Modelling Egyptian ancestry

[nee4speed111]

Continuing on from this thread https://www.theapricity.com/forum/showthread.php?357601-Modern-Copts-are-the-closest-descendants-of-the-ancient-Egyptians, I will attempt to model modern Egyptians using the ancient samples we have on hand to determine a precise model for both Copts & Egyptian muslims.

I've often noticed that the biggest difference between Copts & Egyptian muslims other than the SSA shift is the depressed amounts of Natufian related ancestry Egyptian muslims carry relative to copts. A model to demonstrate what I mean



Target: COPTIC_AVERAGE
Distance: 3.0459% / 0.03045874
50.0 Levant_Natufian
25.2 Anatolia_Barcin_N
12.8 IRN_Wezmeh_N
6.8 GEO_CHG
5.2 Sudanese



Target: Egyptian_muslim_average_scaled
Distance: 2.2673% / 0.02267288
38.2 Levant_Natufian
26.6 Anatolia_Barcin_N
15.8 IRN_Wezmeh_N
6.2 GEO_CHG
6.0 Sudanese
5.0 Yoruba
1.2 Yamnaya_UKR
1.0 MAR_Iberomaurusian


Thanks to the Kulubnarti samples who were Medieval Nubian Christians, we seem to have a good proxy for much of the excess in SSA in both Copts & muslims & thus should be able to get a working model of their ancestral components:


Target: Egyptian_muslim_average_scaled
Distance: 1.0668% / 0.01066770
29.8 Lebanese_Christian
23.4 Levant_Beirut_IAIII_Egyptian
18.6 EGY_Late_Period
16.6 Sudan_MA_Kulubnarti
6.8 England_Roman_Near_Eastern_o
4.8 Yoruba


Target: COPTIC_AVERAGE
Distance: 1.2563% / 0.01256272
46.6 EGY_Late_Period
34.4 England_Roman_Near_Eastern_o
11.6 Sudan_MA_Kulubnarti
7.4 Levant_Beirut_IAIII_Egyptian

Using the Ancient Egyptian samples we have on hand (Egy late period, England_Roman_Near_Eastern_o & Levant_Beirut_IAIII_Egyptian), the Nubian Christian Kulubnarti Samples, a Yoruba & Sudanese source population for any excess SSA affinities not captured by the Medieval Nubians & a levantine proxy using Lebanese Christians, it seems that Copts don't pick up any levantine ancestry but all of their SSA is absorbed by the Kulubnarti samples & the fit is very good. The Egyptian muslims also have all of their East African ancestry absorbed, however a simply 2 way model of AE + SSA doesn't seem to work for Egyptian muslims due to their relatively depressed Natufian related ancestry & they seem to need both levantine ancestry along with West African ancestry. The fits for both populations are quite good, but I will also attempt to model them using only ancient sources to demonstrate what I mean by a levantine pull among Muslim Egyptians:

With Levant_Abel_IA


Target: Egyptian_muslim_average_scaled
Distance: 1.4541% / 0.01454053
30.0 Levant_Beirut_IAIII_Egyptian
22.2 Levant_Abel_IA
21.4 England_Roman_Near_Eastern_o
10.2 EGY_Late_Period
8.2 Sudan_MA_Kulubnarti
5.0 Yoruba
3.0 Sudanese


Target: COPTIC_AVERAGE
Distance: 1.2562% / 0.01256171
46.6 EGY_Late_Period
34.0 England_Roman_Near_Eastern_o
11.6 Sudan_MA_Kulubnarti
7.4 Levant_Beirut_IAIII_Egyptian
0.4 Levant_Abel_IA

With Levant_Baqah_BA


Target: Egyptian_muslim_average_scaled
Distance: 1.5130% / 0.01513006
36.0 Levant_Beirut_IAIII_Egyptian
22.8 Levant_Baqah_BA
20.2 England_Roman_Near_Eastern_o
6.4 Sudan_MA_Kulubnarti
5.8 EGY_Late_Period
4.8 Yoruba
4.0 Sudanese


Target: COPTIC_AVERAGE
Distance: 1.2563% / 0.01256293
47.0 EGY_Late_Period
33.2 England_Roman_Near_Eastern_o
11.8 Sudan_MA_Kulubnarti
6.6 Levant_Beirut_IAIII_Egyptian
1.4 Levant_Baqah_BA

With Levant_Beirut_ERoman


Target: Egyptian_muslim_average_scaled
Distance: 1.3182% / 0.01318168
35.4 Levant_Beirut_IAIII_Egyptian
23.4 Levant_Beirut_ERoman
13.0 England_Roman_Near_Eastern_o
12.0 EGY_Late_Period
8.4 Sudan_MA_Kulubnarti
4.6 Yoruba
3.2 Sudanese


Target: COPTIC_AVERAGE
Distance: 1.2563% / 0.01256272
46.6 EGY_Late_Period
34.4 England_Roman_Near_Eastern_o
11.6 Sudan_MA_Kulubnarti
7.4 Levant_Beirut_IAIII_Egyptian

With Levant_Sidon_MBA


Target: Egyptian_muslim_average_scaled
Distance: 1.4134% / 0.01413351
29.0 Levant_Sidon_MBA
26.6 Levant_Beirut_IAIII_Egyptian
15.2 England_Roman_Near_Eastern_o
12.8 EGY_Late_Period
8.2 Sudan_MA_Kulubnarti
4.6 Yoruba
3.6 Sudanese


Target: COPTIC_AVERAGE
Distance: 1.2560% / 0.01255970
46.6 EGY_Late_Period
33.8 England_Roman_Near_Eastern_o
11.6 Sudan_MA_Kulubnarti
7.4 Levant_Beirut_IAIII_Egyptian
0.6 Levant_Sidon_MBA

Using only ancient sources, the models gets quite interesting, the Sudanese reference highlighted is essentially a Dinka like reference population, when you model both the Coptic & Muslim averages using ancient levantine sources, it seems that Egyptian muslims need a Sudanese source for some of their excess East African ancestry whereas the model consistently absorbs all of the EA in Copts through the Nubian Christian proxy, perhaps a reflection of a slight EA pull in modern Lebanese Christians that doesn't show up in direct admixture results & that the ancient Levantines did not have? Another thing to notice is that once you use the ancient levantine sources, Copts actually have higher Nubian Christian ancestry than the Egyptian muslims do, which does seem to strongly imply that the elevated EA ancestry in modern Copts is probably as a result of Nubian Christian admixture in the medieval period, whereas the elevated SSA ancestry in Egyptian muslims needs both a West African source and a East African source in addition to the Nubian Christian samples.

In 3 out of the 4 models, Copts score minor levantine ancestry on the order of ~1%, however the model is pretty consistent in that approx 88-89% Ancient Egyptian + 11% Medieval Nubian Christians + 0-1% ancient levantine = Modern day Copts. With Egyptian Muslims, the model is approx 60% Ancient Egyptian + 24% ancient levantine + 8% Medieval Nubian Christians + 5% West African + 3% East African.

The model is a pretty good fit for both Copts & Muslims, however considering that the Medieval Nubian Christians almost certainly have some Dynastic Egyptian DNA from earlier periods, I think the model is probably slightly underestimating the actual Ancient Egyptian ancestry in both groups & that more samples from Egypt will help clarify this point.

[Ajeje Brazorf]

If it helps with the models, I made this average consisting of the 3 samples from Egypt + SFI-43. Should fairly well represent the situation in northern Egypt during the Hellenistic era. It remains an unknown what Upper Egyptians were like in the Bronze Age, but rumors say they shouldn't differ much from this average.


Egyptian_Ancient_proxy,0.04496,0.14928275,-0.0482715,-0.11401975,-0.000154,-0.05068825,-0.016098,-0.0047885,0.0474495,0.00560375,0.012098,-0.01536125,0.031739,-0.003303,-0.0003055,-0.00427625,-0.00997425,-0.00015825,-0.003708,0.01106775,0.00539675,0.00265875,-0.00209525,0.00457875,-0.0025145

[nee4speed111]

If it helps with the models, I made this average consisting of the 3 samples from Egypt + SFI-43. Should fairly well represent the situation in northern Egypt during the Hellenistic era. It remains an unknown what Upper Egyptians were like in the Bronze Age, but rumors say they shouldn't differ much from this average.


Egyptian_Ancient_proxy,0.04496,0.14928275,-0.0482715,-0.11401975,-0.000154,-0.05068825,-0.016098,-0.0047885,0.0474495,0.00560375,0.012098,-0.01536125,0.031739,-0.003303,-0.0003055,-0.00427625,-0.00997425,-0.00015825,-0.003708,0.01106775,0.00539675,0.00265875,-0.00209525,0.00457875,-0.0025145

Yes I have heard rumors from reliable sources that from the Middle Kingdom onward, they are basically Coptic-like and very similar to the current Ancient Egyptian samples we have on hand. Apparently the Old Kingdom samples are more shifted in a Neolithic Levantine direction though.

