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Awale
10-30-2017, 11:27 AM
Recently sent David nee4speed111 (http://www.anthrogenica.com/member.php?3491-nee4speed111)'s raw data so that he could throw him into the global-10 PCA as "Egyptian-Copt" (he seems rather representative/typical of Copts, from what I've seen but but I'd no doubt prefer more samples) and here we go:

Egyptian_Copt,0.0034,0.027,-0.0043,0.0406,0.0012,0.0108,-0.0252,-0.0043,-0.0092,-0.004

I ran some models quickly after just for the heck of it:


[1] "distance%=0.9432 / distance=0.009432"

Egyptian_Copt

Natufian 38.8
Iran_ChL 27.4
Tepecik_Ciftlik_N 26.3
Dinka 7.5


39% Natufian, 27% Zagros-Chl, 26% Anatolia_N and 8% Dinka.

--

[1] "distance%=1.1044 / distance=0.011044"

Egyptian_Copt

Levant_N 46.5
Iran_ChL 30.3
Natufian 13.8
Dinka 9.4

47% Levant_N, 30% Zagros-Chl, 14% Natufian and 9% Dinka.

--

[1] "distance%=0.8286 / distance=0.008286"

Egyptian_Copt

Natufian 39.6
Tepecik_Ciftlik_N 36.9
Iran_N 17.4
Dinka 6.1

40% Natufian, 37% Anatolia_N, 17% Zagros_N and 6% Dinka.

--

[1] "distance%=0.7256 / distance=0.007256"

Egyptian_Copt

Tepecik_Ciftlik_N:Tep004 35.10
Natufian:I1072 15.90
Natufian:I0861 13.75
Levant_N:I1704 11.60
Iran_N:WC1 9.60
Iran_N:AH1 7.65
Dinka 6.40

35% Anatolia_N, 30% Natufian, 12% Levant_N, 17% Zagros_N and 6% Dinka.

--

[1] "distance%=2.9821 / distance=0.029821"

Egyptian_Copt

Saharawi 69.0
Satsurblia 31.1

69% Saharawi and 31% CHG.

I don't know what but something's missing for Copts, it seems. Something holding models like the first one from being really good fits (i.e. below or at around 0.5), even using individual samples instead of population averages (for the ancients) like with the 4th model didn't help all that much. It's odd because using the very same samples (+Yorubas) as the 1st model actually produced a decent fit for the usual non-Copt Egyptian samples out there:

[1] "distance%=0.3783 / distance=0.003783"

Egyptian

Natufian 33.80
Iran_ChL 28.85
Tepecik_Ciftlik_N 24.40
Dinka 9.65
Yoruba 3.30

I ran some other models for non-Copt Egyptians as well and I'd say the first and last one below are probably the most sensible ones:


[1] "distance%=0.5151 / distance=0.005151"

Egyptian

Egyptian_Copt 77.0
Palestinian 16.4
Mende_Sierra_Leone 4.1
Bantu_SA_Tswana 2.5
Arab_Israel_1 0.0
Arab_Israel_2 0.0
Samaritan 0.0
Lebanese_Christian 0.0
Lebanese_Muslim 0.0
Druze 0.0
Syrian 0.0
Yoruba 0.0
Bantu_SA_Herero 0.0
Bantu_SA_Ovambo 0.0
Bantu_SA_Pedi 0.0
Bantu_SA_S_Sotho 0.0
Bantu_SA_Zulu 0.0

77% Copt, 16% Southern-Levantine and 7% West-South African.

This first model was pretty crazy... I decided to include every Levantine group out there (xJews & Cypriots) as well as some West-African samples and every Bantu speaker sample available and I expected to get some overfit and wonky result (5% Druze, 6% Palestinian, 2% Lebanese and a fit like 0.03... or something) but the distance is not in overfitting territory and the model surprisingly only chose Palestinians among the Levantines. Seems sensible to me, to be honest.

--

[1] "distance%=0.0354 / distance=0.000354"

Egyptian

Yemenite-Jew 40.90
Moroccan 18.50
Lebanese_Muslim 16.60
Syrian 10.70
Libyan 4.95
Yoruba 2.80
Saudi 2.10
Mende_Sierra_Leone 1.25
Bantu_SA_Ovambo 1.05
Bantu_SA_Pedi 1.05
Arab_Israel_2 0.10

43% Arabian, 27% Northern-Levantine, 24% Maghrebi and 6% West-South African.

Decided to include Arabians like the Saudi and Yemenite Jewish samples as well as some Maghrebis here and see how they'd change things up and, as you can see, the results are interesting but I'd say far-less sensible now. The Arabians (YJs mainly) seem to have usurped Copts and there's way too much Levantine (Northern-Levantine, no less) and Maghrebi to make sense. The distance wreaks of overfitting too.

--

[1] "distance%=0.0968 / distance=0.000968"

Egyptian

Syrian 25.40
Samaritan 18.85
Negev-Bedouin-B 16.35
Moroccan 14.45
Libyan 13.80
Egyptian_Copt 5.20
Bantu_SA_Ovambo 4.95
Yoruba 1.00

61% Levantine, 28% Maghrebi, 5% Copt and 6% West-South African.

Believe all I did here was add Bedouin-Bs and remove YJs and Saudis. As nonsensical to me as the last result.

--

[1] "distance%=0.4552 / distance=0.004552"

Egyptian

Libyan 56.1
Palestinian 21.9
Syrian 20.9
Egyptian_Copt 1.2

56% Maghrebi, 43% Levantine and 1% Copt.

Think I removed the Negevians here but I also definitely removed every Sub-Saharan and/or Sahelian population (I wanted to see, just for fun (not because it would make any sense), what'd happen if Maghrebis proved to be the only thing the models could turn to in order to explain these Egyptians' SSA&orSahelian ancestry. Libyans ended up muddying up everything. As some may know, especially along the east of the country, Libyans often prove to be the most West-Asian or Egyptian shifted Maghrebis.

--

[1] "distance%=0.752 / distance=0.00752"

Egyptian

Palestinian 46.05
Egyptian_Copt 30.60
Moroccan 21.20
Syrian 2.15

46% Southern-Levantine, 31% Copt, 21% Maghrebi and 2% Northern-Levantine.

I removed Libyans here and the run became more interesting, I guess. But eh, I was just having fun at this point... Don't take this result or almost any after the first one seriously at all.

--

[1] "distance%=0.7781 / distance=0.007781"

Egyptian

Egyptian_Copt 46.9
Syrian 33.2
Moroccan 19.9

47% Copt, 33% Northern-Levantine and 20% Maghrebi.

Think all I did here was remove Palestinians.

--

[1] "distance%=0.525 / distance=0.00525"

Egyptian

Egyptian_Copt 77.1
Samaritan 13.4
Mende_Sierra_Leone 4.6
Bantu_SA_Tswana 2.8
Syrian 2.1

77% Copt, 16% Levantine and 7% West-South African.

And finally, I wanted to see what'd happen now if I re-added the West African and Bantu-speaking groups and got another result I think is somewhat sensible. 6-7% West-African related ancestry (most likely owed to the slave-trade?) and ~15% Levantine (mainly Soutern-Levantine again) related admixture.

I'm not all that familiar at all with the Y-DNA and mtDNA differences between Copts and other Egyptian so I'll have to leave it to other folks to comment on whether or not ~15% Southern-Levantine-like admixture really makes sense. Anyway, feel free to share some models you made using nee4speed111/Egyptian_Copt and make some suggestions models for me to run (which samples you think I should put in the input and target folders (http://www.anthrogenica.com/showthread.php?11538-Genetic-origins-of-the-Minoans-and-Mycenaeans&p=271453#post271453) and so on) and I'll try to run 'em when I'm free, though I suggest just figuring out nMonte for yourself as well (it's easy to run).

