Will the Ancient Egyptian samples ever be published?

[FormosanAristocrat]

Is this the paper being referred to?
https://pmc.ncbi.nlm.nih.gov/articles/PMC10809863/

No, that predynastic sample came from Gebelein and was half a century older.

[Pharoah127]

Is this the paper being referred to?
https://pmc.ncbi.nlm.nih.gov/articles/PMC10809863/

No, that predynastic sample came from Gebelein and was half a century older.

It will probably have high ANA and SSA due to being in the very South of Egypt

[FormosanAristocrat]

It is probable, yes. Though as ilabv stated a few days ago, the readings of it being something akin to 40-50% African in total could as well be a subject of contamination or whatever.
IMO, they should occupy a position between the Christian Nubians and Copts.

[Idris]

I forgot to note, there is also the curious fact that there are fully contaminated samples, that are simply North Italians. It makes this a whole lot clearer.

As for the Egypt HG in Africans, there is no reason to assume its a fake population because East Africans dont absorb it much.

1: Sims are awful, sims using low coverage samples are even worse

2: East African fits are still awful, clearly they require another source. It is likely that much of this is an Egyptian HG source, but those who introduced pastoralism seem to have made their way across the Red Sea, which means they came through Arabia. So Arabian HG is likely another source, perhaps mixed with some Levant Neolithic.

The reason for the poor fits for East Africans (notably populations with less recent Arabian from ~3kya: Somali, Oromo) lay not in the proxies for the people who introduced pastoralism to their ancestors, but the population that adopted it - namely the 'proto-Nilotic' or, how I prefer to refer to them as, Ancestral East Africans.

Sudanese7 (+ other modern Nilotic samples) has ~30% Niger-Congo-like ancestry that isn't present in East Africans. It's all to easy to just lump all of SSA into a single mental cluster, but considering how genetically distinct AA-speaking East Africans are from NC-speakers, this makes a massive difference.

Incidentally, the simulated coordinates weren't 'discovered' by way of working backwards using Afroasiatic East Africans; the AEA coordinates were simulated using Mota, removing the excess South African HG. It just so happened to work perfectly as a proxy for Nilotes (as their East African component) and for Afroasiatic East Africans.

I replicated the run here, only replacing the Sudanese coordinates with AEA, and just look at what it does for the distance. 



Not to say that the other proxies are perfect, but they work well. The leaker on Twitter himself, when asked, said that the DNA found in Neolithic Upper Egypt is very close to proto-Cushitic. I think that the role Arabian HG played in introducing pastoralism into Africa is way overstated.

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As for contamination, I recall an R-Pxyz clade found in an Ancient Egyptian actually having a younger coalescence date than the sample itself which is what got the alarm bells ringing initially. Not sure what the consensus is now but yeah people began to become very skeptical of a lot of the older, seemingly out-of-place samples. Very interesting seeing everything come together in your posts. If you aren't on Twitter as you say, it could use someone as well read as you are to educate the biased and the ignorant.

[TellTheTruth]

The leaker JFD said in a Twitter space already, and judging by the tone this character was very likely ilabv