Using the average you provided plus a SSA source (Both Dinka & Yoruba), here are the models for both Copts & Muslims:


Target: Egyptian_muslim_average_scaled
Distance: 2.9556% / 0.02955627
89.8 Egyptian_Ancient_proxy
10.2 Dinka


Target: COPTIC_AVERAGE
Distance: 1.6624% / 0.01662425
95.8 Egyptian_Ancient_proxy
4.2 Dinka

The fit is quite decent for Copts but seems off for Egyptian muslims, here I run the same model but add Lebanese_Christian as one of the source populations:


Target: Egyptian_muslim_average_scaled
Distance: 1.3083% / 0.01308287
56.6 Egyptian_Ancient_proxy
31.6 Lebanese_Christian
8.2 Dinka
3.6 Yoruba


Target: COPTIC_AVERAGE
Distance: 1.5996% / 0.01599632
89.2 Egyptian_Ancient_proxy
6.2 Lebanese_Christian
4.6 Dinka

Seems that both Copts & Muslims need additional Levantine using this proxy, the model improves massively for Muslims and slightly for Copts, but it seems that the fit is not as good for Copts as some of my runs in this thread, still very interesting.

Here I run it again but use Palestinians instead of Lebanese Christians as my levantine proxy:


Target: Egyptian_muslim_average_scaled
Distance: 1.1991% / 0.01199053
50.0 Egyptian_Ancient_proxy
40.4 Palestinian
6.2 Dinka
3.4 Yoruba


Target: COPTIC_AVERAGE
Distance: 1.5828% / 0.01582798
87.4 Egyptian_Ancient_proxy
8.6 Palestinian
4.0 Dinka

Slight increase of levantine ancestry using Palestinians as a proxy in Copts & a quite large increase in Egyptian muslims, however I think alot of this affinity can be explained by Palestinians having Egyptian admixture rather than the other way around, considering how they cluster in comparison to other levantines.

Here are the same models but adding Medieval Nubian Christian in the mix:


Target: Egyptian_muslim_average_scaled
Distance: 1.0928% / 0.01092846
41.6 Egyptian_Ancient_proxy
36.2 Lebanese_Christian
17.4 Sudan_MA_Kulubnarti
4.8 Yoruba


Target: COPTIC_AVERAGE
Distance: 1.4630% / 0.01462961
78.6 Egyptian_Ancient_proxy
11.6 Sudan_MA_Kulubnarti
9.8 Lebanese_Christian

With Palestinians instead of Lebanese Christian as a proxy:


Target: Egyptian_muslim_average_scaled
Distance: 1.1289% / 0.01128919
43.8 Palestinian
39.8 Egyptian_Ancient_proxy
11.8 Sudan_MA_Kulubnarti
4.4 Yoruba
0.2 Dinka


Target: COPTIC_AVERAGE
Distance: 1.4698% / 0.01469841
78.4 Egyptian_Ancient_proxy
11.6 Palestinian
10.0 Sudan_MA_Kulubnarti

[Leto]

So basically there is no Arabian/Bedouin type admixture in Egypt? Don't know much about Egypt of course.

[nee4speed111]

So basically there is no Arabian/Bedouin type admixture in Egypt? Don't know much about Egypt of course.

Based on the averages, no it doesn't seem like it. However heterogeneity among the G25 Egyptian samples means its possible some do & some don't. Here I run all of the individual Egyptian muslim samples, using the AE proxy, lebanese Christian, SSA proxy & Saudi & Yemenite samples:

Target: Egyptian:Egypt9AQ177
Distance: 2.8492% / 0.02849239
44.4 Lebanese_Christian
30.0 Egyptian_Ancient_proxy
11.6 Dinka
6.8 Yemenite_Amran
5.0 Yemenite_Mahra
2.2 Yoruba

Target: Egyptian:Egypt9AQ172
Distance: 2.7736% / 0.02773590
49.0 Egyptian_Ancient_proxy
31.2 Lebanese_Christian
6.6 Dinka
5.8 Yoruba
4.8 Yemenite_Amran
2.6 Yemenite_Mahra

Target: Egyptian:Egypt8AT113
Distance: 2.2385% / 0.02238505
33.6 Egyptian_Ancient_proxy
28.8 Lebanese_Christian
24.4 Yemenite_Al_Jawf
6.6 Dinka
6.6 Yoruba

Target: Egyptian:Egypt7AQ172
Distance: 2.4031% / 0.02403087
51.8 Egyptian_Ancient_proxy
30.2 Lebanese_Christian
8.8 Yemenite_Amran
7.2 Yoruba
2.0 Dinka

Target: Egyptian:Egypt5AQ172
Distance: 3.0930% / 0.03092976
56.4 Egyptian_Ancient_proxy
21.2 Lebanese_Christian
12.6 Yemenite_Amran
6.2 Dinka
3.6 Yoruba

Target: Egyptian:Egypt3AQ172
Distance: 2.9142% / 0.02914211
47.6 Egyptian_Ancient_proxy
36.4 Lebanese_Christian
7.2 Dinka
6.0 Yemenite_Mahra
2.8 Yoruba

Target: Egyptian:Egypt22TD21
Distance: 2.7028% / 0.02702762
46.2 Egyptian_Ancient_proxy
38.2 Lebanese_Christian
11.4 Dinka
4.2 Yemenite_Mahra

Target: Egyptian:Egypt1AQ172
Distance: 2.4466% / 0.02446623
52.8 Egyptian_Ancient_proxy
21.4 Lebanese_Christian
16.4 Yemenite_Amran
9.4 Dinka

Target: Egyptian:Egypt17AQ176
Distance: 2.7940% / 0.02794032
56.0 Egyptian_Ancient_proxy
33.0 Lebanese_Christian
8.8 Dinka
2.2 Yoruba

Target: Egyptian:Egypt15AQ172
Distance: 2.0074% / 0.02007428
65.4 Egyptian_Ancient_proxy
23.8 Lebanese_Christian
5.6 Dinka
5.2 Yoruba

Target: Egyptian:Egypt12AQ172
Distance: 2.8480% / 0.02847998
61.6 Egyptian_Ancient_proxy
27.6 Lebanese_Christian
10.8 Dinka

Target: Egyptian:9AJ129
Distance: 2.6057% / 0.02605701
68.2 Egyptian_Ancient_proxy
21.8 Lebanese_Christian
9.2 Yoruba
0.8 Dinka

Target: Egyptian:8AJ136
Distance: 3.3318% / 0.03331823
43.6 Yemenite_Amran
38.4 Egyptian_Ancient_proxy
8.2 Lebanese_Christian
6.4 Dinka
3.4 Yoruba

Target: Egyptian:8AJ129
Distance: 2.5157% / 0.02515733
40.0 Lebanese_Christian
33.6 Egyptian_Ancient_proxy
14.2 Yemenite_Dhamar
6.8 Yoruba
5.4 Dinka

Target: Egyptian:7AJ136
Distance: 2.9074% / 0.02907378
56.2 Lebanese_Christian
30.0 Egyptian_Ancient_proxy
11.8 Dinka
2.0 Yoruba

Target: Egyptian:7AJ129
Distance: 2.6693% / 0.02669350
34.6 Lebanese_Christian
27.0 Yemenite_Al_Jawf
21.0 Egyptian_Ancient_proxy
12.2 Dinka
5.2 Yoruba

Target: Egyptian:6AJ129
Distance: 2.6749% / 0.02674904
65.0 Egyptian_Ancient_proxy
19.0 Lebanese_Christian
6.8 Yemenite_Amran
4.8 Yemenite_Mahra
3.8 Yoruba
0.6 Dinka

Target: Egyptian:5AJ137
Distance: 2.5283% / 0.02528278
46.8 Egyptian_Ancient_proxy
26.0 Lebanese_Christian
16.2 Dinka
11.0 Yoruba

Target: Egyptian:5AJ136
Distance: 3.6805% / 0.03680453
43.4 Lebanese_Christian
29.6 Egyptian_Ancient_proxy
13.8 Yemenite_Mahra
7.2 Yoruba
6.0 Dinka

Target: Egyptian:4AJ137
Distance: 2.7625% / 0.02762540
57.6 Egyptian_Ancient_proxy
29.2 Lebanese_Christian
13.2 Dinka

Target: Egyptian:4AJ136
Distance: 2.9396% / 0.02939585
43.2 Egyptian_Ancient_proxy
29.6 Yemenite_Amran
18.2 Lebanese_Christian
6.8 Yoruba
2.2 Dinka

Target: Egyptian:3AJ137
Distance: 3.0285% / 0.03028529
54.0 Egyptian_Ancient_proxy
32.4 Lebanese_Christian
5.6 Yoruba
3.2 Dinka
3.2 Yemenite_Amran
1.6 Yemenite_Mahra