NetNomad
10-31-2017, 04:00 AM
Afrocentrists claim that Egyptians have been whitened, but it looks more like they were blackened.

Awale
10-31-2017, 07:57 AM
Afrocentrists claim that Egyptians have been whitened, but it looks more like they were blackened.

Refrain from nonsensical and off-topic postings like this, thank you. Besides, most Afrocentrics I've seen are aware of the difference between Copts and many Muslim Egyptians (some Muslim Egyptians can be recent converts and not all that different from Copts), what they normally claim is that Copts are the more West-Asianized ones... As in, Egyptians before about 1000-1500 BCE or something were much more Dinka-like or what have you but this is very doubtful. North of around Luxor, I doubt any Egyptians were more than ~20% East-Central African at any point since the early Bronze Age. Also, only Afrocentrists could act like there's anything "white" at all about Egypt. West-Asian ≠ "white". Most Egyptians, whether Copt or not would be seen as ethnic brown people in most of the West.

Anyway, either share guidelines for models you want to see run, share some of your own models, comment on the models already present in an intelligent manner or don't comment at all. I'm really not in the mood for this to devolve into some flame war thread.

--

Now on another note, I remember being told by King once that Need4Speed used to point out (I think at ABF?) that Copts and Yemenite Jews maybe similar but not at all nearly identical and that, based on ADMIXTURE results, Copts were more Anatolian-Neolithic shifted and less pre-historic Zagrosian so I wanted to see if that was the case:

[1] "distance%=0.9066 / distance=0.009066"

Yemenite_Jew

Natufian 57.6
Iran_ChL 41.8
Tepecik_Ciftlik_N 0.6

--

[1] "distance%=0.9094 / distance=0.009094"

Egyptian_Copt

Natufian 39.95
Iran_ChL 32.15
Barcin_N 20.45
Dinka 7.45


So it seems Need4Speed was correct, Copts are basically more Anatolian-Neolithic-shifted than Yemenite Jews and also show less Zagros-Chalcolithic related ancestry (albeit there's Anatolian-Neolithic related ancestry in this ancestry). I ran in the same populations for both groups to get the above results:

Iran_ChL,0.01224,0.02376,-0.0045,0.02978,0.0133,-0.04126,-0.01008,0.0048,0.02584,0.00164
Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Barcin_N,0.0163053,0.0352053,-0.0025368,0.0242368,0.0039474,0.0469684,-0.0141105,-0.0004632,-0.0013684,0.005
Boncuklu_N,0.014375,0.03175,-0.003025,0.011675,0.003525,0.044425,-0.00485,0.001725,0.00105,0.006875
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143

TuaMan
10-31-2017, 10:01 PM
Can you do some runs using the ancient Egyptian samples from this past summer? I would be curious to see how closely modern Copts match them, and I'd also like to see some of their own ancestral breakdown in their own right.

Awale
11-01-2017, 01:53 PM
Can you do some runs using the ancient Egyptian samples from this past summer? I would be curious to see how closely modern Copts match them, and I'd also like to see some of their own ancestral breakdown in their own right.

I'd love to but those ancient samples aren't in the Global-10 PCA (I assume there aren't enough markers, otherwise David would have them up). But I've seen people like Need4Speed meticulously pore over them via ADMIXTURE calcs over at Gedmatch and they looked very very similar to Copts which makes sense, to be honest.

Poldo
11-02-2017, 03:04 AM
Would Copts (And by extension, Ancient Egyptians) cluster with North Africans like Berbers?

Awale
11-09-2017, 02:59 PM
Would Copts (And by extension, Ancient Egyptians) cluster with North Africans like Berbers?

No. They'd seem generally Arabian-Levantine-North-African along a global PCA. As in, part of the cline between Southern-Europe and negligibly (or not) Eurasian admixed groups from Eastern, Southern, Central & Western Africa. But in a regional plot like a "Pan-West-Eurasia" one; I've seen Copts and Muslim Egyptians mainly cluster close to Southern-Levantines and Arabians rather than Maghrebis (see here (https://drive.google.com/file/d/0B2ARnUeK-Y8WWEx4bnFWSTc2dWM/view?usp=sharing), there are no Copts but the usual Egyptian samples are there). I guess the reason is that they're far more "eastern-shifted" than Maghrebis. All that Zagros-Chalcolithic related ancestry and probably less IAM-like ancestry as well.

--

Anyway, funny seeing your question when I got back to this thread as I'd returned to share these results:


Copt + More Western Maghrebi group:

distance%=0.7618 / distance=0.007618

Libyan

Tunisian 60.2
Egyptian_Copt 39.8

--

distance%=0.3159 / distance=0.003159

Tunisian

Algerian 75.8
Egyptian_Copt 24.1

--

distance%=0.753 / distance=0.00753

Algerian

Moroccan 90.85
Egyptian_Copt 9.15

--

distance%=0.7084 / distance=0.007084

Moroccan

Saharawi 76.2
Egyptian_Copt 23.8

--

distance%=1.1107 / distance=0.011107

Saharawi

Mozabite 66.2
Egyptian_Copt 33.8

---

Copt + More Western Maghrebi group + East & West African groups:

distance%=0.7425 / distance=0.007425

Libyan

Tunisian 56.6
Egyptian_Copt 41.6
Dinka 1.7

--

distance%=0.2177 / distance=0.002177

Tunisian

Algerian 72.8
Egyptian_Copt 25.4
Mende_Sierra_Leone 1.8

--

distance%=0.616 / distance=0.00616

Algerian

Moroccan 86.8
Egyptian_Copt 9.9
Mende_Sierra_Leone 3.3

--

distance%=0.6163 / distance=0.006163

Moroccan

Saharawi 74.5
Egyptian_Copt 22.9
Yoruba 2.5

--

distance%=0.7415 / distance=0.007415

Saharawi

Mozabite 64.5
Egyptian_Copt 29.6
Mende_Sierra_Leone 5.9

---

Iran-Chl & Levant_N + More Western Maghrebi group + East & West African groups:

distance%=0.5572 / distance=0.005572

Libyan

Tunisian 51.95
Levant_N 32.20
Iran_ChL 8.65
Dinka 7.20

--

distance%=0.2631 / distance=0.002631

Tunisian

Algerian 77.65
Levant_N 12.20
Iran_ChL 7.25
Dinka 2.40
Mende_Sierra_Leone 0.50

--

distance%=0.5766 / distance=0.005766

Algerian

Moroccan 92.9
Iran_ChL 4.8
Mende_Sierra_Leone 1.6
Yoruba 0.7

--

distance%=0.6577 / distance=0.006577

Moroccan

Saharawi 74.75
Levant_N 15.80
Iran_ChL 4.60
Luo 3.65
Yoruba 1.20

--

distance%=0.4333 / distance=0.004333

Saharawi

Mozabite 61.90
Levant_N 25.20
Mende_Sierra_Leone 7.50
Iran_ChL 3.55
Dinka 1.85

Decided to try and use Copts to gauge whether or not there was "eastern admixture" in the various Maghrebi populations available in the Global-10 PCA and it does look like there's a very clear east-pulling-cline. Moroccans being more east-shifted than Saharawis, Algerians being more east-shifted than Moroccans, Tunisians being more east-shifted than Algerians and Libyans being more east-shifted than Tunisians.

