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Thread: Modelling Egyptian ancestry

  1. #1
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    Modelling Egyptian ancestry

    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. Thanks to another user on a different forum, here are the attempts to model both groups:

    Target: Levant_Beirut_IAIII_Egyptian
    Distance: 3.2342% / 0.03234200
    49.0 Levant_Natufian
    26.2 Anatolia_Barcin_N
    11.6 IRN_Wezmeh_N
    11.2 GEO_CHG
    1.4 Yoruba
    0.6 Sudanese
    Target: England_Roman_Near_Eastern_o
    Distance: 3.7740% / 0.03774015
    46.2 Levant_Natufian
    27.8 Anatolia_Barcin_N
    13.4 IRN_Wezmeh_N
    11.8 GEO_CHG
    0.8 Yoruba
    Target: EGY_Late_Period
    Distance: 3.3708% / 0.03370801
    53.0 Levant_Natufian
    26.4 Anatolia_Barcin_N
    10.4 IRN_Wezmeh_N
    9.6 GEO_CHG
    0.6 Sudanese
    Target: Copt5_scaled
    Distance: 3.7530% / 0.03752960
    48.2 Levant_Natufian
    26.6 Anatolia_Barcin_N
    13.0 IRN_Wezmeh_N
    6.2 GEO_CHG
    6.0 Sudanese
    Target: Egyptian:Coptic_Egyptian
    Distance: 2.9577% / 0.02957678
    49.6 Levant_Natufian
    24.2 Anatolia_Barcin_N
    14.0 IRN_Wezmeh_N
    7.0 GEO_CHG
    4.0 Sudanese
    1.2 Yoruba
    Target: Copt4_scaled
    Distance: 2.9772% / 0.02977171
    49.6 Levant_Natufian
    25.6 Anatolia_Barcin_N
    14.0 IRN_Wezmeh_N
    5.6 Sudanese
    5.2 GEO_CHG
    Target: Copt3_scaled
    Distance: 3.1947% / 0.03194723
    51.0 Levant_Natufian
    25.2 Anatolia_Barcin_N
    12.2 IRN_Wezmeh_N
    7.6 GEO_CHG
    3.8 Sudanese
    0.2 Yoruba
    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
    Target: Coptsudan_scaled
    Distance: 3.0965% / 0.03096483
    48.8 Levant_Natufian
    25.4 Anatolia_Barcin_N
    13.8 IRN_Wezmeh_N
    6.0 GEO_CHG
    6.0 Sudanese
    Target: Nee4speed111_scaled
    Distance: 4.0726% / 0.04072620
    52.0 Levant_Natufian
    24.8 Anatolia_Barcin_N
    10.6 IRN_Wezmeh_N
    8.0 GEO_CHG
    3.8 Sudanese
    0.8 Yoruba
    Target: Copt1_scaled (Potential Armenian acestry)
    Distance: 2.8835% / 0.02883488
    41.8 Levant_Natufian
    31.0 Anatolia_Barcin_N
    19.6 IRN_Wezmeh_N
    3.4 Yamnaya_UKR
    2.8 Sudanese
    1.4 Yoruba
    The fundamental difference between copts & our Egyptian samples seems to be AEA ancestry, best proxied by either Sudanese or Dinka like ancestry although this is probably an imperfect fit for this AEA component. 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, some models to display what I mean.

    Target: Egyptian_muslim_average_scaled
    Distance: 1.2448% / 0.01244809
    26.2 Levant_Beirut_IAIII_Egyptian
    25.8 EGY_Late_Period
    21.8 Lebanese_Christian
    14.8 England_Roman_Near_Eastern_o
    7.0 Sudanese
    4.4 Yoruba
    Target: COPTIC_AVERAGE
    Distance: 1.4128% / 0.01412847
    57.6 EGY_Late_Period
    32.6 England_Roman_Near_Eastern_o
    5.0 Levant_Beirut_IAIII_Egyptian
    4.8 Sudanese
    When I attempt to model an average of Copts & Egyptian muslims using both the Egyptian samples on hand along with both an extra SSA source and a levantine proxy using Lebanese christians, the copts don't need a levantine source and their ancestry can be modeled as a two way mix of Egyptian & Sudanese, whereas the Egyptian muslim average does pick up a levantine source. Attempting to model this levantine ancestry with some ancient samples produces the following results:

    With Levant_Abel_IA

    Target: Egyptian_muslim_average_scaled
    Distance: 1.4630% / 0.01463009
    31.8 Levant_Beirut_IAIII_Egyptian
    24.2 England_Roman_Near_Eastern_o
    18.0 Levant_Abel_IA
    14.8 EGY_Late_Period
    6.4 Sudanese
    4.8 Yoruba
    Target: COPTIC_AVERAGE
    Distance: 1.4128% / 0.01412847
    57.6 EGY_Late_Period
    32.6 England_Roman_Near_Eastern_o
    5.0 Levant_Beirut_IAIII_Egyptian
    4.8 Sudanese
    With Levant_Baqah_BA

    Target: Egyptian_muslim_average_scaled
    Distance: 1.5134% / 0.01513414
    35.2 Levant_Beirut_IAIII_Egyptian
    22.2 England_Roman_Near_Eastern_o
    20.2 Levant_Baqah_BA
    11.0 EGY_Late_Period
    6.8 Sudanese
    4.6 Yoruba
    Target: COPTIC_AVERAGE
    Distance: 1.4128% / 0.01412847
    57.6 EGY_Late_Period
    32.6 England_Roman_Near_Eastern_o
    5.0 Levant_Beirut_IAIII_Egyptian
    4.8 Sudanese
    With Levant_Beirut_ERoman

    Target: Egyptian_muslim_average_scaled
    Distance: 1.3490% / 0.01349006
    35.0 Levant_Beirut_IAIII_Egyptian
    20.2 Levant_Beirut_ERoman
    17.4 EGY_Late_Period
    16.2 England_Roman_Near_Eastern_o
    6.8 Sudanese
    4.4 Yoruba
    Target: COPTIC_AVERAGE
    Distance: 1.4128% / 0.01412847
    57.6 EGY_Late_Period
    32.6 England_Roman_Near_Eastern_o
    5.0 Levant_Beirut_IAIII_Egyptian
    4.8 Sudanese
    With Levant_Sidon_MBA

    Target: Egyptian_muslim_average_scaled
    Distance: 1.4367% / 0.01436744
    28.6 Levant_Beirut_IAIII_Egyptian
    23.8 Levant_Sidon_MBA
    19.0 England_Roman_Near_Eastern_o
    17.2 EGY_Late_Period
    7.0 Sudanese
    4.4 Yoruba
    Target: COPTIC_AVERAGE
    Distance: 1.4128% / 0.01412847
    57.6 EGY_Late_Period
    32.6 England_Roman_Near_Eastern_o
    5.0 Levant_Beirut_IAIII_Egyptian
    4.8 Sudanese
    As the results seem to show, while both Copts & Muslims are both majority descendant of these Ancient Egyptian samples, it seems that once you account for the excess SSA ancestry (which in Copts at least is either due to the facts Copts are ancestrally descendant from Upper Egypt or actual Nubian Christian ancestry), there is a levantine pull in Egyptian muslims as they seem to consistently require a Levantine source for a portion of their ancestry in all the models.
    Last edited by nee4speed111; 01-15-2022 at 10:51 AM.

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  3. #2
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    Here I attempt to discern the source of the excess SSA ancestry in modern Egyptians, thanks to the Kulubnarti samples we seem to have a good proxy for much of the excess in SSA in both Copts & muslims, I will run the same pop's but include Kulubnarti as one of the source populations:

    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 Lebanese Christian sample, it seems that Copts still don't pick up any levantine ancestry but all of their SSA is absorbed by the Kulubnarti samples & the fits improve, the Egyptian muslims also have their AEA like ancestry absorbed but their is still a West African signal along with an increase in Levantine ancestry compared to before.

    Using the ancient samples:

    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
    Interestingly enough, 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 AEA ancestry whereas the model consistently absorbs all of the AEA in Copts through the Nubian Christian proxy, perhaps a reflection of a slight AEA pull in modern Lebanese Christians that doesn't show up in direct admixture results & that the ancient Levantines did not have?

    Also interesting is that in 3 out of the 4 ancient models, Copts show a very slight levantine pull, around ~1% of their ancestry, which also seems to correspond to the Muslim Egyptian results as their levantine ancestry increases by around 2-5%.

    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 AEA 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.
    Last edited by nee4speed111; 01-15-2022 at 11:18 AM.

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    Interesting stuff! Are there any Lower Egyptian Copts (without recent Upper Egyptian ancestry) to compare with? I believe most of the academic Egyptian Muslim samples are from Lower Egypt.