Target: Egyptian:2AJ137
Distance: 2.0888% / 0.02088810
72.6 Egyptian_Ancient_proxy
16.2 Lebanese_Christian
5.8 Dinka
5.4 Yoruba

Target: Egyptian:1AJ137
Distance: 2.7179% / 0.02717934
42.6 Lebanese_Christian
38.8 Egyptian_Ancient_proxy
8.6 Dinka
8.0 Yemenite_Amran
2.0 Yoruba

Target: Egyptian:16AJ137
Distance: 2.9097% / 0.02909701
52.4 Egyptian_Ancient_proxy
36.0 Lebanese_Christian
8.2 Dinka
3.4 Yoruba

Target: Egyptian:15AJ137
Distance: 3.1526% / 0.03152574
54.6 Egyptian_Ancient_proxy
24.2 Lebanese_Christian
9.4 Dinka
7.8 Yemenite_Amran
4.0 Yoruba

Target: Egyptian:12AJ136
Distance: 2.4664% / 0.02466434
41.2 Egyptian_Ancient_proxy
34.4 Lebanese_Christian
13.0 Yemenite_Ma'rib
10.2 Dinka
1.2 Yoruba

Target: Egyptian:12AJ129
Distance: 3.3353% / 0.03335306
44.2 Egyptian_Ancient_proxy
32.0 Lebanese_Christian
12.6 Yemenite_Amran
11.2 Dinka

Target: Egyptian:10AJ137
Distance: 2.5674% / 0.02567416
44.8 Lebanese_Christian
42.4 Egyptian_Ancient_proxy
10.6 Dinka
2.2 Yoruba

Target: Egyptian:10AJ136
Distance: 2.8636% / 0.02863648
41.2 Egyptian_Ancient_proxy
32.6 Lebanese_Christian
17.8 Yemenite_Amran
4.4 Dinka
4.0 Yoruba

As you can see, it ranges from not needed a Arabian source at all to needing 40%+ of a Yemenite source. However I don't think all or even most of it is actual Arabian ancestry, alot of it could be shared ancestry between Egyptians & Arabians from a Natufian like source. Although the heterogeneity of it does imply that some of it is real.

[Leto]

Wow, some of those samples are over 15% black (Dinka + Yoruba). And that's not including the minor African that might be in the other components.

[nee4speed111]

Wow, some of those samples are over 15% black (Dinka + Yoruba). And that's not including the minor African that might be in the other components.

Yes there is a large variability in SSA ancestry, from almost Coptic Egyptian levels to some like Egyptian:5AJ137 having around 27%. I don't know where these Egyptian samples are from so I can't exactly say how representative they are

[Ajeje Brazorf]

Yes I have heard rumors from reliable sources that from the Middle Kingdom onward, they are basically Coptic-like and very similar to the current Ancient Egyptian samples we have on hand. Apparently the Old Kingdom samples are more shifted in a Neolithic Levantine direction though.

Wow, that means they would be even less shifted towards Africa than these later samples are. I would have expected the opposite, I admit, ancient DNA always has surprises for us.


Seems that both Copts & Muslims need additional Levantine using this proxy, the model improves massively for Muslims and slightly for Copts, but it seems that the fit is not as good for Copts as some of my runs in this thread, still very interesting.

Yes, there is considerable Levantine ancestry in modern Egyptians, and you can see this in the percentage of Iran_N compared to ancient Egyptians. Also interesting is the percentage of Taforalt, which cannot be explained simply by ancient Egyptians, Blacks and Levantines. There is something else from the west in the mix.

https://i.imgur.com/UkomyQc.png


So basically there is no Arabian/Bedouin type admixture in Egypt? Don't know much about Egypt of course.

Interestingly, modern Egyptians compared to ancient ones saw a decrease in "Arab-like" ancestry (which is practically Neolithic Levantine).


Distance difference: ( AC - BC ) ↓
A: Egyptian
B: Egyptian_Ancient_proxy
C: ↴
0.04724672 Yemenite_Jew
0.04712126 Yemenite_Mahra
0.04570310 Yemenite_Al_Jawf
0.04468401 Yemenite_Ma'rib
0.04294587 Saudi
0.04078825 Samaritan

[nee4speed111]

Wow, that means they would be even less shifted towards Africa than these later samples are. I would have expected the opposite, I admit, ancient DNA always has surprises for us.



Yes, there is considerable Levantine ancestry in modern Egyptians, and you can see this in the percentage of Iran_N compared to ancient Egyptians. Also interesting is the percentage of Taforalt, which cannot be explained simply by ancient Egyptians, Blacks and Levantines. There is something else from the west in the mix.

https://i.imgur.com/UkomyQc.png



Interestingly, modern Egyptians compared to ancient ones saw a decrease in "Arab-like" ancestry (which is practically Neolithic Levantine).


Distance difference: ( AC - BC ) ↓
A: Egyptian
B: Egyptian_Ancient_proxy
C: ↴
0.04724672 Yemenite_Jew
0.04712126 Yemenite_Mahra
0.04570310 Yemenite_Al_Jawf
0.04468401 Yemenite_Ma'rib
0.04294587 Saudi
0.04078825 Samaritan

Yes, this is the information we have so far on older Egyptian DNA


Based on some pca plots which I've seen (but can't publish), I can say that Old Kingdom samples are closer to Levant_Neolithic samples and Mid Kingdom samples are closer to Levant_BA samples. New Kingdom samples seem to be closer to Old Kingdom samples.
I don't have any idea about when related paper(s) will be published.


There is some upcoming data from Old and Middle Kingdom Egypt that I've seen, some of it has been discussed already on the forum. Basically the Old Kingdom samples look North African with a small amount of Seh_Gabi_C-type ancestry, and very little SSA, then during the Middle Kingdom there's a shift towards a SW Asian/Near Eastern profile which resembles that of the few ancient Egyptians we have and present-day Copts, this corresponds with the large influx of "Asiatics" starting from the 1st intermediate period. SSA ancestry also increases in time. Haplogroups so far are E-M35 and J1-P58

So it seems like the modern Coptic profile has been around since the Middle Kingdom period, which is quite a long time & implies a lot of continuity.

https://www.theapricity.com/forum/attachment.php?attachmentid=112089&d=1642290446

I believe this was the same test you did for me on Anthrogenica? I seem to be very close to your Ancient Egyptian proxy. So you believe adding a North African source to the models will improve the fits?

[Cernunnos]

Yes there is a large variability in SSA ancestry, from almost Coptic Egyptian levels to some like Egyptian:5AJ137 having around 27%. I don't know where these Egyptian samples are from so I can't exactly say how representative they are

I would imagine Moh Sallah to score that quantity of SSA.

[Ajeje Brazorf]

Yes, this is the information we have so far on older Egyptian DNA


Based on some pca plots which I've seen (but can't publish), I can say that Old Kingdom samples are closer to Levant_Neolithic samples and Mid Kingdom samples are closer to Levant_BA samples. New Kingdom samples seem to be closer to Old Kingdom samples. I don't have any idea about when related paper(s) will be published.


There is some upcoming data from Old and Middle Kingdom Egypt that I've seen, some of it has been discussed already on the forum. Basically the Old Kingdom samples look North African with a small amount of Seh_Gabi_C-type ancestry, and very little SSA, then during the Middle Kingdom there's a shift towards a SW Asian/Near Eastern profile which resembles that of the few ancient Egyptians we have and present-day Copts, this corresponds with the large influx of "Asiatics" starting from the 1st intermediate period. SSA ancestry also increases in time. Haplogroups so far are E-M35 and J1-P58

These are very interesting rumors, but they didn't specify (for obvious reasons, they couldn't reveal everything) where the samples came from. In Luxor governorate there was a profile similar to the one described above and that we already have in part? I hope these are questions that one day will be answered.

https://i.imgur.com/QmBYqPO.png


So it seems like the modern Coptic profile has been around since the Middle Kingdom period, which is quite a long time & implies a lot of continuity.

https://www.theapricity.com/forum/attachment.php?attachmentid=112089&d=1642290446

I believe this was the same test you did for me on Anthrogenica? I seem to be very close to your Ancient Egyptian proxy.