I also used Levantine-Neolithic and Zagros-Chalcolithic along with some mostly unadmixed Western and Eastern African samples to see if this shift wasn't just some Anatolian-Neolithic related one but had something to do with the sort of ANE-rich ancestry that characterizes much of the Chalcolithic Zagrosians' ancestry:


distance%=0.5399 / distance=0.005399"

Iran_Chl

Iran_N 37.1
Levant_N 31.6
CHG 31.3

And, as you can see, they all did end up showing both Levant_N and Iran_Chl.

All the non-Maghrebi samples used in the Maghrebi models:

Egyptian_Copt,0.0034,0.027,-0.0043,0.0406,0.0012,0.0108,-0.0252,-0.0043,-0.0092,-0.004
Iran_ChL,0.01224,0.02376,-0.0045,0.02978,0.0133,-0.04126,-0.01008,0.0048,0.02584,0.00164
Levant_N,0.0099333,0.0326333,-0.0052667,0.0503667,0.0047667,0.0396,-0.0398333,0.0021,-0.0131,0.0038333
Mende_Sierra_Leone,-0.1163,0.00592,0.0065,-0.00024,-0.0411,-0.00424,0.01038,-0.00126,0.00796,0.01228
Yoruba,-0.1168645,0.0060323,0.0071194,0.0004387,-0.0461,-0.0047419,0.0123645,-0.0002097,0.007829,-0.0155419
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Luo,-0.1095,0.00582,0.00494,0.00342,-0.02512,-0.0038,0.00282,4e-04,-0.01,-0.03874

Poldo
11-09-2017, 05:19 PM
So, Copts (and apparently Ancient Egyptians) are more or less Arabs?

Awale
11-09-2017, 06:49 PM
So, Copts (and apparently Ancient Egyptians) are more or less Arabs?

No. Rather similar, on an autosomal level, to some "Arabs" like those in parts of the Southern-Levant and Arabia, sure, hence the close clustering on a "West-Eurasia" scale. But, when you look a little bit deeper, they're clearly a distinct population of their own if you look at them and say Yemenite Jews or even them and Palestinians:


distance%=0.5757 / distance=0.005757

Arab_Israel_2

Iran_ChL 46.4
Barcin_N 32.8
Natufian 11.6
Dinka 7.1
Boncuklu_N 1.3
Yoruba 0.8

47% Chalcolithic-Zagrosian, 34% Neolithic-Anatolian, 12% Levantine Hunter-Gatherer, 7% Dinka and 1% Yoruba.

--

distance%=0.386 / distance=0.00386"

Palestinian

Iran_ChL 42.95
Tepecik_Ciftlik_N 34.10
Natufian 18.30
Luo 2.35
Yoruba 2.30

43% Chalcolithic-Zagrosian, 34% Neolithic-Anatolian, 18% Levantine Hunter-Gatherer, 2% Luo and 2% Yoruba.

--

distance%=0.9094 / distance=0.009094

Egyptian_Copt

Natufian 39.95
Iran_ChL 32.15
Barcin_N 20.45
Dinka 7.45

40% Levantine Hunter-Gatherer, 32% Chalcolithic-Zagrosian, 21% Neolithic-Anatolian and 8% Dinka.

It really depends for some of the earliest Ancient-Egyptians, however. They may have not had the Zagros-related ancestry the recent 2-2.8kya samples had (and Copts also have) and may have been much more Natufian~Levantine-Neolithic-like than any modern population. We'll see in due time.

pegasus
11-09-2017, 07:01 PM
Awale can u post Iran recent and Iron Age Iran results

Awale
11-09-2017, 07:25 PM
Awale can u post Iran recent and Iron Age Iran results

Sure. In another thread but sure.

jesus
11-09-2017, 07:33 PM
Awale can u post Iran recent and Iron Age Iran results

I remember playing around with the sample(with the sheikh Awale). They were mainly Iran ChL + 15-20% steppe.

pegasus
11-10-2017, 05:48 AM
Sure. In another thread but sure.

I just wanted to see how CHG and Levantine components increase over time

Dewsloth
11-10-2017, 06:30 AM
I'd love to but those ancient samples aren't in the Global-10 PCA (I assume there aren't enough markers, otherwise David would have them up). But I've seen people like Need4Speed meticulously pore over them via ADMIXTURE calcs over at Gedmatch and they looked very very similar to Copts which makes sense, to be honest.

What about 3Drif-26? He was supposed to look Copt-like.

nee4speed111
11-10-2017, 11:28 AM
Hey Awale, I've got the raw data of another copt from 23andme if you would like it, along with something like 27 or so coptic Gedmatch kits. I'm pretty representative of copts based on the results I've seen, just slightly less Dinka shifted than the average coptic sample.

Awale
11-10-2017, 02:09 PM
Hey Awale, I've got the raw data of another copt from 23andme if you would like it, along with something like 27 or so coptic Gedmatch kits. I'm pretty representative of copts based on the results I've seen, just slightly less Dinka shifted than the average coptic sample.

Do email that Copt's raw data! Thanks. :)


What about 3Drif-26? He was supposed to look Copt-like.

I was under the impression that he wasn't in the Global-10 PCA but I think this might be him:

England_Roman_outlier:3DT26,0.0066,0.0308,-0.0053,0.0435,0.0061,0.012,-0.0297,0.0027,-0.0048,-0.0008

I'll run some models soon and see if it is and try and see if he fits better with Copts or Levantines.

nee4speed111
11-15-2017, 08:32 AM
Recently sent David nee4speed111 (http://www.anthrogenica.com/member.php?3491-nee4speed111)'s raw data so that he could throw him into the global-10 PCA as "Egyptian-Copt" (he seems rather representative/typical of Copts, from what I've seen but but I'd no doubt prefer more samples) and here we go:

Egyptian_Copt,0.0034,0.027,-0.0043,0.0406,0.0012,0.0108,-0.0252,-0.0043,-0.0092,-0.004

I ran some models quickly after just for the heck of it:


[1] "distance%=0.9432 / distance=0.009432"

Egyptian_Copt

Natufian 38.8
Iran_ChL 27.4
Tepecik_Ciftlik_N 26.3
Dinka 7.5


39% Natufian, 27% Zagros-Chl, 26% Anatolia_N and 8% Dinka.

--

[1] "distance%=1.1044 / distance=0.011044"

Egyptian_Copt

Levant_N 46.5
Iran_ChL 30.3
Natufian 13.8
Dinka 9.4

47% Levant_N, 30% Zagros-Chl, 14% Natufian and 9% Dinka.

--

[1] "distance%=0.8286 / distance=0.008286"

Egyptian_Copt

Natufian 39.6
Tepecik_Ciftlik_N 36.9
Iran_N 17.4
Dinka 6.1

40% Natufian, 37% Anatolia_N, 17% Zagros_N and 6% Dinka.

--

[1] "distance%=0.7256 / distance=0.007256"

Egyptian_Copt

Tepecik_Ciftlik_N:Tep004 35.10
Natufian:I1072 15.90
Natufian:I0861 13.75
Levant_N:I1704 11.60
Iran_N:WC1 9.60
Iran_N:AH1 7.65
Dinka 6.40

35% Anatolia_N, 30% Natufian, 12% Levant_N, 17% Zagros_N and 6% Dinka.

--

[1] "distance%=2.9821 / distance=0.029821"

Egyptian_Copt

Saharawi 69.0
Satsurblia 31.1

69% Saharawi and 31% CHG.