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  7. #4
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    Quote Originally Posted by Lank View Post
    Interesting stuff! Are there any Lower Egyptian Copts (without recent Upper Egyptian ancestry) to compare with? I believe most of the academic Egyptian Muslim samples are from Lower Egypt.
    I believe the Copt3 sample above was born in Alexandria, however the thing you have to realize with Copts is that due to historical events (revolts etc), almost all modern day Copts have ancestral origins in Middle-Upper Egypt from Beni Suef to Sohag. Around 1800 there were virtually no Christians living in the Delta, with the Christian communities in Cairo and Alexandria being very small. Major pockets in Middle Egypt, however, had remained isolated until 1800 and Christians there formed a substantial size of the population and, in several places, even constituted the majority.

    To put it another way, when Napolean invades Egypt in 1798, the french conduct a survey of Egypt to determine the population size & while their estimates should be taken with a grain of salt, there was supposedly only around 10,000 Copts in Cairo at the time & even fewer in Alexandria, its only during the days of Muhammad Ali and his successors many Upper Egyptians, including Christians, were encouraged to work in the Delta.

    Christians in the Delta repeatedly tell stories explaining that their forefathers came from Upper Egypt but came to the Delta and the Suez Canal region for economic opportunities in the 19th and first half of the 20th century; for example cotton production around Al-Zaqāzīq and building the Suez Canal for many Christians living in Ismailia. It was suggested practically no Christians lived in the Delta, with the exception of Alexandria, prior to Khedive Muhammad Ali.

    I believe this also explains the very high levels of genetic homogeneity Copts display, as from Alexandria all the way to Khartoum in Sudan Copts are essentially the same genetically, with only little variation.
    Last edited by nee4speed111; 01-15-2022 at 11:49 AM.

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    Are you sure England_Roman_Near_Eastern_o wasn't a Nabataean?

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    Thanks to another user for pointing out that there may also be a Northwest African Berber like signature in some Modern Egyptian samples, as they seem to have Taforalt ancestry that cannot be explained as a 3 way model of AE, Levantine & SSA, so to investigate I will run the exact same source populations but will also add Canary_Islands_Guanche ancient samples.

    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 he was correct, 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'm not 100% sure what to make of this, but it does seem to strongly imply that there was a very complex admixture process in Egypt over the past millennia.

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    Quote Originally Posted by Seabass View Post
    Are you sure England_Roman_Near_Eastern_o wasn't a Nabataean?
    Almost certain, he displays a East African signal that none of his contemporary levantine ancient populations do, he is significantly Natufian enriched compared to any Roman Era sample, he clusters with our current Egyptian samples, he has a Taforalt signal unlike any levantine population & the actual study that the sampled was sourced from does a Sr and O isotope analysis in the supplementary material and they state the following on his likely geographic origins

    Turning to the Levant, citing amongst others study of rainfall in the Upper Jordan Valleyestimated an upper limit of only *4.5 ‰ for most of the Levantine coast, with values reducing further, east of the Levantine coastal plain, suggesting none of these regions would provide a place of origin for 3DRIF*26.
    Similarly, who conducted a survey of water δ18O data in modern day Israel and Jordan reported valuesabove *3‰ only for individual coastal aquifers in the south, with the majority of values in the region well below *4‰

    The mean value for 87Sr/86Sr in Theban limestones and Nile sediments is reported to be 0.70777 59,95, a value identical to that of 3DRIF*26
    The best fit for3DRIF*26’s carbon and nitrogen isotope data are therefore currently human populations from the Lower Nile Valley in Egypt, possibly also from Nubia, although a greater C4 component in diet of most individuals and relatively low δ15N in human groups that best fit the time*frame 13 makes the latter appear less likely
    Last edited by nee4speed111; 01-16-2022 at 12:37 AM.

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    Quote Originally Posted by nee4speed111 View Post
    Thanks to another user for pointing out that there may also be a Northwest African Berber like signature in some Modern Egyptian samples, as they seem to have Taforalt ancestry that cannot be explained as a 3 way model of AE, Levantine & SSA, so to investigate I will run the exact same source populations but will also add Canary_Islands_Guanche ancient samples.

    Using the Lebanese Christian sample





    It does seem like he was correct, 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





    With Levant_Baqah_BA





    With Levant_Beirut_ERoman





    With 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'm not 100% sure what to make of this, but it does seem to strongly imply that there was a very complex admixture process in Egypt over the past millennia.
    I would be careful when using the Guanche samples to model the Egyptians' excess Taforalt, they seem to have picked up something more Eastern (likely via something similar to the Chalcolithic North African samples) which could be causing the extra affinity.


