An ancient haplogroup split in Y-DNA haplogroup E has been rediscovered

[Riverman]

After 15 years, an ancient haplogroup split in Y-DNA haplogroup E has been rediscovered through one tester who received a Y-DNA haplogroup from his Family Finder test.
Y-DNA haplogroup E is one of the main haplogroups on the Tree of Humankind. With the highest frequency in Africa, it is found today all over the world. The two most common and well-known lineages are:

• E-M2, with the highest frequency in Subsahara
  
• E-M35 with the highest frequency in North & East Africa, Arab Peninsula, and South & East Europe.
  

These two haplogroup E lineages share a common paternal line ancestor who lived around 42,000 years ago. 
How have advancements refined the deep ancestral lineage of the two most common haplogroup E lineages? Let’s take a look.
The Split in Y-DNA Haplogroup E Was First Discovered in 2008
Before 2008, this common ancestor between E-M2 and E-M35 was known as “E3-P2”. In 2008, Karafet et al. published the paper “New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree” which updated the YCC (Y Chromosome Consortium) tree with additional refinement. What used to be the E3-P2 branch was split into two branches that became known as E1b-P177 and E1b1-P2.


The split between P177 and P2 was based on Y-SNP test results from Michael Hammer’s lab in Arizona, where he and Tatiana Karafet performed Y-DNA research with the technology available at the time. Their test method involved testing individual Y-SNPs either one by one or in smaller Y-SNP panels. Tatiana informs us that the sample that caused the P177>P2 split was from South Africa, Zulu tribe of East Bantu, and that it was found to have the private mutation P75.


Y-Chromosome Phylogenetic Tree (2008) poster published by FamilyTreeDNA

Big Y-700 Testing Could Not Confirm The Split

With the introduction of NGS testing and the Big Y in 2014, the Y-DNA tree exploded with Y-SNPs and branches. However, even as the years passed and tens of thousands of samples from all corners of the world were tested, no new test result came out in support of the P177/P2 haplogroup split.
This caused some analytical problems when additional high-level Y-SNPs were added to haplogroup E. Without any NGS test results with positive Y-SNP calls for the E1b-P177 Y-SNPs and negative Y-SNP calls for the E1b1-P2 Y-SNPs, it was impossible to determine which Y-SNPs belonged upstream and which belonged downstream.
Without knowing the Y-SNP length of the branches, it would also not be possible for FamilyTreeDNA’s then-upcoming TMRCA (Time to Most Recent Common Ancestor) algorithm to estimate the time of the E-P177 haplogroup split.
The Haplogroup Split Was Removed Leaving Only E-P177
Eventually, in April 2019, the launch of the Big Y-700 allowed even more Y-SNPs to be discovered. The E1b-P177 and E1b1-P2 branches were collapsed on the FamilyTreeDNA Y-DNA haplotree, meaning that the split was removed and all that remained was the E1b-P177 haplogroup with 100 SNPs.
Of course, the split would be easy to reinstate again; if the P177 haplogroup had been observed before, it would eventually appear again in a new Big Y result.
A Family Finder Y-DNA Haplogroup Showed a Potential Haplogroup E Split
It would take almost five more years until the launch of the Family Finder™ Y-DNA haplogroup feature at the end of 2023 for a change to occur. One of the first 40,000 Family Finder kits that had been assigned a Y-DNA haplogroup stood out to the FamilyTreeDNA research team. The customer was positive for the P177 Y-SNP but negative for several of the other tested branch Y-SNPs, which was a strong indication that this customer belonged to the elusive breaker lineage!



Initial Family Finder Y-DNA Haplotree results for the E-P177 customer

Haydar Alyassery, FamilyTreeDNA’s Arab World Account Manager, contacted the customer, who has paternal ancestry from Yemen. Fortunately, he was available and agreed to a research-sponsored Big Y-700 upgrade to confirm the lineage and the split.
In January 2024, the Big Y-700 result arrived back from the lab, and FamilyTreeDNA’s phylogenetic specialist Michael Sager could confirm and redo the split on the tree, this time with Y-SNP call information for all the 100+ SNPs.