I don't know what but something's missing for Copts, it seems. Something holding models like the first one from being really good fits (i.e. below or at around 0.5), even using individual samples instead of population averages (for the ancients) like with the 4th model didn't help all that much. It's odd because using the very same samples (+Yorubas) as the 1st model actually produced a decent fit for the usual non-Copt Egyptian samples out there:

[1] "distance%=0.3783 / distance=0.003783"

Egyptian

Natufian 33.80
Iran_ChL 28.85
Tepecik_Ciftlik_N 24.40
Dinka 9.65
Yoruba 3.30

I ran some other models for non-Copt Egyptians as well and I'd say the first and last one below are probably the most sensible ones:


[1] "distance%=0.5151 / distance=0.005151"

Egyptian

Egyptian_Copt 77.0
Palestinian 16.4
Mende_Sierra_Leone 4.1
Bantu_SA_Tswana 2.5
Arab_Israel_1 0.0
Arab_Israel_2 0.0
Samaritan 0.0
Lebanese_Christian 0.0
Lebanese_Muslim 0.0
Druze 0.0
Syrian 0.0
Yoruba 0.0
Bantu_SA_Herero 0.0
Bantu_SA_Ovambo 0.0
Bantu_SA_Pedi 0.0
Bantu_SA_S_Sotho 0.0
Bantu_SA_Zulu 0.0

77% Copt, 16% Southern-Levantine and 7% West-South African.

This first model was pretty crazy... I decided to include every Levantine group out there (xJews & Cypriots) as well as some West-African samples and every Bantu speaker sample available and I expected to get some overfit and wonky result (5% Druze, 6% Palestinian, 2% Lebanese and a fit like 0.03... or something) but the distance is not in overfitting territory and the model surprisingly only chose Palestinians among the Levantines. Seems sensible to me, to be honest.

--

[1] "distance%=0.0354 / distance=0.000354"

Egyptian

Yemenite-Jew 40.90
Moroccan 18.50
Lebanese_Muslim 16.60
Syrian 10.70
Libyan 4.95
Yoruba 2.80
Saudi 2.10
Mende_Sierra_Leone 1.25
Bantu_SA_Ovambo 1.05
Bantu_SA_Pedi 1.05
Arab_Israel_2 0.10

43% Arabian, 27% Northern-Levantine, 24% Maghrebi and 6% West-South African.

Decided to include Arabians like the Saudi and Yemenite Jewish samples as well as some Maghrebis here and see how they'd change things up and, as you can see, the results are interesting but I'd say far-less sensible now. The Arabians (YJs mainly) seem to have usurped Copts and there's way too much Levantine (Northern-Levantine, no less) and Maghrebi to make sense. The distance wreaks of overfitting too.

--

[1] "distance%=0.0968 / distance=0.000968"

Egyptian

Syrian 25.40
Samaritan 18.85
Negev-Bedouin-B 16.35
Moroccan 14.45
Libyan 13.80
Egyptian_Copt 5.20
Bantu_SA_Ovambo 4.95
Yoruba 1.00

61% Levantine, 28% Maghrebi, 5% Copt and 6% West-South African.

Believe all I did here was add Bedouin-Bs and remove YJs and Saudis. As nonsensical to me as the last result.

--

[1] "distance%=0.4552 / distance=0.004552"

Egyptian

Libyan 56.1
Palestinian 21.9
Syrian 20.9
Egyptian_Copt 1.2

56% Maghrebi, 43% Levantine and 1% Copt.

Think I removed the Negevians here but I also definitely removed every Sub-Saharan and/or Sahelian population (I wanted to see, just for fun (not because it would make any sense), what'd happen if Maghrebis proved to be the only thing the models could turn to in order to explain these Egyptians' SSA&orSahelian ancestry. Libyans ended up muddying up everything. As some may know, especially along the east of the country, Libyans often prove to be the most West-Asian or Egyptian shifted Maghrebis.

--

[1] "distance%=0.752 / distance=0.00752"

Egyptian

Palestinian 46.05
Egyptian_Copt 30.60
Moroccan 21.20
Syrian 2.15

46% Southern-Levantine, 31% Copt, 21% Maghrebi and 2% Northern-Levantine.

I removed Libyans here and the run became more interesting, I guess. But eh, I was just having fun at this point... Don't take this result or almost any after the first one seriously at all.

--

[1] "distance%=0.7781 / distance=0.007781"

Egyptian

Egyptian_Copt 46.9
Syrian 33.2
Moroccan 19.9

47% Copt, 33% Northern-Levantine and 20% Maghrebi.

Think all I did here was remove Palestinians.

--

[1] "distance%=0.525 / distance=0.00525"

Egyptian

Egyptian_Copt 77.1
Samaritan 13.4
Mende_Sierra_Leone 4.6
Bantu_SA_Tswana 2.8
Syrian 2.1

77% Copt, 16% Levantine and 7% West-South African.

And finally, I wanted to see what'd happen now if I re-added the West African and Bantu-speaking groups and got another result I think is somewhat sensible. 6-7% West-African related ancestry (most likely owed to the slave-trade?) and ~15% Levantine (mainly Soutern-Levantine again) related admixture.

I'm not all that familiar at all with the Y-DNA and mtDNA differences between Copts and other Egyptian so I'll have to leave it to other folks to comment on whether or not ~15% Southern-Levantine-like admixture really makes sense. Anyway, feel free to share some models you made using nee4speed111/Egyptian_Copt and make some suggestions models for me to run (which samples you think I should put in the input and target folders (http://www.anthrogenica.com/showthread.php?11538-Genetic-origins-of-the-Minoans-and-Mycenaeans&p=271453#post271453) and so on) and I'll try to run 'em when I'm free, though I suggest just figuring out nMonte for yourself as well (it's easy to run).

Hey Awale, I've sent you the coptic genomes by email. What do you think is preventing any of the models from being good fits for me, Especially considering that muslim Egyptian samples can be fitted pretty well?

TuaMan
11-15-2017, 05:08 PM
Do Copts ever show evidence of Dinka or other Nilo-Saharan ancestry via D stats?

nee4speed111
11-16-2017, 11:32 PM
Do Copts ever show evidence of Dinka or other Nilo-Saharan ancestry via D stats?

I would imagine we do, considering every other sort of model has copts showing it. I've never seen D stats of copts before though, so I could be wrong

Awale
11-19-2017, 09:50 PM
Hey Awale, I've sent you the coptic genomes by email. What do you think is preventing any of the models from being good fits for me, Especially considering that muslim Egyptian samples can be fitted pretty well?

Not sure, to be honest. Maybe there's something from North-Africa missing here? I'll try with the samples you sent me. David got them into the PCA alongside an average:


Egyptian_Copt-1,0.0034,0.027,-0.0043,0.0406,0.0012,0.0108,-0.0252,-0.0043,-0.0092,-0.004
Egyptian_Copt-2,0.001,0.0284,-0.0018,0.0447,0.0034,0.0145,-0.0308,0.0011,-0.0083,-0.0023
Egyptian_Copt-3,0.0018,0.0294,-0.0028,0.0478,0.0024,0.0155,-0.0317,-0.0014,-0.0042,-0.0037

(You're the first sample)

The average: Egyptian_Copt,0.0020667,0.0282667,-0.0029667,0.0443667,0.0023333,0.0136,-0.0292333,-0.0015333,-0.0072333,-0.0033333

Just a little busy with Uni this week but I'll try to pump some stuff out soon. :P

Do Copts ever show evidence of Dinka or other Nilo-Saharan ancestry via D stats?

If Lebanese Christians (https://drive.google.com/file/d/0B2ARnUeK-Y8WNjFrOXpTeWpqTGc/view?usp=sharing) and Ashkenazi Jews (https://drive.google.com/file/d/0B2ARnUeK-Y8Wd3RqYTE1OGNUM00/view?usp=sharing) can show such an "SSA" shift via D-stats, I'm quite sure Copts can too, though I've never seen stats attempted for them.