You're very close to the ancient average, which is exceptional considering it's been over 2000 years since the samples used lived. You should be living in a museum, man! XD


Distance to: Egyptian_Ancient_proxy
0.02441176 EGY_Late_Period:JK2911
0.02554559 Levant_Beirut_IAIII_Egyptian:SFI-43
0.02661113 EGY_Late_Period:JK2134
0.03078707 nee4speed111_scaled
0.03179397 England_Roman_Near_Eastern_o:3DT26
0.03629304 EGY_Hellenistic_contam:JK2888
0.03633276 Levant_Beirut_IAIII_Egyptian:SFI-44
0.03727830 lifeisdandy/oblivion_scaled
0.03934866 Egyptian:6AJ129
0.03952264 BedouinA:HGDP00639
0.03972376 BedouinB:HGDP00608
0.04175174 Yemenite_Amran:Y517
0.04194446 Yemenite_Dhamar:Y038
0.04204391 Yemenite_Dhamar:Y031
0.04229777 nee4speed111_friend_scaled
0.04321479 Yemenite_Ma'rib:Y237
0.04489333 Yemenite_Ma'rib:Y241
0.04497328 Yemenite_Amran:Y542
0.04701479 Levant_JOR_EBA:I1730
0.04712183 Yemenite_Jew:YemeniteJew4695
0.04724900 Yemenite_Dhamar:Y382
0.04771740 Yemenite_Dhamar:Y025
0.04772098 Yemenite_Amran:Y506
0.04830971 BedouinA:HGDP00642
0.04849460 Levant_Megiddo_IBA:I4521
0.04870395 Yemenite_Amran:Y522
0.04874220 BedouinB:HGDP00624
0.04901769 Yemenite_Amran:Y544
0.04907426 Yemenite_Dhamar:Y036
0.04931219 Copt5_scaled
0.04949366 Yemenite_Amran:Y519
0.04950061 BedouinB:HGDP00651
0.04981180 Yemenite_Amran:Y504
0.04987955 Yemenite_Amran:Y529
0.04994509 Yemenite_Jew:YemeniteJew4938


So you believe adding a North African source to the models will improve the fits?

When I talk about general Egyptians I am referring to the majority of the population who is Muslim, not Coptic. I believe, however, that even in the case of the Copts it is there: the East African ancestry has increased (note the lack of West African ancestry unlike the rest of the population) but Taforalt has remained the same.

[nee4speed111]

These are very interesting rumors, but they didn't specify (for obvious reasons, they couldn't reveal everything) where the samples came from. In Luxor governorate there was a profile similar to the one described above and that we already have in part? I hope these are questions that one day will be answered.

From what I understand, the papers should be released soon enough & apparently they cover 4000 years of Ancient Egyptian history, with a full sampling across the Nile valley including both Upper & Lower Egypt.


You're very close to the ancient average, which is exceptional considering it's been over 2000 years since the samples used lived. You should be living in a museum, man! XD

Ha, it was certainly a surprise how close I clustered to these samples, I believe Copt_3 is even closer than me though last time I checked.


When I talk about general Egyptians I am referring to the majority of the population who is Muslim, not Coptic. I believe, however, that even in the case of the Copts it is there: the East African ancestry has increased (note the lack of West African ancestry unlike the rest of the population) but Taforalt has remained the same.

Interesting theory, I decided to test it out by running the same models I did initially but adding a Guanche source:

Using the Lebanese Christian sample


Target: Egyptian_muslim_average_scaled
Distance: 0.9422% / 0.00942153
29.8 Lebanese_Christian
23.0 Levant_Beirut_IAIII_Egyptian
16.4 Sudan_MA_Kulubnarti
12.8 EGY_Late_Period
9.0 England_Roman_Near_Eastern_o
4.8 Canary_Islands_Guanche
4.2 Yoruba



Target: COPTIC_AVERAGE
Distance: 1.2563% / 0.01256272
46.6 EGY_Late_Period
34.4 England_Roman_Near_Eastern_o
11.6 Sudan_MA_Kulubnarti
7.4 Levant_Beirut_IAIII_Egyptian

It does seem like you were correct, however there is no change in the Coptic average once I add Canary_islands_Guanche but the Egyptian muslim average does seem to pick up some Guanche ancestry and slightly depress the AE ancestry, with the fit improving slightly.

Now with the ancient samples:

With Levant_Abel_IA


Target: Egyptian_muslim_average_scaled
Distance: 1.1712% / 0.01171184
27.8 Levant_Abel_IA
24.2 Levant_Beirut_IAIII_Egyptian
20.4 England_Roman_Near_Eastern_o
9.0 Canary_Islands_Guanche
6.4 Sudan_MA_Kulubnarti
4.4 EGY_Late_Period
4.0 Sudanese
3.8 Yoruba


Target: COPTIC_AVERAGE
Distance: 1.2562% / 0.01256171
46.6 EGY_Late_Period
34.0 England_Roman_Near_Eastern_o
11.6 Sudan_MA_Kulubnarti
7.4 Levant_Beirut_IAIII_Egyptian
0.4 Levant_Abel_IA

With Levant_Baqah_BA


Target: Egyptian_muslim_average_scaled
Distance: 0.9850% / 0.00985037
43.4 Levant_Baqah_BA
21.4 Levant_Beirut_IAIII_Egyptian
13.4 Canary_Islands_Guanche
7.4 England_Roman_Near_Eastern_o
6.8 Sudanese
3.0 Sudan_MA_Kulubnarti
2.8 Yoruba
1.8 EGY_Late_Period


Target: COPTIC_AVERAGE
Distance: 1.2563% / 0.01256293
47.0 EGY_Late_Period
33.2 England_Roman_Near_Eastern_o
11.8 Sudan_MA_Kulubnarti
6.6 Levant_Beirut_IAIII_Egyptian
1.4 Levant_Baqah_BA

With Levant_Beirut_ERoman


Target: Egyptian_muslim_average_scaled
Distance: 1.0811% / 0.01081103
33.4 Levant_Beirut_IAIII_Egyptian
25.2 Levant_Beirut_ERoman
14.0 England_Roman_Near_Eastern_o
7.6 Canary_Islands_Guanche
6.0 EGY_Late_Period
6.0 Sudan_MA_Kulubnarti
4.2 Sudanese
3.6 Yoruba


Target: COPTIC_AVERAGE
Distance: 1.2563% / 0.01256272
46.6 EGY_Late_Period
34.4 England_Roman_Near_Eastern_o
11.6 Sudan_MA_Kulubnarti
7.4 Levant_Beirut_IAIII_Egyptian

With Levant_Sidon_MBA


Target: Egyptian_muslim_average_scaled
Distance: 0.9837% / 0.00983693
40.2 Levant_Sidon_MBA
17.0 Levant_Beirut_IAIII_Egyptian
11.0 Canary_Islands_Guanche
10.0 England_Roman_Near_Eastern_o
7.8 EGY_Late_Period
5.8 Sudan_MA_Kulubnarti
5.4 Sudanese
2.8 Yoruba


Target: COPTIC_AVERAGE
Distance: 1.2564% / 0.01256374
47.4 EGY_Late_Period
33.2 England_Roman_Near_Eastern_o
11.8 Sudan_MA_Kulubnarti
6.2 Levant_Beirut_IAIII_Egyptian
1.4 Levant_Sidon_MBA

While the Coptic average remains completely unchanged with the Canary_Islands_Guanche added as a source population, the Egyptian muslim average improves quite significantly with the Guanches compared to the previous run using only ancient populations, with basically all the ancestry proportions changing. It seems to increase the Ancient Levantine signal in Egyptian muslims and depress the amount of AE ancestry being registered, along with a Guanche like signal being picked up on in every run.

I believe the reason Copts don't need a Guanche signal is that Kulubnarti already has Taforalt ancestry, so the increase in East African was accompanied by some Taforalt ancestry.

[Ajeje Brazorf]

From what I understand, the papers should be released soon enough & apparently they cover 4000 years of Ancient Egyptian history, with a full sampling across the Nile valley including both Upper & Lower Egypt.

Great!


Ha, it was certainly a surprise how close I clustered to these samples, I believe Copt_3 is even closer than me though last time I checked.

Copt3 is literally a time traveler.


Distance to: Egyptian_Ancient_proxy
0.02340962 Copt3_scaled
0.02441176 EGY_Late_Period:JK2911
0.02554559 Levant_Beirut_IAIII_Egyptian:SFI-43
0.02661113 EGY_Late_Period:JK2134
0.03078707 nee4speed111_scaled
0.03179397 England_Roman_Near_Eastern_o:3DT26
0.03385544 Copt4_scaled
0.03629304 EGY_Hellenistic_contam:JK2888
0.03633276 Levant_Beirut_IAIII_Egyptian:SFI-44
0.03727830 lifeisdandy/oblivion_scaled


I believe the reason Copts don't need a Guanche signal is that Kulubnarti already has Taforalt ancestry, so the increase in East African was accompanied by some Taforalt ancestry.

Yes, it is very likely. Kulubnarti itself has about 8% Taforalt.

[nee4speed111]

I would imagine Moh Sallah to score that quantity of SSA.

I doubt it, that much SSA ancestry is very apparent in the phenotype, Mohamed Salah does not look it at all.

[T_Maniac]

Is being shifted towards Levant_N considered North African? Are the rumors in agreement with each other?