Leaks from JFD.
-ANA from SSA not separated.
-qpf4 broad not fine scale.
-poor sample.  Naqadans pilot between high SSA Up Ug and Sudanese Nubians, overwhelming no way back.
-unidentified talked about in unpublished Nile HG - lune/miro/marwan.  High ANA populations epipaleolthic/Mesolithic Nile.  40% in Natufian.
-lot of papers upcoming.  2 OK 1 of which (i2507)  Gizans (North)…..3 Nilotic. 15% total African.  Already higher African than Copts.  Copt like profile very homo middle an new kingdom to antiquity.
No less that 20 African un uppers E.  Floor is 25.
-my question. Uniparental data enforcing Nile HG.  A “i would have to look up the specific clade but there are a bunch of E clades and a bunch of B clades including E-M2 clades. I would have to check all the info.
-1 new kingdom. E-V22. Upper E priest.  2 lates era. G2a and J1.
-(my question unknown) Nile HP predicting intra African substructure for contemporary Saharan/SSA/ rift valley folks?
-process announced to sequel al these royal mummies may come out this year 2024 “ why are you even saying that. You are going to disappoint all these people and its going to take 1000 years”.also Hyksos data They also mentioned late this year (2024) or early next year but it may be never.  Maybe 2027.
2022 works was supposed to come out…nada
Jordan, Palestine, Syria.  Never came out.
-(my commen on the going to the Africa genetic confrerence in 2012) and data presented in the conference has not been published yet and or published only in 2022.  10 year wait. Academics are hoarding the data. Assholism.
-why so many samples outside the continent. 
tried sequencing data from Saudi Arabia. Never worked.
A few samples on G25 of midevil studies.  Look very similar to Mahra Yemenis.
Some samples from Yemen that are very old and have very good covereage.  Not sure if those are the E-M2 ones.  “I can check their haplos right now.
Yemen Iron Age exists.,
mtDNA R1 (contamination) HV1abc (high coverage  883795 snps) K1a19 (mt contamination) H (critical contamination) Embargo. Many of the list have not been released and they have been on the sheet for years.  Been on the list since the beginning of the autosomal ancient dna rush.
Yemen unknown 8000bc sample Exist
Omani data exist.
“I say total African, i know people want to differentiate.  ANA and SSA.  We dont have a good understanding on how ANA relates to this Population” “more like Africans than eurasians” not differentiated.  25-40% 15% needs to be the floor.
Lower Predynastic Levantine EPA diluted whatever NileHG+Levantine Neolithic exists.  Didn’t affect upper Egyptian Levantine Neolithic ancestors
Predynastic upper has a base of 25% ANA and as much as 20% Nilotic.  By Middle Kingdom a profile exists that is similar to comps across the entire country.  Genetic flattening effect. It has always existed. Based profile substrata.  Middle kingdoms = Arab times.
Copts most similar to the AE Average…but its a NEW profile that is about 3000 years old.
Abusir samples are weird.  They have very little SSA… a little not a lot 3% very small.  Don’t think they are separate for an AE average. The AE average they have for middle. . New / 4% Nilotic”.  Qpadm or G25.  55-70 of the A E average.  A bunch of Iron Age Berber.  Excess Nilotic 3-5% West Africa. Total African 8-9%.  E Muslims have  a lot of Near midevil Levantine ancestry diluting the AE ancestry
Nobody can differentiate from SSA and ANA . This Lower coverage 100x lower coverage than a bad shitty sample. 0.1. Coverage.  Converted and aligned  SNP count was 1841  _Fastq file.
Natural selection, sexual selections, drift as a reasons regardless of ancestral makeup.
(My question) does Nile HG resolved Africa in substructure that we have yet to see in modern models.  “Seem like a very significant amount of Levantine Neolithic stuff that East Africans have is Nile Hunter Gatherer.  Seems to get absorbed.”
No affect on Dinka. “ I think we need more data from the Sahara”.  The paternal linages don’t really indicate such a thing, not certain.
A lot of those lines originate Nile HG population… a lot of Natufian clades originate in Egyptians.  People have informed that IBM is the contributor to Natufian Materal culture and DNA.  People are skipping over the Nile Ghost population.  Same with the NWA samples…model with Levantine Neolithic, i think is Egypt Neolithic or Egyptian Chacolithic.
-converted the Naqadans low converage one to PLINK.  Sending over the whole set to avoid aligned and conversion.
JFD origin of proto AA…..Egypt along the Red Sea..  Coincided with Nile HG mixing into the Native with Kebaran To make Natufian.  Natufian is like 40% Nile HG.
70% ANA for Takarkori.
Data from private Harvard data sheet.
leaked, MIRO has access. Davidski has the sheet from Reich.  Entire data based of unpublished Samples.
3000 unpublished samples, told is ok to discuss them, weird club of deuchbags that dont discuss it.  data hoarding assholes.
(My question) Anything NDA’d
Nigerian maples R1b (really old) obvious V88. 600-400BC
10000 Samples unpublished 3000 on G25
Saudi/Iron/Bronze age - J1a2b on all. Minor contamination on X chromosome.  L2a1, i1b, u4c1,



It is settled, the Predynastics are closest to Sudanese.