TuaMan
11-19-2017, 11:52 PM
If Lebanese Christians (https://drive.google.com/file/d/0B2ARnUeK-Y8WNjFrOXpTeWpqTGc/view?usp=sharing) and Ashkenazi Jews (https://drive.google.com/file/d/0B2ARnUeK-Y8Wd3RqYTE1OGNUM00/view?usp=sharing) can show such an "SSA" shift via D-stats, I'm quite sure Copts can too, though I've never seen stats attempted for them.

I hate to sound like a total noob, but I just want to be clear - in those runs the SSA groups in column two are the target pops, the groups in columns three and four are the test pops? Leb Christian and AJ are the column fours, so if there's a positive stat that means the SSA groups have more drift with them over the column threes?

nee4speed111
11-20-2017, 12:25 AM
Would it be possible to model some sudanese/nubian samples, while including coptic reference pops to see how well the model fits?

Awale
01-19-2018, 12:50 PM
What about 3Drif-26? He was supposed to look Copt-like.

Well, I'm finally free from my exams and about a month ago I tried running him and some modern groups through nMonte:


Model 1 based on:

Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Levant_N,0.0099333,0.0326333,-0.0052667,0.0503667,0.0047667,0.0396,-0.0398333,0.0021,-0.0131,0.0038333
Iran_ChL,0.01224,0.02376,-0.0045,0.02978,0.0133,-0.04126,-0.01008,0.0048,0.02584,0.00164
Iran_N,0.00645,0.0141,-0.0066333,0.0267,0.0158833,-0.09005,0.0025333,0.00365,0.0293167,-0.0009667
CHG,0.01255,0.0206,-0.0027,0.0061,0.01215,-0.0631,0.01045,0.00565,0.05515,-0.00175
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Barcin_N,0.0163053,0.0352053,-0.0025368,0.0242368,0.0039474,0.0469684,-0.0141105,-0.0004632,-0.0013684,0.005
Boncuklu_N,0.014375,0.03175,-0.003025,0.011675,0.003525,0.044425,-0.00485,0.001725,0.00105,0.006875
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
WHG,0.01775,0.0183,6e-04,-0.08685,-0.0187,0.0627,0.0655,-0.0048,-0.0487,-0.0038

Results:

distance%=0.3662 / distance=0.003662

England_Roman_outlier

Levant_N 47.55
Iran_ChL 18.95
Natufian 14.95
Tepecik_Ciftlik_N 8.05
Iran_N 7.75
Dinka 2.75

--

distance%=0.3305 / distance=0.003305

Samaritan

Tepecik_Ciftlik_N 33.9
Levant_N 33.4
Iran_ChL 20.7
Iran_N 12.1

--

distance%=0.2922 / distance=0.002922

Palestinian

Natufian 36.15
CHG 31.15
Tepecik_Ciftlik_N 26.25
Iran_N 3.35
Dinka 2.75
Levant_N 0.35

--

distance%=0.8847 / distance=0.008847

Yemenite_Jew

Natufian 49.5
Iran_ChL 40.4
Levant_N 10.1

--

distance%=0.6126 / distance=0.006126

Egyptian_Copt

Levant_N 49.10
Iran_N 16.75
Natufian 15.15
Tepecik_Ciftlik_N 12.05
Dinka 6.95

____________________________________

Model 2 based on:

Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Iran_ChL,0.01224,0.02376,-0.0045,0.02978,0.0133,-0.04126,-0.01008,0.0048,0.02584,0.00164
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
WHG,0.01775,0.0183,6e-04,-0.08685,-0.0187,0.0627,0.0655,-0.0048,-0.0487,-0.0038

Results:

distance%=0.4195 / distance=0.004195

England_Roman_outlier

Natufian 43.5
Iran_ChL 30.9
Tepecik_Ciftlik_N 24.4
Dinka 1.3

--

distance%=0.4077 / distance=0.004077

Palestinian

Iran_ChL 42.55
Tepecik_Ciftlik_N 36.60
Natufian 15.70
Dinka 5.15

--

distance%=0.372 / distance=0.00372

Samaritan

Tepecik_Ciftlik_N 41.3
Iran_ChL 39.4
Natufian 19.3

--

distance%=0.9066 / distance=0.009066

Yemenite_Jew

Natufian 57.6
Iran_ChL 41.8
Tepecik_Ciftlik_N 0.6

--

distance%=0.6463 / distance=0.006463

Egyptian_Copt

Natufian 44.2
Iran_ChL 26.4
Tepecik_Ciftlik_N 23.3
Dinka 6.1

_____________________________________

Model 3 based on:

Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Iran_N,0.00645,0.0141,-0.0066333,0.0267,0.0158833,-0.09005,0.0025333,0.00365,0.0293167,-0.0009667
CHG,0.01255,0.0206,-0.0027,0.0061,0.01215,-0.0631,0.01045,0.00565,0.05515,-0.00175
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
WHG,0.01775,0.0183,6e-04,-0.08685,-0.0187,0.0627,0.0655,-0.0048,-0.0487,-0.0038

Results:

distance%=0.4953 / distance=0.004953

England_Roman_outlier

Natufian 51.55
Tepecik_Ciftlik_N 26.40
CHG 12.30
Iran_N 9.75

--

distance%=0.2922 / distance=0.002922

Palestinian

Natufian 36.2
CHG 30.9
Tepecik_Ciftlik_N 26.6
Iran_N 3.5
Dinka 2.7

--

distance%=0.5371 / distance=0.005371

Samaritan

Tepecik_Ciftlik_N 50.40
Natufian 23.95
Iran_N 17.20
CHG 8.45

--

distance%=1.0221 / distance=0.010221

Yemenite_Jew

Natufian 70.00
CHG 23.95
Iran_N 6.05

--

distance%=0.6608 / distance=0.006608

Egyptian_Copt

Natufian 49.55
Tepecik_Ciftlik_N 27.40
Iran_N 10.70
CHG 7.55
Dinka 4.80

The Roman sample seems to have possibly been an Egyptian. He consistently looks more similar to Egyptian Copts (average of 3 representative Copts) than to Yemenite Jews, Palestinians or Samaritans, though there is a difference.


Would it be possible to model some sudanese/nubian samples, while including coptic reference pops to see how well the model fits?

I'll see what can be done with the new Nubian and Sudani Arab samples we have, Bejas should be intriguing as well.


I hate to sound like a total noob, but I just want to be clear - in those runs the SSA groups in column two are the target pops, the groups in columns three and four are the test pops? Leb Christian and AJ are the column fours, so if there's a positive stat that means the SSA groups have more drift with them over the column threes?

If there's a positive stat, it means there's been gene flow from the group in the second column (ignoring the "result" column) into the group in the 4th column and anything above positive 3 is pretty significant.

nee4speed111
01-19-2018, 07:30 PM
It looks like dinka admixture is the biggest difference between modern copts and 3drif26.

Umer
01-19-2018, 08:56 PM
How much Subsaharan African do the Copt Egytpians have?

nee4speed111
01-20-2018, 01:00 AM
How much Subsaharan African do the Copt Egytpians have?

10-15%, although tbh the ssa admixture has never seemed particularly consistent, with it varying quite a bit depending on the sample pop's tested.

Umer
01-20-2018, 01:35 AM
What populations south of the Sahara match the Copts' Subsaharan African?

nee4speed111
01-20-2018, 01:42 AM
What populations south of the Sahara match the Copts' Subsaharan African?

Some sort of ancestral nilotic population I believe, without the current west/central african admixture in present day nilotic populations.

Umer
01-20-2018, 05:04 AM
What about modern ones?

nee4speed111
01-21-2018, 06:59 PM
What about modern ones?