[nee4speed111]

I was running my Egyptian samples through the updated ancient averages spreadsheet when I noticed that a Anatolian Byzantine sample seemed to consistently come up in my averages, so I decided to investigate further


TUR_Marmara_Iznik_Basilica_RomByz_B,0.034147,0.143 1895,-0.0369575,-0.0899555,0.0141565,-0.035001,-0.0125735,-0.0043845,0.047654,0.016766,0.008282,-0.010416,0.026313,-0.0011695,0.0042075,-0.005635,-0.005802,-0.009312,-0.019986,0.0072535,-0.006426,-0.0133545,0.0059775,-0.0048195,0.0020355
First a run of the sample to determine its more basal components:


Target: TUR_Marmara_Iznik_Basilica_RomByz_B
Distance: 2.8015% / 0.02801544
37.8 Anatolia_Neolithic_Farmer_TUR_Barcin_N
30.8 Levant_Natufian_Hunter-Gatherer_Levant_Natufian
12.8 Morocco_Early_Neolithic_Farmer_MAR_EN
10.0 Iran_Neolithic_Farmer_IRN_Ganj_Dareh_N
5.6 Caucasus_Hunter-Gatherer_GEO_CHG
2.0 Pontic_Steppe_Yamnaya_Pastoralist_Yamnaya_RUS_Sama ra
1.0 Nilotic_Pastoralist_KEN_Kakapel_900BP

First thing that is obvious is the seeming low level of West-African ancestry in a population with a seemingly high level of IBM related ancestry, along with what seems like elevated Iran-N and Caucasus ancestry in comparison to other pops with significant IBM ancestry,but to confirm further a comparison with some other North African pop's



Target: Guanche_Canary_Islands
Distance: 2.0318% / 0.02031781
40.6 Anatolia_Neolithic_Farmer_TUR_Barcin_N
33.8 Morocco_Early_Neolithic_Farmer_MAR_EN
8.6 Pontic_Steppe_Yamnaya_Pastoralist_Yamnaya_RUS_Sama ra
8.0 Levant_Natufian_Hunter-Gatherer_Levant_Natufian
5.6 West_Africa-Bantu_Farmer_COG_Kindoki_230BP
1.8 West_Europe_Hunter-Gatherer_WHG
1.6 Nilotic_Pastoralist_KEN_Kakapel_900BP


Target: Libyan
Distance: 2.7073% / 0.02707345
33.0 Levant_Natufian_Hunter-Gatherer_Levant_Natufian
29.0 Anatolia_Neolithic_Farmer_TUR_Barcin_N
14.2 Morocco_Early_Neolithic_Farmer_MAR_EN
9.4 West_Africa-Bantu_Farmer_COG_Kindoki_230BP
6.0 Iran_Neolithic_Farmer_IRN_Ganj_Dareh_N
5.2 Pontic_Steppe_Yamnaya_Pastoralist_Yamnaya_RUS_Sama ra
2.4 Caucasus_Hunter-Gatherer_GEO_CHG
0.8 Nilotic_Pastoralist_KEN_Kakapel_900BP


Target: Sardinia_CA_(North_African_Profile)
Distance: 4.7061% / 0.04706059
43.6 Morocco_Early_Neolithic_Farmer_MAR_EN
35.0 Anatolia_Neolithic_Farmer_TUR_Barcin_N
12.4 Levant_Natufian_Hunter-Gatherer_Levant_Natufian
5.2 Nilotic_Pastoralist_KEN_Kakapel_900BP
3.4 West_Africa-Bantu_Farmer_COG_Kindoki_230BP
0.4 West_Africa_Hunter-Gatherer_CMR_Shum_Laka_3000BP


Target: Iberia_Central_CA_(North_African_Profile)
Distance: 3.7205% / 0.03720482
47.6 Anatolia_Neolithic_Farmer_TUR_Barcin_N
29.0 Morocco_Early_Neolithic_Farmer_MAR_EN
10.6 Levant_Natufian_Hunter-Gatherer_Levant_Natufian
8.2 Nilotic_Pastoralist_KEN_Kakapel_900BP
2.6 West_Africa-Bantu_Farmer_COG_Kindoki_230BP
2.0 West_Europe_Hunter-Gatherer_WHG


Target: Levant_IAIII_Beirut_o_(Egyptian_Profile)
Distance: 4.5867% / 0.04586710
57.0 Levant_Natufian_Hunter-Gatherer_Levant_Natufian
24.0 Anatolia_Neolithic_Farmer_TUR_Barcin_N
11.0 Caucasus_Hunter-Gatherer_GEO_CHG
6.2 Iran_Neolithic_Farmer_IRN_Ganj_Dareh_N
1.8 Nilotic_Pastoralist_KEN_Kakapel_900BP


Based off these results, it seems that the Guanches or the Iberia_Central_CA/Sardinian_NA represent the IBM side of this sample best, however it needs a significantly Anatolia & Natufian enriched source for its non-NA side which rules out Arabian admixture as they don't have enough Anatolian admix & probably rules out levantines of the time period as their Natufian ancestry is too low. Thus Egyptian seems to be the most probable.

To test this theory out, I ran the sample with every singe ancient average on a distance of 0.5x so as to not overfit and got the following results.



Target: TUR_Marmara_Iznik_Basilica_RomByz_B
Distance: 1.8435% / 0.01843464 | ADC: 0.5x RC
33.0 Levant_Beirut_IAIII_Egyptian
32.0 England_Roman_Near_Eastern_o
23.4 Canary_Islands_Guanche
11.6 ITA_Etruscan_o1

Interestingly enough, it selects a fit of essentially 65% Egyptian, 23% NA with the remainder being an NA admixed Italic population. I am not sure if this sample was essentially some sort of mixed Egyptian/Libyan, a Egyptian from the Western deserts with ancient IBM admix or perhaps some sort of relic ancient Libyan population, but it is clear that this individual has clear genetic links to both Egypt and North Africa more broadly. To further test this out, I ran the Marmara individual against both modern & ancient averages as per below:


Distance to: TUR_Marmara_Iznik_Basilica_RomByz_B
0.04379666 Levant_Beirut_IAIII_Egyptian
0.05087497 EGY_Late_Period
0.05280943 England_Roman_Near_Eastern_o
0.06379327 EGY_Hellenistic_contam
0.07063559 TUR_Aegean_Bodrum_Halikarnassos_Anc2
0.07591590 Levant_Megiddo_IBA
0.07974130 Levant_Ashkelon_IA2
0.08070766 Levant_Sidon_MBA
0.08124410 Levant_JOR_EBA
0.08336751 Levant_Beirut_IAIII
0.08365187 Levant_Beirut_Hellenistic
0.08540025 Levant_Hazor_MLBA
0.08590909 Levant_LBN_MA
0.08591116 Levant_Megiddo_MLBA
0.08642149 Levant_Beirut_IAII
0.08660442 Levant_Beirut_ERoman
0.08696118 Levant_Baqah_BA
0.08734408 Levant_LBN_Roman
0.08737478 Levant_Abel_IA
0.08782347 Levant_Megiddo_IA
0.09065634 Levant_Yehud_IBA
0.09096413 DEU_MA_Erfurt1
0.09118548 Levant_Shadud_MLBA
0.09148508 TUR_SE_Sirnak_C_B
0.09201583 Levant_Ashkelon_LBA


Distance to: TUR_Marmara_Iznik_Basilica_RomByz_B
0.04424173 Egyptian_Copt_average
0.04641424 Egyptian_Copt_Sudan_average
0.05388370 BedouinA
0.05953447 Tunisian_Jew
0.06031092 Libyan_Jew
0.06155819 Palestinian
0.06278454 Egyptian
0.06466109 Jordanian
0.07228449 Yemenite_Amran
0.07251935 SaudiB
0.07292818 Moroccan_Jew
0.07428315 Yemenite_Dhamar
0.07660152 Tunisian_Rbaya
0.07916885 Samaritan
0.08129089 Yemenite_Al_Bayda
0.08212890 Berber_Tunisia_Sen
0.08260869 Tunisian_Berber_Zraoua
0.08278739 Yemenite_Ma'rib
0.08280102 Karaite_Egypt
0.08475870 SaudiA
0.08638892 Lebanese_Muslim
0.08653060 Sephardic_Jew
0.08675395 Syrian_Jew
0.08678497 Libyan
0.08692195 Romaniote_Jew

As I mentioned earlier, I noticed this sample because my runs of my Egyptian samples seemed to constantly want this as a source population, which brings me to believe it may offer an improvement over my earlier runs, especially as I identified earlier in this thread that both Copts & Muslims have excess IBM when modeled as Ancient Egyptian, Medieval Nubians & Levantine, so hopefully the fits improve.