    Code:
    Target: Canary_Islands_Guanche:gun012
    Distance: 1.9507% / 0.01950698 | ADC: 0.25x RC
    33.6	ITA_Sardinia_Punic
    25.4	MAR_Taforalt
    20.8	Sudan_MA_Kulubnarti
    18.8	MAR_LN
    1.4	Iberia_Southeast_c.10-16CE
    
    Target: Canary_Islands_Guanche:gun011
    Distance: 1.9045% / 0.01904518 | ADC: 0.25x RC
    39.0	ITA_Rome_Imperial
    24.0	MAR_Taforalt
    19.2	Iberia_Southeast_c.10-16CE
    11.0	ITA_Sardinia_Punic
    6.8	Sudan_MA_Kulubnarti
    
    Target: Canary_Islands_Guanche:gun008
    Distance: 1.9849% / 0.01984869 | ADC: 0.25x RC
    33.6	Iberia_Southeast_c.10-16CE
    23.4	MAR_Taforalt
    23.0	TUR_Catalhoyuk_N_Ceramic
    13.8	ITA_Sardinia_Punic
    3.8	Sudan_MA_Kulubnarti
    2.4	BWA_Taukome_1100BP
    
    Target: Canary_Islands_Guanche:gun005
    Distance: 2.6938% / 0.02693764 | ADC: 0.25x RC
    36.8	Iberia_Southeast_c.10-16CE
    25.0	MAR_LN
    13.8	MAR_Taforalt
    8.6	BGR_Bacho_Kiro_MUP
    8.6	ITA_Sardinia_Punic
    7.2	Sudan_MA_Kulubnarti
    
    Target: Canary_Islands_Guanche:gun002
    Distance: 2.8150% / 0.02815031 | ADC: 0.25x RC
    38.4	ITA_Sardinia_Punic
    24.8	ITA_Rome_Imperial
    14.0	MAR_Taforalt
    9.2	MAR_EN
    7.2	MAR_LN
    4.8	COG_Kindoki_230BP
    1.6	Sudan_MA_Kulubnarti

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  17. #9
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    Quote Originally Posted by Mnemonics View Post
    I would be careful when using the Guanche samples to model the Egyptians' excess Taforalt, they seem to have picked up something more Eastern (likely via something similar to the Chalcolithic North African samples) which could be causing the extra affinity.


    Code:
    Target: Canary_Islands_Guanche:gun012
    Distance: 1.9507% / 0.01950698 | ADC: 0.25x RC
    33.6	ITA_Sardinia_Punic
    25.4	MAR_Taforalt
    20.8	Sudan_MA_Kulubnarti
    18.8	MAR_LN
    1.4	Iberia_Southeast_c.10-16CE
    
    Target: Canary_Islands_Guanche:gun011
    Distance: 1.9045% / 0.01904518 | ADC: 0.25x RC
    39.0	ITA_Rome_Imperial
    24.0	MAR_Taforalt
    19.2	Iberia_Southeast_c.10-16CE
    11.0	ITA_Sardinia_Punic
    6.8	Sudan_MA_Kulubnarti
    
    Target: Canary_Islands_Guanche:gun008
    Distance: 1.9849% / 0.01984869 | ADC: 0.25x RC
    33.6	Iberia_Southeast_c.10-16CE
    23.4	MAR_Taforalt
    23.0	TUR_Catalhoyuk_N_Ceramic
    13.8	ITA_Sardinia_Punic
    3.8	Sudan_MA_Kulubnarti
    2.4	BWA_Taukome_1100BP
    
    Target: Canary_Islands_Guanche:gun005
    Distance: 2.6938% / 0.02693764 | ADC: 0.25x RC
    36.8	Iberia_Southeast_c.10-16CE
    25.0	MAR_LN
    13.8	MAR_Taforalt
    8.6	BGR_Bacho_Kiro_MUP
    8.6	ITA_Sardinia_Punic
    7.2	Sudan_MA_Kulubnarti
    
    Target: Canary_Islands_Guanche:gun002
    Distance: 2.8150% / 0.02815031 | ADC: 0.25x RC
    38.4	ITA_Sardinia_Punic
    24.8	ITA_Rome_Imperial
    14.0	MAR_Taforalt
    9.2	MAR_EN
    7.2	MAR_LN
    4.8	COG_Kindoki_230BP
    1.6	Sudan_MA_Kulubnarti
    I see, then it could be a case of overfitting. What source population do you think should be used to test for excess Taforalt ancestry in Egyptians?

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  19. #10
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    I would try including an EEF source, Taforalt, Kindoki and a Steppe source to try to determine if its actually excess modern Northwest African type ancestry or more of the pristinely excess Taforalt type stuff you find in Kulubnarti_MA and the Ancient Egyptians.

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