FamilyTreeDNA Y-DNA Haplotree after the E-P177 split

A Big Y-700 Upgrade Confirmed the Original Split and a New Y-DNA Haplogroup
The result? Upstream E-P177 with 8 Y-SNPs and downstream E-P2 with 113 Y-SNPs. The high proportion of Y-SNPs assigned to the downstream branch means that the branch is old—7000 years older than the previous E-P177 estimate. FamilyTreeDNA’s Age Estimation method could date the new E-P177 split to ca. 47,000 BCE. The new Big Y result also shared the private variant P75, which allowed us to assign the name E-P75 to the new brother lineage of E-P2.

Discover Haplogroup Story for E-P177 and E-P2
And that’s the story of how a 49,000-year-old lineage took 15+ years from discovery to TMRCA estimate!

FamilyTreeDNA TMRCA estimates for the new E-P177 split - Scientific Details
A new 49,000-year-old lineage found in two men, one from the Arabian Peninsula and one from South Africa, raises some interesting questions that we hope to get back to in the future. Has this lineage been in the Arabian Peninsula for tens of thousands of years or is it a more recent migration? More Y-DNA test results are needed to help uncover the story of this rediscovered lineage. Now that we have an idea of the lineage’s Y-STR profile and that more Family Finder Y-DNA haplogroup results are on their way, more FamilyTreeDNA customers may be contacted and offered a research upgrade.
So keep an eye on your inbox!

https://blog.familytreedna.com/ydna-hapl...kRM1bCjl5U

Excellent job by FTDNA, congratulations to their fantastic work. The only criticism I could make is that their own frequency maps are flawed for some countries, because of the disproportional testing frequency of Ashkenazi Jews. This disproportional testing by Ashkenazi Jews with their earliest known ancestor from specific countries like Belorussia, Ukraine and Romania lead to the absurd situation that E gets higher total frequencies (like due to Ashkenazi branches under E-M34) than it would get otherwise, while other branches, including specific E branches like E-V13 decrease drastically.

In fact, ethnic Belorussians have significantly less haplogroup E-M35 than Germans and Serbs.

That's the only minor criticism, otherwise just a lovely job.

Now we got two samples for this very basal position, one from Yemen, the other from South Africa. Worth to note that it could go either way, since South Africa received Afro-Asiatic influences through pastoralists which mixed with Bantu people, while at the same time lineages from East Africa moved to Yemen.

Like Göran wrote, the debate goes and we still don't know whether it was a back migration from the Near East to Africa, or E developed on and even E-M35 is a more recent migrant to the South West Asia.

Yet its quite intriguing that the sample comes from Yemen, since its my personal opinion for quite some time is that Southern Arabia, the Red Sea to Persian Gulf region was the original homeland of both Basal Eurasians and haplogroup E-M35 from the start, with a later influx from the Northern Levante-Caucasus (basically Semites-Arabs) replacing most of the haplogroup E variation which existed in the region before.

More samples might help to clear that up. In any case, we already know, that the Arabian peninsula has a lot of haplogroup E diversity, but we don't know whether its a more recent import, or was born in the region.

[Southpaw]

Probably either an ancient or recent migrant from Africa.

It's highly unlikely Y-DNA E or E-M35 originates in Middle East. Its homeland is probably Ethiopian Mountains, Yemen is not far away.

[Riverman]

Probably either an ancient or recent migrant from Africa.

It's highly unlikely Y-DNA E or E-M35 originates in Middle East. Its homeland is probably Ethiopian Mountains, Yemen is not far away.

I think Southern Arabia/Southern Levante, Egypt or Horn of Africa are equally likely going by the current data. We need more data and conclusive evidence.

[Southpaw]

Probably either an ancient or recent migrant from Africa.

It's highly unlikely Y-DNA E or E-M35 originates in Middle East. Its homeland is probably Ethiopian Mountains, Yemen is not far away.

I think Southern Arabia/Southern Levante, Egypt or Horn of Africa are equally likely going by the current data. We need more data and conclusive evidence.

You should let it go, Eastern/Northern Africa is like 99.9999999% probability, Southern Arabia/Southern Levant has like 0.000000001% chance.