So then what makes you so confident that Upper Egyptians are going to be significantly more African than Lower Egyptians if you acknowledge the samples themselves are garbage? Again, if these OK samples are legit than it seems more likely that Naqadans are going to be overwhelming Levantine in origin too and not some heavily admixed native Egyptian HG that adopted agriculture.

The Old Kingdom Giza samples are approximately 50% Levant EBA + Levant N

Why would upper Egypt have even more? It should have less. This goes well with the archaeology that shows the most Levantine influence in the north, and also with physical anthropology which shows a Caucasoid population in the north and a ‘mixed Caucasoid-Negroid’ population in the south.

I doubt that there's going to be any significant difference between Lower and Upper Egyptians at all. The neolithic in Egypt was a result of demic diffusion from the Levant, if Lower Egyptians were essentially 100% Near Eastern, I doubt Upper Egyptians are going to be much different, at best maybe marginal leftover Nile HG ancestry. The Upper Egyptians didn't just take the Neolithic package from Levantine-origin Lower Egyptians, they'll be mostly Near Eastern derived themselves, because they largely descend from agriculturalists from Lower Egypt.

Anyway, if there are really even genuine samples out there then they need to be finally published and formally analyzed, this willful obscurantism on the part of professional geneticists is pathetic.

Huh, where are you getting this idea that Upper Egyptians largely descend from agriculturalists from Lower Egypt, looking at predynastic and early dynastic Upper Egypt their material culture is largely a local development that really doesn't owe much to Lower Egypt. Also, its been established since the late 19th century that their was an appreciable difference between early Upper and Lower Egyptians skulls, with predynastic Upper Egyptians in many analyses, mainly craniometric, being most similar to north Ethio-Semitic peoples and Beja Sudanis/Eritreans, in other analyses, cranial non-metric, they're closest to present day North Africans.

[TellTheTruth]

It is probable, yes. Though as ilabv stated a few days ago, the readings of it being something akin to 40-50% African in total could as well be a subject of contamination or whatever.
IMO, they should occupy a position between the Christian Nubians and Copts.

Agreed. I think they'll plot around Mozab/Saharawi.

[ilabv]

It is probable, yes. Though as ilabv stated a few days ago, the readings of it being something akin to 40-50% African in total could as well be a subject of contamination or whatever.
IMO, they should occupy a position between the Christian Nubians and Copts.

Agreed. I think they'll plot around Mozab/Saharawi.

I think this is reasonable for the Egypt/Nile HG population (though still distant to them), but after Levant N and later Levant EBA (both of which likely trickled into Upper Egypt), I suspect they'd be pushed a bit genetically north.

[Inquirer]

It is probable, yes. Though as ilabv stated a few days ago, the readings of it being something akin to 40-50% African in total could as well be a subject of contamination or whatever.
IMO, they should occupy a position between the Christian Nubians and Copts.

Agreed. I think they'll plot around Mozab/Saharawi.

I think this is reasonable for the Egypt/Nile HG population (though still distant to them), but after Levant N and later Levant EBA (both of which likely trickled into Upper Egypt), I suspect they'd be pushed a bit genetically north.

Have the unreleased, low-coverage Egyptian hunter-gatherer samples yielded yDNA and / or mtDNA? If so, which haplogroups? And are they notably distinct from the two Natufian samples that have yielded DNA?