Using Ancient Egyptians, SSA sources (Kindoki & Kakapel ), Kulubnarti Nubian & TUR_Marmara_Iznik_Basilica_RomByz_B :




Target: Egyptian_Copt_average
Distance: 1.1940% / 0.01193962
81.2 AE
9.4 SDN_MA_Kulubnarti
9.4 TUR_Marmara_Iznik_Basilica_RomByz_B


Target: Egyptian_Copt_Sudan_average
Distance: 1.2489% / 0.01248900
79.2 AE
12.8 SDN_MA_Kulubnarti
8.0 TUR_Marmara_Iznik_Basilica_RomByz_B

Interestingly enough, it seems that the fit does improve and both the Egyptian Copts & Sudanese Copts pick up on 8-9% of this individuals ancestry, it is very telling as if you scroll to the beginning of the thread you will notice that the Coptic average would not pick up on any Levantine ancestry in the models I ran, only a few of the samples ever picked up anything and it was approx 1-2% so I do believe this is a big indicator that either this individual or individuals similar to them were around in Classical/Medieval Egypt and were possibly absorbed into the general population.

Now I will run the Egyptian Muslim averages



Target: Egyptian
Distance: 1.5588% / 0.01558754
63.0 AE
26.0 TUR_Marmara_Iznik_Basilica_RomByz_B
6.0 KEN_Kakapel_900BP
5.0 COG_Kindoki_230BP


Target: Egyptian_Cairo
Distance: 1.6513% / 0.01651282
67.6 AE
21.4 TUR_Marmara_Iznik_Basilica_RomByz_B
7.0 KEN_Kakapel_900BP
4.0 COG_Kindoki_230BP


Target: Egyptian_Intermediate_Profile
Distance: 2.3360% / 0.02336019
35.0 TUR_Marmara_Iznik_Basilica_RomByz_B
34.4 AE
13.6 COG_Kindoki_230BP
9.2 KEN_Kakapel_900BP
7.8 SDN_MA_Kulubnarti


Target: Egyptian_Kafar_Sheikh
Distance: 2.2666% / 0.02266589
61.4 TUR_Marmara_Iznik_Basilica_RomByz_B
29.8 AE
8.0 KEN_Kakapel_900BP
0.8 COG_Kindoki_230BP


Target: Egyptian_Mansoura
Distance: 1.7441% / 0.01744127
64.4 AE
25.8 TUR_Marmara_Iznik_Basilica_RomByz_B
5.8 KEN_Kakapel_900BP
4.0 COG_Kindoki_230BP


Target: Egyptian_Tanta
Distance: 3.1914% / 0.03191364
58.0 AE
34.0 TUR_Marmara_Iznik_Basilica_RomByz_B
4.6 COG_Kindoki_230BP
3.4 KEN_Kakapel_900BP


Target: Egyptianmuslim_scaled
Distance: 1.4995% / 0.01499516
61.6 AE
28.0 TUR_Marmara_Iznik_Basilica_RomByz_B
5.8 KEN_Kakapel_900BP
4.6 COG_Kindoki_230BP

Some very interesting results also, every single sample average got significant amounts of this Egyptian-Berber individual in their runs, even forming the majority of the Kafar Sheikh sample. Another interesting observation is that other than the Intermediate_Profile who seems significantly SSA admixed and might have actual Nubian ancestry, every other Egyptian muslim sample loses the Kulubnarti ancestry and instead prefers Kakapel & Kindoki ancestry, which seems very different to the Coptic averages who only seem to want Kulubnarti ancestry for their excess SSA in relation to the Egyptian samples.

I had theorized previously that Copts seemed to have more actual Kulubnarti ancestry than Egyptian muslims once you introduced other SSA sources into the model & that this may indicate real ancestry rather than mere shared affinities. I believe these results do support that supposition as the trend seems to repeat itself, the other possible model is that as Coptic ancestry is from Upper Egypt, these affinities may have been built in to our genome and it is simply shared affinities rather than actual admixture.

[nee4speed111]

Is being shifted towards Levant_N considered North African? Are the rumors in agreement with each other?

I believe that the first rumour is in regards to where they plot and the second one is about their admixture. I think the implication with the North african looking Old Kingdom Egyptians implies a more Natufian like sample with minor Iran-Chl ancestry, which probably would cluster in the levant neolithic direction.

[nee4speed111]

Some more models, this time with Basal ancestry and modelling the AE samples on hand along with modern averages for Egyptians:

https://i.imgur.com/4FXY0Ln.jpeg

[nee4speed111]

Some models of Egyptians

First one is Ancient Egyptians, Levantines & a West & East SSA source, second one I add the medieval Arabian sources we have & the third one I add Guanches to the model

https://cdn.discordapp.com/attachments/980212761982296124/1061043973004734525/image.png

https://cdn.discordapp.com/attachments/980212761982296124/1061043973558378516/image.png

https://cdn.discordapp.com/attachments/980212761982296124/1061043974082658434/image.png

Source populations used


Canary_Islands_Guanche,-0.0393828,0.1314096,-0.0023384,-0.0687344,0.0337292,-0.0363672,-0.0299874,0.008261,0.0708878,0.0305428,0.0075674,-0.0059948,0.0182554,-0.0176982,0.0232082,-0.0130468,0.0031814,-0.019206,-0.044321,0.010405,-0.0134762,-0.0377142,0.0232692,-0.0011806,0.0046224
Arab:Levant_SYR_Tell_Masaikh,0.0819525,0.131511,-0.0560025,-0.083819,-0.0136945,-0.0308175,-0.008108,-0.0080765,0.0259745,-0.004465,0.008769,-0.01716,0.036645,0.000275,0.001018,0.018629,-0.0170805,0.000887,0.0001885,0.013131,0.0134765,0. 004699,-0.0086275,0.006085,-0.0017365
Arab:Levant_Tell_Qarassa_Early_Antiquity,0.0671555 ,0.1518215,-0.0554365,-0.1225795,-0.003231,-0.055081,-0.0151585,-0.0119995,0.065652,0.007107,0.01835,-0.028999,0.06608,0.0039225,0.008618,0.019159,-0.0372895,-0.0015205,0.0018225,0.034642,0.020589,0.0174355,-0.005793,0.004579,-0.0126935
COG_Kindoki_230BP,-0.6231815,0.058393,0.019422,0.018088,0.0007695,0.0 133865,-0.007168,0.0170765,-0.035587,0.017495,0.0048715,-0.002248,-0.0031215,-0.0052985,-0.0021715,0.0088835,-0.0058675,-0.004941,-0.0042735,0.0078785,0.0061765,-0.0012985,0.002465,-0.0030125,0.0029935
KEN_Kakapel_900BP,-0.513342,0.05687,-0.010936,-0.00969,-0.007386,-0.013666,-0.00658,0.014769,0.075674,-0.113898,-0.032478,0.028924,-0.049207,-0.010046,0.015065,-0.020419,0.018645,-0.000507,0.022877,-0.027138,-0.002496,0.007172,-0.027238,-0.000241,0.004071
Levant:Levant_Megiddo_MLBA,0.0861261,0.1455592,-0.0646134,-0.1002072,-0.014596,-0.0394563,-0.0045434,-0.0097249,0.0131382,0.0089382,0.0103465,-0.0088707,0.0219027,0.0020119,-0.007316,0.005411,-0.0024898,0.004217,0.0036812,0.0073607,0.0047534,0 .0040982,-0.0049357,-0.0025361,-0.0014427
Levant:Levant_Sidon_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant:Levant_Beirut_ERoman,0.0859368,0.1406508,-0.0576052,-0.0909245,-0.0153875,-0.0312358,-0.0051112,-0.005596,0.007465,0.010524,0.0064958,-0.0090293,0.0178392,-0.0026492,-0.0099752,0.0170377,0.0113435,-0.0044975,0.0018855,0.0016572,0.0022772,0.0048845,-0.0008625,0.0039462,-0.0029638
Levant:Levant_Baqah_BA,0.0878146,0.1485719,-0.0613198,-0.1046686,-0.0111404,-0.038222,-0.0059575,-0.008215,0.0145723,0.0087018,0.0110425,-0.0114123,0.0239046,0.0015208,-0.0082111,0.0121054,-0.0002609,0.003712,0.003708,0.0065595,0.0049349,0. 0068132,-0.0056694,0.000506,
Levant:Levant_Abel_IA,0.087644,0.149283,-0.05506,-0.100776,-0.014156,-0.032072,-0.002115,-0.006231,0.012476,0.007654,0.011205,-0.003297,0.01888,0.003716,0.002443,0.010475,0.0033 9,0.008235,-0.001006,-0.003252,0.005366,0.009027,-0.002835,0.000482,-0.004071
Ancient_Egyptian:Egypt_Late_Period,0.050082,0.1467 44,-0.042426,-0.1183805,-0.0020005,-0.049782,-0.015628,-0.004731,0.0474495,0.006196,0.0090125,-0.011465,0.029732,-0.005849,-0.0008145,-0.0020555,-0.0074315,-0.0019635,-0.0035195,0.0120055,0.005615,0.0016695,0.0036355,0 .003916,-0.0005985
Ancient_Egyptian:Levant_IAIII_Beirut_o_(Egyptian_P rofile),0.0387,0.144205,-0.052797,-0.11725,0.003385,-0.042391,-0.00987,-0.001385,0.046427,0.002551,0.01494,-0.018733,0.033151,0.002615,-0.004343,0.002652,-0.000913,-0.004054,-0.002765,0.02051,0.014974,-0.000989,-0.003081,0.005181,-0.002874

[Jingle Bell]

Why not use Nilotic & West African samples instead the Congolese one?