The Natufian E-M35 were not native to Levant, they were Iberomaurusian intruders who mixed with Dudzuana-like UHG people.

[Capsian20]

Probably either an ancient or recent migrant from Africa.

It's highly unlikely Y-DNA E or E-M35 originates in Middle East. Its homeland is probably Ethiopian Mountains, Yemen is not far away.

Yes is seems to me Hg E1b1b is origin in Northern Eastern Africa (Egypt)

[Riverman]

Probably either an ancient or recent migrant from Africa.

It's highly unlikely Y-DNA E or E-M35 originates in Middle East. Its homeland is probably Ethiopian Mountains, Yemen is not far away.

I think Southern Arabia/Southern Levante, Egypt or Horn of Africa are equally likely going by the current data. We need more data and conclusive evidence.

You should let it go, Eastern/Northern Africa is like 99.9999999% probability, Southern Arabia/Southern Levant has like 0.000000001% chance.

The Natufian E-M35 were not native to Levant, they were Iberomaurusian intruders who mixed with Dudzuana-like UHG people.

To be sure we need Pre-Natufian samples, otherwise it remains speculative. Anthropologically there is no evidence for an IBM Intrusion and archaeologically the direction of the flows being disputed as well.

[Southpaw]

Probably either an ancient or recent migrant from Africa.

It's highly unlikely Y-DNA E or E-M35 originates in Middle East. Its homeland is probably Ethiopian Mountains, Yemen is not far away.

I think Southern Arabia/Southern Levante, Egypt or Horn of Africa are equally likely going by the current data. We need more data and conclusive evidence.

You should let it go, Eastern/Northern Africa is like 99.9999999% probability, Southern Arabia/Southern Levant has like 0.000000001% chance.

The Natufian E-M35 were not native to Levant, they were Iberomaurusian intruders who mixed with Dudzuana-like UHG people.

To be sure we need Pre-Natufian samples, otherwise it remains speculative. Anthropologically there is no evidence for an IBM Intrusion and archaeologically the direction of the flows being disputed as well.

Doesn't get clearer than this: https://en.wikipedia.org/wiki/Mushabian_culture

Also Paleolithic-Mesolithic Levant is devoid of advanced prehistoric culture unlike Egypt where we have first instances of flint mining in Paleolithic Egypt and first instances of Pre-Agricultural instances unlike Levant.

[Riverman]

Doesn't get clearer than this: https://en.wikipedia.org/wiki/Mushabian_culture

Also Paleolithic-Mesolithic Levant is devoid of advanced prehistoric culture unlike Egypt where we have first instances of flint mining in Paleolithic Egypt and first instances of Pre-Agricultural instances unlike Levant.

i know your opinion on the matter and I'm not saying you're wrong, but its not like all scholars agree on the matter of how the forth and back migrations between Egypt and the Southern Levante worked out genetically. What I want to stress in particular is that while the Natufians are the opposite end of the spectrum in many respects compared to IBM specimen, the Neolithic was spread by Natufian-like people. Therefore, before we have no actual data from Pre-Natufians in the Near East, it could very well have gone the other way around too.
Both remains possible at this point, that's all I'm saying.

[Capsian20]

Doesn't get clearer than this: https://en.wikipedia.org/wiki/Mushabian_culture

Also Paleolithic-Mesolithic Levant is devoid of advanced prehistoric culture unlike Egypt where we have first instances of flint mining in Paleolithic Egypt and first instances of Pre-Agricultural instances unlike Levant.

i know your opinion on the matter and I'm not saying you're wrong, but its not like all scholars agree on the matter of how the forth and back migrations between Egypt and the Southern Levante worked out genetically. What I want to stress in particular is that while the Natufians are the opposite end of the spectrum in many respects compared to IBM specimen, the Neolithic was spread by Natufian-like people. Therefore, before we have no actual data from Pre-Natufians in the Near East, it could very well have gone the other way around too.
Both remains possible at this point, that's all I'm saying.

I think Kebaran are ancestor of Natufian in side mtDNA and and Mushabian ancestor of Natufian in side Y-DNA , is clear Hg E1b1b is North African Haplogroup and after is spread to Levant and Balkan and Horn Africa