Not sure what you mean, which modern ones?

Awale
01-21-2018, 07:24 PM
It looks like dinka admixture is the biggest difference between modern copts and 3drif26.

Yeah, he mostly looks like a slightly less East-African Copt to me. Although, nMonte sometimes has trouble spotting SSA in populations that have substantive Basal-Eurasian ancestry when you're modeling them with ancients like Natufians, Levant_Ns and so on. It can't even register the mild East-African in Samaritans and the notable amount in Yemenite Jews (usually 10-15% like Copts) so it might, for whatever weird reason possibly relating to Basal Eurasian, not be registering as much with this guy but it can definitely tell he's part Dinka-like which sets him apart from the Levantines and Yemeni group and looks much more like something you'd see with a North-African.


What populations south of the Sahara match the Copts' Subsaharan African?


Some sort of ancestral nilotic population I believe, without the current west/central african admixture in present day nilotic populations.

Basically a population that doesn't exist anymore and they were probably from around the eastern and central areas of the Sahel, in my humble opinion. Modern groups like Dinkas and Anuaks are pretty close but they have notable West-African related admixture which is missing in groups and individuals like Somalis, Mota, Copts etc. So, we all look to have ancestry from whatever Dinkas' ancestors were like before the West-African elements began being incurred, however long ago that was.

nee4speed111
01-21-2018, 07:41 PM
Yeah, he mostly looks like a slightly less East-African Copt to me. Although, nMonte sometimes has trouble spotting SSA in populations that have substantive Basal-Eurasian ancestry when you're modeling them with ancients like Natufians, Levant_Ns and so on. It can't even register the mild East-African in Samaritans and the notable amount in Yemenite Jews (usually 10-15% like Copts) so it might, for whatever weird reason possibly relating to Basal Eurasian, not be registering as much with this guy but it can definitely tell he's part Dinka-like which sets him apart from the Levantines and Yemeni group and looks much more like something you'd see with a North-African.





Basically a population that doesn't exist anymore and they were probably from around the eastern and central areas of the Sahel, in my humble opinion. Modern groups like Dinkas and Anuaks are pretty close but they have notable West-African related admixture which is missing in groups and individuals like Somalis, Mota, Copts etc. So, we all look to have ancestry from whatever Dinkas' ancestors were like before the West-African elements began being incurred, however long ago that was.

Yeah, the nmonte model of copts also seems to understate the amount of SSA we have, we are closer to 15% than 6%, its something that seems to occur when a population has lots of natufian related admixture I believe, which seems to absorb some of the east african admix.

nee4speed111
01-21-2018, 08:07 PM
Well, I'm finally free from my exams and about a month ago I tried running him and some modern groups through nMonte:


Model 1 based on:

Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Levant_N,0.0099333,0.0326333,-0.0052667,0.0503667,0.0047667,0.0396,-0.0398333,0.0021,-0.0131,0.0038333
Iran_ChL,0.01224,0.02376,-0.0045,0.02978,0.0133,-0.04126,-0.01008,0.0048,0.02584,0.00164
Iran_N,0.00645,0.0141,-0.0066333,0.0267,0.0158833,-0.09005,0.0025333,0.00365,0.0293167,-0.0009667
CHG,0.01255,0.0206,-0.0027,0.0061,0.01215,-0.0631,0.01045,0.00565,0.05515,-0.00175
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Barcin_N,0.0163053,0.0352053,-0.0025368,0.0242368,0.0039474,0.0469684,-0.0141105,-0.0004632,-0.0013684,0.005
Boncuklu_N,0.014375,0.03175,-0.003025,0.011675,0.003525,0.044425,-0.00485,0.001725,0.00105,0.006875
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
WHG,0.01775,0.0183,6e-04,-0.08685,-0.0187,0.0627,0.0655,-0.0048,-0.0487,-0.0038

Results:

distance%=0.3662 / distance=0.003662

England_Roman_outlier

Levant_N 47.55
Iran_ChL 18.95
Natufian 14.95
Tepecik_Ciftlik_N 8.05
Iran_N 7.75
Dinka 2.75

--

distance%=0.3305 / distance=0.003305

Samaritan

Tepecik_Ciftlik_N 33.9
Levant_N 33.4
Iran_ChL 20.7
Iran_N 12.1

--

distance%=0.2922 / distance=0.002922

Palestinian

Natufian 36.15
CHG 31.15
Tepecik_Ciftlik_N 26.25
Iran_N 3.35
Dinka 2.75
Levant_N 0.35

--

distance%=0.8847 / distance=0.008847

Yemenite_Jew

Natufian 49.5
Iran_ChL 40.4
Levant_N 10.1

--

distance%=0.6126 / distance=0.006126

Egyptian_Copt

Levant_N 49.10
Iran_N 16.75
Natufian 15.15
Tepecik_Ciftlik_N 12.05
Dinka 6.95

____________________________________

Model 2 based on:

Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Iran_ChL,0.01224,0.02376,-0.0045,0.02978,0.0133,-0.04126,-0.01008,0.0048,0.02584,0.00164
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
WHG,0.01775,0.0183,6e-04,-0.08685,-0.0187,0.0627,0.0655,-0.0048,-0.0487,-0.0038

Results:

distance%=0.4195 / distance=0.004195

England_Roman_outlier

Natufian 43.5
Iran_ChL 30.9
Tepecik_Ciftlik_N 24.4
Dinka 1.3

--

distance%=0.4077 / distance=0.004077

Palestinian

Iran_ChL 42.55
Tepecik_Ciftlik_N 36.60
Natufian 15.70
Dinka 5.15

--

distance%=0.372 / distance=0.00372

Samaritan

Tepecik_Ciftlik_N 41.3
Iran_ChL 39.4
Natufian 19.3

--

distance%=0.9066 / distance=0.009066

Yemenite_Jew

Natufian 57.6
Iran_ChL 41.8
Tepecik_Ciftlik_N 0.6

--

distance%=0.6463 / distance=0.006463

Egyptian_Copt

Natufian 44.2
Iran_ChL 26.4
Tepecik_Ciftlik_N 23.3
Dinka 6.1

_____________________________________

Model 3 based on:

Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Iran_N,0.00645,0.0141,-0.0066333,0.0267,0.0158833,-0.09005,0.0025333,0.00365,0.0293167,-0.0009667
CHG,0.01255,0.0206,-0.0027,0.0061,0.01215,-0.0631,0.01045,0.00565,0.05515,-0.00175
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
WHG,0.01775,0.0183,6e-04,-0.08685,-0.0187,0.0627,0.0655,-0.0048,-0.0487,-0.0038

Results:

distance%=0.4953 / distance=0.004953

England_Roman_outlier

Natufian 51.55
Tepecik_Ciftlik_N 26.40
CHG 12.30
Iran_N 9.75

--

distance%=0.2922 / distance=0.002922

Palestinian

Natufian 36.2
CHG 30.9
Tepecik_Ciftlik_N 26.6
Iran_N 3.5
Dinka 2.7

--

distance%=0.5371 / distance=0.005371

Samaritan

Tepecik_Ciftlik_N 50.40
Natufian 23.95
Iran_N 17.20
CHG 8.45

--

distance%=1.0221 / distance=0.010221

Yemenite_Jew

Natufian 70.00
CHG 23.95
Iran_N 6.05

--

distance%=0.6608 / distance=0.006608

Egyptian_Copt

Natufian 49.55
Tepecik_Ciftlik_N 27.40
Iran_N 10.70
CHG 7.55
Dinka 4.80

The Roman sample seems to have possibly been an Egyptian. He consistently looks more similar to Egyptian Copts (average of 3 representative Copts) than to Yemenite Jews, Palestinians or Samaritans, though there is a difference.