[nee4speed111]

Why not use Nilotic & West African samples instead the Congolese one?

I was trying to only use ancient pops instead of modern ones, doesn't make too much of a difference with the results, I re-ran the last model with a Nilotic and West African source

https://cdn.discordapp.com/attachments/1061059385113198594/1061059430336180324/image.png

[Zanzibar]

Based on the averages, no it doesn't seem like it. However heterogeneity among the G25 Egyptian samples means its possible some do & some don't. Here I run all of the individual Egyptian muslim samples, using the AE proxy, lebanese Christian, SSA proxy & Saudi & Yemenite samples:

Target: Egyptian:Egypt9AQ177
Distance: 2.8492% / 0.02849239
44.4 Lebanese_Christian
30.0 Egyptian_Ancient_proxy
11.6 Dinka
6.8 Yemenite_Amran
5.0 Yemenite_Mahra
2.2 Yoruba

Target: Egyptian:Egypt9AQ172
Distance: 2.7736% / 0.02773590
49.0 Egyptian_Ancient_proxy
31.2 Lebanese_Christian
6.6 Dinka
5.8 Yoruba
4.8 Yemenite_Amran
2.6 Yemenite_Mahra

Target: Egyptian:Egypt8AT113
Distance: 2.2385% / 0.02238505
33.6 Egyptian_Ancient_proxy
28.8 Lebanese_Christian
24.4 Yemenite_Al_Jawf
6.6 Dinka
6.6 Yoruba

Target: Egyptian:Egypt7AQ172
Distance: 2.4031% / 0.02403087
51.8 Egyptian_Ancient_proxy
30.2 Lebanese_Christian
8.8 Yemenite_Amran
7.2 Yoruba
2.0 Dinka

Target: Egyptian:Egypt5AQ172
Distance: 3.0930% / 0.03092976
56.4 Egyptian_Ancient_proxy
21.2 Lebanese_Christian
12.6 Yemenite_Amran
6.2 Dinka
3.6 Yoruba

Target: Egyptian:Egypt3AQ172
Distance: 2.9142% / 0.02914211
47.6 Egyptian_Ancient_proxy
36.4 Lebanese_Christian
7.2 Dinka
6.0 Yemenite_Mahra
2.8 Yoruba

Target: Egyptian:Egypt22TD21
Distance: 2.7028% / 0.02702762
46.2 Egyptian_Ancient_proxy
38.2 Lebanese_Christian
11.4 Dinka
4.2 Yemenite_Mahra

Target: Egyptian:Egypt1AQ172
Distance: 2.4466% / 0.02446623
52.8 Egyptian_Ancient_proxy
21.4 Lebanese_Christian
16.4 Yemenite_Amran
9.4 Dinka

Target: Egyptian:Egypt17AQ176
Distance: 2.7940% / 0.02794032
56.0 Egyptian_Ancient_proxy
33.0 Lebanese_Christian
8.8 Dinka
2.2 Yoruba

Target: Egyptian:Egypt15AQ172
Distance: 2.0074% / 0.02007428
65.4 Egyptian_Ancient_proxy
23.8 Lebanese_Christian
5.6 Dinka
5.2 Yoruba

Target: Egyptian:Egypt12AQ172
Distance: 2.8480% / 0.02847998
61.6 Egyptian_Ancient_proxy
27.6 Lebanese_Christian
10.8 Dinka

Target: Egyptian:9AJ129
Distance: 2.6057% / 0.02605701
68.2 Egyptian_Ancient_proxy
21.8 Lebanese_Christian
9.2 Yoruba
0.8 Dinka

Target: Egyptian:8AJ136
Distance: 3.3318% / 0.03331823
43.6 Yemenite_Amran
38.4 Egyptian_Ancient_proxy
8.2 Lebanese_Christian
6.4 Dinka
3.4 Yoruba

Target: Egyptian:8AJ129
Distance: 2.5157% / 0.02515733
40.0 Lebanese_Christian
33.6 Egyptian_Ancient_proxy
14.2 Yemenite_Dhamar
6.8 Yoruba
5.4 Dinka

Target: Egyptian:7AJ136
Distance: 2.9074% / 0.02907378
56.2 Lebanese_Christian
30.0 Egyptian_Ancient_proxy
11.8 Dinka
2.0 Yoruba

Target: Egyptian:7AJ129
Distance: 2.6693% / 0.02669350
34.6 Lebanese_Christian
27.0 Yemenite_Al_Jawf
21.0 Egyptian_Ancient_proxy
12.2 Dinka
5.2 Yoruba

Target: Egyptian:6AJ129
Distance: 2.6749% / 0.02674904
65.0 Egyptian_Ancient_proxy
19.0 Lebanese_Christian
6.8 Yemenite_Amran
4.8 Yemenite_Mahra
3.8 Yoruba
0.6 Dinka

Target: Egyptian:5AJ137
Distance: 2.5283% / 0.02528278
46.8 Egyptian_Ancient_proxy
26.0 Lebanese_Christian
16.2 Dinka
11.0 Yoruba

Target: Egyptian:5AJ136
Distance: 3.6805% / 0.03680453
43.4 Lebanese_Christian
29.6 Egyptian_Ancient_proxy
13.8 Yemenite_Mahra
7.2 Yoruba
6.0 Dinka

Target: Egyptian:4AJ137
Distance: 2.7625% / 0.02762540
57.6 Egyptian_Ancient_proxy
29.2 Lebanese_Christian
13.2 Dinka

Target: Egyptian:4AJ136
Distance: 2.9396% / 0.02939585
43.2 Egyptian_Ancient_proxy
29.6 Yemenite_Amran
18.2 Lebanese_Christian
6.8 Yoruba
2.2 Dinka

Target: Egyptian:3AJ137
Distance: 3.0285% / 0.03028529
54.0 Egyptian_Ancient_proxy
32.4 Lebanese_Christian
5.6 Yoruba
3.2 Dinka
3.2 Yemenite_Amran
1.6 Yemenite_Mahra

Target: Egyptian:2AJ137
Distance: 2.0888% / 0.02088810
72.6 Egyptian_Ancient_proxy
16.2 Lebanese_Christian
5.8 Dinka
5.4 Yoruba

Target: Egyptian:1AJ137
Distance: 2.7179% / 0.02717934
42.6 Lebanese_Christian
38.8 Egyptian_Ancient_proxy
8.6 Dinka
8.0 Yemenite_Amran
2.0 Yoruba

Target: Egyptian:16AJ137
Distance: 2.9097% / 0.02909701
52.4 Egyptian_Ancient_proxy
36.0 Lebanese_Christian
8.2 Dinka
3.4 Yoruba

Target: Egyptian:15AJ137
Distance: 3.1526% / 0.03152574
54.6 Egyptian_Ancient_proxy
24.2 Lebanese_Christian
9.4 Dinka
7.8 Yemenite_Amran
4.0 Yoruba

Target: Egyptian:12AJ136
Distance: 2.4664% / 0.02466434
41.2 Egyptian_Ancient_proxy
34.4 Lebanese_Christian
13.0 Yemenite_Ma'rib
10.2 Dinka
1.2 Yoruba

Target: Egyptian:12AJ129
Distance: 3.3353% / 0.03335306
44.2 Egyptian_Ancient_proxy
32.0 Lebanese_Christian
12.6 Yemenite_Amran
11.2 Dinka

Target: Egyptian:10AJ137
Distance: 2.5674% / 0.02567416
44.8 Lebanese_Christian
42.4 Egyptian_Ancient_proxy
10.6 Dinka
2.2 Yoruba

Target: Egyptian:10AJ136
Distance: 2.8636% / 0.02863648
41.2 Egyptian_Ancient_proxy
32.6 Lebanese_Christian
17.8 Yemenite_Amran
4.4 Dinka
4.0 Yoruba

As you can see, it ranges from not needed a Arabian source at all to needing 40%+ of a Yemenite source. However I don't think all or even most of it is actual Arabian ancestry, alot of it could be shared ancestry between Egyptians & Arabians from a Natufian like source. Although the heterogeneity of it does imply that some of it is real.

Interesting. I notice that Yemenites, Bedouins, Saudians and other Peninsular Arabians are closest modern populations to ancient Egyptians? So the close distance and genetic similarity comes from their massive shared Natufian ancestry?

This would means its possible that ancient Egyptians could have Arabid phenotypes and resemble modern day Peninsular Arabs in looks then?

