africa in current populations


So far as I know the yDna analysis of Ramses is correct, which means he was indeed, as you pointed out, E1b1a. However, he was from the 20th Dynasty (his rule started in 1186 BC). Expredel stated that Tutankhamen, who was from the 18th dynasty (he ruled from 1361 to 1352 BC), was yDna R1b M269, and he was assuming, I believe, that as Tut was from an earlier dynasty than Ramses, his R1b lineage is the original lineage of the Pharaohs of Egypt.

The only so called "proof" that Tut was R1b is that during a presentation about the testing of Tut's remains a screen shot of yDna results was shown when they were describing the testing, and when the values from that screen shot were run through a predictor it's claimed that the values are those of someone who is R1b. That may in fact be the case, but we don't know if the screen shot was of a default result, perhaps that of one of the scientists, and was just used for demonstration purposes, or if it was indeed a screen shot of Tutankhamen's results. 

Anyway, my point was that *even if* Tutankhamen was R1b, that would not be any proof that all the prior Egyptian dynasties were R1b, much less M269. 

My comment about the Hyksos was because some people used to speculate that the Hyksos were an Indo-European group related to the Hittites. That's no longer considered a mainstream idea, with most experts now believing they were a Semitic speaking group related to Canaanites. Of course, there _is_ R1b in the Near East, and not just of the V88 variety, so it's possible there was some in the Hyksos, although I doubt it was M269. Still, ancient dna can surprise, so I never say never. :)
http://en.wikipedia.org/wiki/Hyksos

When people talk about the back-migration of Eurasians into Africa they can be talking about the very early movement of the "E" lineages back to Africa (if the researcher thinks early forms of "E" might have been in Arabia or in the Levant, for example), or the movement of R1b herders (V88) down into Africa, or perhaps the "J" lineages.

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## Hauteville

Weren't the early Egyptians of Berber caucasoid stock?

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## Sile

> Why is that Angela? Just out of curiosity the dna analises of Ramses is not conclusive?
> 
> 
> 
> Thats correct but that would be the V88 type. Do we have a time when R1b migrated back to Africa? If not mistaken the re migration took place through Iberia. Would it have spread back to North Africa by that time?. I know some of the R1b V88 is present in North Africa in current populations


*Haplogroup R1b1c-V88 has a Eurasian origin and entered Northeast Africa from the Near East. The number of sublineages(L=5) stemming from R1b1c-V88 indicates an expansion.

When the J1 and R1b1c-V88 expansions are compared, two differences become apparent. (i)Their geographic signature differs. The former spreads in the circum-Saharan region and the Arabian Peninsula, whereas the latter describes a migration path via the Levant to the region of present-day northern Cameroon (Cruciani et al.2010). (ii) Their phylogenetic signature is different.The attribution of a single V88 mutation to theR1b1c migration differs from the expected participation of many sublineages in the J1migration. Although the confidence interval of both expansions overlaps, the R1b1c migration may have happened slightly before the J1migration.


*from post#18

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## bicicleur

> *Haplogroup R1b1c-V88 has a Eurasian origin and entered Northeast Africa from the Near East. The number of sublineages(L=5) stemming from R1b1c-V88 indicates an expansion.
> 
> When the J1 and R1b1c-V88 expansions are compared, two differences become apparent. (i)Their geographic signature differs. The former spreads in the circum-Saharan region and the Arabian Peninsula, whereas the latter describes a migration path via the Levant to the region of present-day northern Cameroon (Cruciani et al.2010). (ii) Their phylogenetic signature is different.The attribution of a single V88 mutation to theR1b1c migration differs from the expected participation of many sublineages in the J1migration. Although the confidence interval of both expansions overlaps, the R1b1c migration may have happened slightly before the J1migration.
> 
> 
> *from post#18