I'll see what can be done with the new Nubian and Sudani Arab samples we have, Bejas should be intriguing as well.



If there's a positive stat, it means there's been gene flow from the group in the second column (ignoring the "result" column) into the group in the 4th column and anything above positive 3 is pretty significant.

Also, do you think copts are more genetically similar to samaritans or yemenite jews?

pegasus
01-23-2018, 01:07 AM
Can you model with KEB and Neolithic Africans now? I would expect the fits to improve. Though I think fits will improve much more for Berber related populations.

Sapporo
01-23-2018, 09:13 PM
@Awale

Do you have any coastal North African samples such as Riffians/Kabyle/Tunisians you can run through nnmonte with slightly modified populations to compare to Egyptian Copts? I want to see the differences in European versus Near Eastern like admixture as well as the difference in West African versus East African like contributions that North African components on admixture calculators tend to incorporate.

nee4speed111
02-18-2018, 09:00 AM
Well, I'm finally free from my exams and about a month ago I tried running him and some modern groups through nMonte:


Model 1 based on:

Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Levant_N,0.0099333,0.0326333,-0.0052667,0.0503667,0.0047667,0.0396,-0.0398333,0.0021,-0.0131,0.0038333
Iran_ChL,0.01224,0.02376,-0.0045,0.02978,0.0133,-0.04126,-0.01008,0.0048,0.02584,0.00164
Iran_N,0.00645,0.0141,-0.0066333,0.0267,0.0158833,-0.09005,0.0025333,0.00365,0.0293167,-0.0009667
CHG,0.01255,0.0206,-0.0027,0.0061,0.01215,-0.0631,0.01045,0.00565,0.05515,-0.00175
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Barcin_N,0.0163053,0.0352053,-0.0025368,0.0242368,0.0039474,0.0469684,-0.0141105,-0.0004632,-0.0013684,0.005
Boncuklu_N,0.014375,0.03175,-0.003025,0.011675,0.003525,0.044425,-0.00485,0.001725,0.00105,0.006875
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
WHG,0.01775,0.0183,6e-04,-0.08685,-0.0187,0.0627,0.0655,-0.0048,-0.0487,-0.0038

Results:

distance%=0.3662 / distance=0.003662

England_Roman_outlier

Levant_N 47.55
Iran_ChL 18.95
Natufian 14.95
Tepecik_Ciftlik_N 8.05
Iran_N 7.75
Dinka 2.75

--

distance%=0.3305 / distance=0.003305

Samaritan

Tepecik_Ciftlik_N 33.9
Levant_N 33.4
Iran_ChL 20.7
Iran_N 12.1

--

distance%=0.2922 / distance=0.002922

Palestinian

Natufian 36.15
CHG 31.15
Tepecik_Ciftlik_N 26.25
Iran_N 3.35
Dinka 2.75
Levant_N 0.35

--

distance%=0.8847 / distance=0.008847

Yemenite_Jew

Natufian 49.5
Iran_ChL 40.4
Levant_N 10.1

--

distance%=0.6126 / distance=0.006126

Egyptian_Copt

Levant_N 49.10
Iran_N 16.75
Natufian 15.15
Tepecik_Ciftlik_N 12.05
Dinka 6.95

____________________________________

Model 2 based on:

Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Iran_ChL,0.01224,0.02376,-0.0045,0.02978,0.0133,-0.04126,-0.01008,0.0048,0.02584,0.00164
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
WHG,0.01775,0.0183,6e-04,-0.08685,-0.0187,0.0627,0.0655,-0.0048,-0.0487,-0.0038

Results:

distance%=0.4195 / distance=0.004195

England_Roman_outlier

Natufian 43.5
Iran_ChL 30.9
Tepecik_Ciftlik_N 24.4
Dinka 1.3

--

distance%=0.4077 / distance=0.004077

Palestinian

Iran_ChL 42.55
Tepecik_Ciftlik_N 36.60
Natufian 15.70
Dinka 5.15

--

distance%=0.372 / distance=0.00372

Samaritan

Tepecik_Ciftlik_N 41.3
Iran_ChL 39.4
Natufian 19.3

--

distance%=0.9066 / distance=0.009066

Yemenite_Jew

Natufian 57.6
Iran_ChL 41.8
Tepecik_Ciftlik_N 0.6

--

distance%=0.6463 / distance=0.006463

Egyptian_Copt

Natufian 44.2
Iran_ChL 26.4
Tepecik_Ciftlik_N 23.3
Dinka 6.1

_____________________________________

Model 3 based on:

Natufian,0.00305,0.0273,-0.0063,0.05895,0.00265,0.04,-0.05225,0.00175,-0.0328,-0.00015
Iran_N,0.00645,0.0141,-0.0066333,0.0267,0.0158833,-0.09005,0.0025333,0.00365,0.0293167,-0.0009667
CHG,0.01255,0.0206,-0.0027,0.0061,0.01215,-0.0631,0.01045,0.00565,0.05515,-0.00175
Dinka,-0.1001857,0.0044286,0.0039143,0.0139571,-0.0233,-0.0034286,-0.0071429,0.0022143,-0.0291429,-0.0331143
Tepecik_Ciftlik_N,0.013925,0.034,-0.00205,0.028625,0.0048,0.030825,-0.017475,0.00095,0.004975,0.003875
WHG,0.01775,0.0183,6e-04,-0.08685,-0.0187,0.0627,0.0655,-0.0048,-0.0487,-0.0038

Results:

distance%=0.4953 / distance=0.004953

England_Roman_outlier

Natufian 51.55
Tepecik_Ciftlik_N 26.40
CHG 12.30
Iran_N 9.75

--

distance%=0.2922 / distance=0.002922

Palestinian

Natufian 36.2
CHG 30.9
Tepecik_Ciftlik_N 26.6
Iran_N 3.5
Dinka 2.7

--

distance%=0.5371 / distance=0.005371

Samaritan

Tepecik_Ciftlik_N 50.40
Natufian 23.95
Iran_N 17.20
CHG 8.45

--

distance%=1.0221 / distance=0.010221

Yemenite_Jew

Natufian 70.00
CHG 23.95
Iran_N 6.05

--

distance%=0.6608 / distance=0.006608

Egyptian_Copt

Natufian 49.55
Tepecik_Ciftlik_N 27.40
Iran_N 10.70
CHG 7.55
Dinka 4.80

The Roman sample seems to have possibly been an Egyptian. He consistently looks more similar to Egyptian Copts (average of 3 representative Copts) than to Yemenite Jews, Palestinians or Samaritans, though there is a difference.



I'll see what can be done with the new Nubian and Sudani Arab samples we have, Bejas should be intriguing as well.



If there's a positive stat, it means there's been gene flow from the group in the second column (ignoring the "result" column) into the group in the 4th column and anything above positive 3 is pretty significant.

Well, on the question of 3Drif-26's Egyptian affinities, I got Lukas to model some copts on his K36 oracles based on ancients, to see what ancient populations copts could be modeled as.