[nee4speed111]

Copts are the closest modern pop, Arabians are pretty close but the big difference is Arabians have less Anatolian ancestry and more Iranian ancestry.

[Zanzibar]

Copts are the closest modern pop, Arabians are pretty close but the big difference is Arabians have less Anatolian ancestry and more Iranian ancestry.

Where do both ancient Egyptians, Copts and Arabians get their massive Natufian ancestry to makes them pretty close together?

Is it possible that ancient Egyptians might have resemble Copts and the less Iranian and more Anatolian-shifted Arabs such as Yemenis from Amran?

Do Arabians also have more Steppe than Copts or similar amounts?

[abceff]

Do Arabians also have more Steppe than Copts or similar amounts?

"real" unmixed arabs have no steppe

Target: Saudi
Distance: 5.5222% / 0.05522179
63.2 Levant_Natufian_contam
26.4 Iran_Neolithic
10.4 EEF

some gulf arabs have elevated iran_n+steppe from their persian admixture

Target: EmiratiC
Distance: 1.9120% / 0.01912021
37.0 Iran_Neolithic
29.4 Levant_Natufian_contam
17.0 EEF
10.6 Steppe_Pastoralist
4.4 AA_AASI
1.6 SSA

Target: Omani_(Intermediate_Profile)
Distance: 3.4156% / 0.03415630
27.4 SSA
26.0 Iran_Neolithic
25.0 Levant_Natufian_contam
14.0 EEF
4.8 AA_AASI
2.6 Steppe_Pastoralist
0.2 Caucasus_Hunter-gatherer

Target: Omani
Distance: 3.0316% / 0.03031555
42.8 Levant_Natufian_contam
34.2 Iran_Neolithic
13.0 EEF
5.8 Steppe_Pastoralist
4.2 SSA

whereas the coptic average gets no steppe

Target: Egyptian_Copt
Distance: 2.4927% / 0.02492696
46.6 Levant_Natufian_contam
26.0 EEF
17.2 Iran_Neolithic
5.4 SSA
4.8 Caucasus_Hunter-gatherer

[nee4speed111]

Where do both ancient Egyptians, Copts and Arabians get their massive Natufian ancestry to makes them pretty close together?

Is it possible that ancient Egyptians might have resemble Copts and the less Iranian and more Anatolian-shifted Arabs such as Yemenis from Amran?

Do Arabians also have more Steppe than Copts or similar amounts?

Arabians seem to have alot of ancestry from a yet undiscovered hunter gatherer population very similar to Natufians, this combined with Bronze Age Levantine makes up most of the genome of modern day Arabians. In Egypt, I would guess that Natufian type ancestry has been around since even before the Neolithic period, it consistently pops up in large amounts in ancient DNA remains from East Africa, the earliest Kenyan Neolithic pastoralist samples have huge amounts of it.

Steppe is very low to non-existent in both Copts & Arabs.

[Zanzibar]

"real" unmixed arabs have no steppe

Target: Saudi
Distance: 5.5222% / 0.05522179
63.2 Levant_Natufian_contam
26.4 Iran_Neolithic
10.4 EEF

some gulf arabs have elevated iran_n+steppe from their persian admixture

Target: EmiratiC
Distance: 1.9120% / 0.01912021
37.0 Iran_Neolithic
29.4 Levant_Natufian_contam
17.0 EEF
10.6 Steppe_Pastoralist
4.4 AA_AASI
1.6 SSA

Target: Omani_(Intermediate_Profile)
Distance: 3.4156% / 0.03415630
27.4 SSA
26.0 Iran_Neolithic
25.0 Levant_Natufian_contam
14.0 EEF
4.8 AA_AASI
2.6 Steppe_Pastoralist
0.2 Caucasus_Hunter-gatherer

Target: Omani
Distance: 3.0316% / 0.03031555
42.8 Levant_Natufian_contam
34.2 Iran_Neolithic
13.0 EEF
5.8 Steppe_Pastoralist
4.2 SSA

whereas the coptic average gets no steppe

Target: Egyptian_Copt
Distance: 2.4927% / 0.02492696
46.6 Levant_Natufian_contam
26.0 EEF
17.2 Iran_Neolithic
5.4 SSA
4.8 Caucasus_Hunter-gatherer

That Omani sample (not the Intermediate one) seems to be too low in terms of SSA.

How did those Arabs, Copts, Samaritans, Western Georgians manage to avoid Steppe admixture while almost every one else in the MENA region have it?

[Zanzibar]

Arabians seem to have alot of ancestry from a yet undiscovered hunter gatherer population very similar to Natufians, this combined with Bronze Age Levantine makes up most of the genome of modern day Arabians. In Egypt, I would guess that Natufian type ancestry has been around since even before the Neolithic period, it consistently pops up in large amounts in ancient DNA remains from East Africa, the earliest Kenyan Neolithic pastoralist samples have huge amounts of it.

Steppe is very low to non-existent in both Copts & Arabs.

Is Natufian also hiding some African/ANA-related ancestry in these Peninsular Arabs?

I see. In terms of African ancestry, Copts and Peninsular Arabs have similar amounts?

[nee4speed111]

Is Natufian also hiding some African/ANA-related ancestry in these Peninsular Arabs?

I see. In terms of African ancestry, Copts and Peninsular Arabs have similar amounts?

Natufian has African ancestry built into it, although we don't have the samples yet for this ANA-related ancestry so models are pretty rough.

Depends on the Arabian, generally Copts have more than unadmixed Arabs but there are alot of outliers in the Yemeni population & to a lesser extent Saudi population that have quite large amounts.

[abceff]

That Omani sample (not the Intermediate one) seems to be too low in terms of SSA.

their SSA seems to be in line with what other omanis score, here are three omani coords i have

Target: Oman_North:27631_APPG7555958
Distance: 4.8572% / 0.04857183
58.2 Levant_Natufian_EpiP
29.6 Iran_N
12.2 SSA

Target: Oman_North:27582_APPG7555960
Distance: 4.0083% / 0.04008288
44.8 Levant_Natufian_EpiP
40.8 Iran_N
10.8 SSA
3.0 GEO_CHG
0.4 Yamnaya
0.2 AASI

Target: Oman_o:27582_APPG7555959
Distance: 4.3172% / 0.04317224
36.4 SSA
32.0 Levant_Natufian_EpiP
27.6 Iran_N
4.0 AASI


How did those Arabs, Copts, Samaritans, Western Georgians manage to avoid Steppe admixture while almost every one else in the MENA region have it?

i am not sure to be entirely honest but the genetic continuity of Samaritans especially is very interesting, they are almost identical to bronze age levantines


Target: Samaritan
Distance: 3.5345% / 0.03534484
39.0 Anatolia_N
29.2 Levant_Natufian_EpiP
25.0 Iran_N
6.2 GEO_CHG
0.6 Yamnaya

Target: Levant_Baqah_BA
Distance: 4.2022% / 0.04202170
37.2 Anatolia_N
32.2 Levant_Natufian_EpiP
23.4 Iran_N
7.2 GEO_CHG

[Zanzibar]

their SSA seems to be in line with what other omanis score, here are three omani coords i have

Target: Oman_North:27631_APPG7555958
Distance: 4.8572% / 0.04857183
58.2 Levant_Natufian_EpiP
29.6 Iran_N
12.2 SSA

Target: Oman_North:27582_APPG7555960
Distance: 4.0083% / 0.04008288
44.8 Levant_Natufian_EpiP
40.8 Iran_N
10.8 SSA
3.0 GEO_CHG
0.4 Yamnaya
0.2 AASI

Target: Oman_o:27582_APPG7555959
Distance: 4.3172% / 0.04317224
36.4 SSA
32.0 Levant_Natufian_EpiP
27.6 Iran_N
4.0 AASI



i am not sure to be entirely honest but the genetic continuity of Samaritans especially is very interesting, they are almost identical to bronze age levantines


Target: Samaritan
Distance: 3.5345% / 0.03534484
39.0 Anatolia_N
29.2 Levant_Natufian_EpiP
25.0 Iran_N
6.2 GEO_CHG
0.6 Yamnaya

Target: Levant_Baqah_BA
Distance: 4.2022% / 0.04202170
37.2 Anatolia_N
32.2 Levant_Natufian_EpiP
23.4 Iran_N
7.2 GEO_CHG

Hmm that other Omani is only 4.2% SSA while these three coords have much higher. Are the Northern Omanis from Muscat, Sohar or Musandam?

If I remembered correctly, the Iraqi Jews also have very low to negligible amounts of Steppe compared to their neighbors in the region. Agreed, a long time ago, I did some modelling for Samaritans, and they were getting 88-95%+ Bronze Age Levantine depending on the ancient averages used. They have less non-native admixture than even Levantine Christians.

It's probably because of endogamy and refusal to absorb outsiders I think that's why the Samaritans have such a high genetic continuity from their ancient forefathers. They are literally living fossils.