IMO the Arabic expansion of J1-P58 happened as late as 2500 BC
the main branch was a colonisation of Yemen by people from the Levant

http://en.wikipedia.org/wiki/Ancient...story_of_Yemen

later on they also colonised parts of Ethiopia to control the trade in frankincense and myrhe
it was the era of the queen of Sheba

HG_J1_(ADN-Y).PNG

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## Maleth

> So far as I know the yDna analysis of Ramses is correct, which means he was indeed, as you pointed out, E1b1a. However, he was from the 20th Dynasty (his rule started in 1186 BC). Expredel stated that Tutankhamen, who was from the 18th dynasty (he ruled from 1361 to 1352 BC), was yDna R1b M269, and he was assuming, I believe, that as Tut was from an earlier dynasty than Ramses, his R1b lineage is the original lineage of the Pharaohs of Egypt.


Thats understandable. One need to look at the time line which is quite a long one. It seems often that the lineage is fragmented too unlike European Royal heraldry which seems more consistent (as far as we know) The first 'Pharaoh who united lower with upper Egypt looks pretty much sub sub Saharan in my opinion, even though one cannot judge by looks and we also not taking Mtdna in consideration.






> The only so called "proof" that Tut was R1b is that during a presentation about the testing of Tut's remains a screen shot of yDna results was shown when they were describing the testing, and when the values from that screen shot were run through a predictor it's claimed that the values are those of someone who is R1b. That may in fact be the case, but we don't know if the screen shot was of a default result, perhaps that of one of the scientists, and was just used for demonstration purposes, or if it was indeed a screen shot of Tutankhamen's results.


.

According to lifescience the issue is used as a publicity stunt 




> Anyway, my point was that *even if* Tutankhamen was R1b, that would not be any proof that all the prior Egyptian dynasties were R1b, much less M269.


indeed and while everything is possible, there are other factors to take in consideration including the history and haplogroup percentages in the area. On the other hand the area has always seem to be a mixed bag of haplogroups and it does not seem to differ much from modern populations. The current highest HG are E-78 and J at 20% each G's and R's (R1a and b) are some 10% each. Maybe deeper classification would help.

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## Maleth

> *Haplogroup R1b1c-V88 has a Eurasian origin and entered Northeast Africa from the Near East. The number of sublineages(L=5) stemming from R1b1c-V88 indicates an expansion.
> 
> When the J1 and R1b1c-V88 expansions are compared, two differences become apparent. (i)Their geographic signature differs. The former spreads in the circum-Saharan region and the Arabian Peninsula, whereas the latter describes a migration path via the Levant to the region of present-day northern Cameroon (Cruciani et al.2010). (ii) Their phylogenetic signature is different.The attribution of a single V88 mutation to theR1b1c migration differs from the expected participation of many sublineages in the J1migration. Although the confidence interval of both expansions overlaps, the R1b1c migration may have happened slightly before the J1migration.
> 
> 
> *from post#18


Interesting. Do we have a time when these expansions happen? Wiki says this about R-v88 *R1b1c (R-V88)[edit]*

R1b1c (formerly R1b1a) is defined by the presence of SNP marker V88, the discovery of which was announced in 2010 by Cruciani et al.[23] *The V88 group in Africa may be linked with Chadic languages and an Iberian* *origin*.[67] Apart from individuals in southern Europe and Western Asia, the majority of R-V88 was found in northern and central Africa:

http://en.wikipedia.org/wiki/Haplogr...1c_.28R-V88.29

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## Maleth

> Weren't the early Egyptians of Berber caucasoid stock?


Blood typing and DNA sampling on ancient Egyptian mummies is scant; however, blood typing of dynastic mummies found ABO frequencies to be most similar to modern Egyptians,[14] and some also to NorthernHaratin populations. ABO blood group distribution shows that the Egyptians form a sister group to North African populations, including Berbers, Nubians and Canary Islanders.[15]

http://en.wikipedia.org/wiki/DNA_history_of_Egypt

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