First copt (This is actually a composite of around ~50 or so copts Eurogenes K36 results)


Amerindian -
Arabian 18.37
Armenian 2.94
Basque -
Central_African -
Central_Euro -
East_African -
East_Asian -
East_Balkan -
East_Central_Asian -
East_Central_Euro -
East_Med 22.85
Eastern_Euro -
Fennoscandian -
French -
Iberian -
Indo-Chinese -
Italian 2.72
Malayan -
Near_Eastern 26.84
North_African 7.15
North_Atlantic -
North_Caucasian -
North_Sea -
Northeast_African 15.17
Oceanian -
Omotic -
Pygmy -
Siberian -
South_Asian -
South_Central_Asian -
South_Chinese -
Volga-Ural -
West_African -
West_Caucasian -
West_Med 3.74

Bronze to Iron age samples, nMonte3


First person



[1] "1. CLOSEST SINGLE ITEM DISTANCE%"
IA_Levant-Egypt_Gladiator_3DRIF26 BA_Sydon
11.04718 17.43005
Egyptian_mumy_I_JK2888_ Egyptian_mummy_III_jk2911_
17.98873 18.98169
EBA_Jordan__I1730 BA_Levant_I0867
21.37956 23.72306
EBA_Jordan__I1705 Egyptian_mummy_II_JK2134_
24.46102 26.78722


[1] "distance%=10.7415"

IA_Levant-Egypt_Gladiator_3DRIF26, 87.4
Egyptian_mumy_I_JK2888_, 10.4
Amerindian_Kennewick,0.4
BA_Afanasievo_RISE509,0.2
BA_Karasuk_RISE492,0.2
BA_Levant_I0867,0.2
BA_Unetice__Germany_I0116,0.2
BA_Unetice_LNBA_Czech_RISE586,0.2
IA_AltaI_RISE601,0.2
IA_EastKazachstan_Ze6,0.2
Lapita_Vanuatu_Il_370,0.2
LBA_Denmark_RISE276,0.2


without Levant gladiator


[1] "1. CLOSEST SINGLE ITEM DISTANCE%"
BA_Sydon Egyptian_mumy_I_JK2888_
17.43005 17.98873
Egyptian_mummy_III_jk2911_ EBA_Jordan__I1730
18.98169 21.37956
BA_Levant_I0867 EBA_Jordan__I1705
23.72306 24.46102
Egyptian_mummy_II_JK2134_ Late_Medieval_Iran_I1955
26.78722 38.27475



[1] "distance%=14.6749"

Egyptian_mumy_I_JK2888_,39.4
BA_Sydon,28.6
EBA_Jordan__I1730,12.8
Egyptian_mummy_III_jk2911_,11.4
EBA_Jordan__I1705,3.2
LBA_Armenia_RISE396,0.6
IA_EastKazachstan_Is2,0.4
MBA_Armenia_RISE423,0.4
Mesolithic_East-Asian_MOS_5_Devil's_Gate,0.4
Aborigine_Australia,0.2
Ameridnian_Chachapoya,0.2
Amerindian_Mikmaq_MARC1492,0.2
BA_Afanasievo_RISE507,0.2
BA_Andronovo_ISE512_outlier,0.2
BA_Andronovo_RISE500,0.2
BA_Srubnaya_I0232,0.2
BA_Srubnaya_I0234,0.2
BA_Srubnaya_I0235,0.2
EIA_F38_Iran,0.2
IA_Altai_RISE600,0.2
IA_Britain_York_6DRIF23,0.2
IA_Pazyryk_Be9_I05622,0.2
Lapita_Vanuatu_Il_370,0.2

Second copt (This was a random copt selected from my samples)


Amerindian -
Arabian 18.64
Armenian 3.48
Basque -
Central_African -
Central_Euro -
East_African -
East_Asian -
East_Balkan -
East_Central_Asian -
East_Central_Euro -
East_Med 20.94
Eastern_Euro -
Fennoscandian -
French -
Iberian -
Indo-Chinese -
Italian -
Malayan -
Near_Eastern 25.2
North_African 11.64
North_Atlantic -
North_Caucasian -
North_Sea -
Northeast_African 13.96
Oceanian -
Omotic -
Pygmy -
Siberian -
South_Asian -
South_Central_Asian -
South_Chinese -
Volga-Ural -
West_African -
West_Caucasian -
West_Med 6.09

Second person



[1] "1. CLOSEST SINGLE ITEM DISTANCE%"
IA_Levant-Egypt_Gladiator_3DRIF26 Egyptian_mumy_I_JK2888_
12.62219 16.03487
Egyptian_mummy_III_jk2911_ BA_Sydon
18.29927 19.91044
BA_Levant_I0867 EBA_Jordan__I1730
21.30817 23.34229
Egyptian_mummy_II_JK2134_ EBA_Jordan__I1705
24.08830 26.43327




[1] "distance%=11.3144"

IA_Levant-Egypt_Gladiator_3DRIF26, 69
Egyptian_mumy_I_JK2888_, 26.4
BA_Levant_I0867,1.6
Egyptian_mummy_II_JK2134_,0.8
Ameridnian_Chachapoya,0.2
Amerindian_Mikmaq_MARC1492,0.2
BA_Afanasievo_511,0.2
BA_Andronovo_RISE503,0.2
BA_Srubnaya_I0232,0.2
BA_Unetice_Poland_RISE150,0.2
IA_Britain_York_6DRIF21,0.2
IA_EastKazachstan_Is2,0.2
IA_Wielbark_Kow_22_PL,0.2
Lapita_Vanuatu_Il_369,0.2
LBA_Afontova_Gora_RISE554,0.2


without Levant gladiator


[1] "1. CLOSEST SINGLE ITEM DISTANCE%"
Egyptian_mumy_I_JK2888_ Egyptian_mummy_III_jk2911_
16.03487 18.29927
BA_Sydon BA_Levant_I0867
19.91044 21.30817
EBA_Jordan__I1730 Egyptian_mummy_II_JK2134_
23.34229 24.08830
EBA_Jordan__I1705 Late_Medieval_Iran_I1955
26.43327 38.57505


[1] "distance%=14.194"

nfs

Egyptian_mumy_I_JK2888_,56.2
Egyptian_mummy_III_jk2911_,25.4
EBA_Jordan__I1730,4.8
BA_Sydon,4.2
EBA_Jordan__I1705,2.6
Late_Medieval_Iran_I1955,1
Egyptian_mummy_II_JK2134_,0.8
EBA_Anatolia_Kum4,0.6
EIA_F38_Iran,0.6
Lapita_Vanuatu_Il_369,0.4
Amerindian_Kennewick,0.2
Amerindian_Pericues,0.2
BA_Afanasievo_511,0.2
BA_Afanasievo_RISE510,0.2
BA_Okunevo_RISE516,0.2
BA_Srubnaya_I0234,0.2
BA_Unetice_Poland_RISE109,0.2
EBA_Armenia_I1658,0.2
EBA_Poland_N17,0.2
HG_Ethiopia_Mota1,0.2
IA_Altai_RISE600,0.2
IA_Kytmanovo_RISE504,0.2
IA_Pazyryk_Be11_I0563,0.2
IA_Pazyryk_Be9_I05622,0.2
IA_Wielbark_Kow_45_PL,0.2
MBA_Armenia_RISE413,0.2
MBA_Armenia_RISE423,0.2[/QUOTE]

So it looks pretty clear cut to me, that 3drif-26 was of Egyptian origins, these results plus his isotope analysis which put his likely birth place as the Delta, seem to indicate pretty strongly that he was an ethnic Egyptian.

The Saite
02-04-2019, 07:30 PM
Guys can u provide me with any info about the ancient egyptian samples kit numbs in ged match ?
I found some but they are probably outdated

nee4speed111
02-10-2019, 09:56 PM
Guys can u provide me with any info about the ancient egyptian samples kit numbs in ged match ?
I found some but they are probably outdated

I think they all have been removed from Gedmatch.

Mingle
02-13-2019, 04:28 PM
I'm not sure if this has already been discussed, but do they have significant Peninsular Arab ancestry? Any estimates on how much?