I ran a qpAdm grid for my target, labeled Eurasiatic, using an AADR-based PLINK dataset plus my target sample.

The full initial grid ran 160/160 models, but none of the feasible models passed with the original right set. The best “least bad” direction was repeatedly around:

Tanzania_Swahili-oNearEast / Tanzania_Swahili / Kenya_Swahili + Egyptian / Northeast African / Levant-like sources

The strongest reduced-right result I found was:

Target: Eurasiatic
Left/source model:

• Tanzania_Swahili-oNearEast
• Egypt_AbusirelMeleq_Ptolemaic
• Georgia_Satsurblia_LateUP

Right set:

• Mbuti
• Russia_UstIshim_IUP
• Russia_Kostenki_UP
• Georgia_KotiasKlde_Mesolithic
• Iran_GanjDareh_N
• Israel_Natufian
• Papuan
• Karitiana
• Mixe

This model excludes Han and Morocco_Iberomaurusian from the earlier right set.

qpAdm result:

• p = 0.555
• chisq = 4.91
• dof = 6
• feasible = TRUE

Weights:

• Tanzania_Swahili-oNearEast = 47.1% ± 2.8%
• Egypt_AbusirelMeleq_Ptolemaic = 45.9% ± 6.5%
• Georgia_Satsurblia_LateUP = 7.0% ± 5.1%

My interpretation is that I am being modeled best as a mix of an East African / Swahili-oNearEast-like proxy, an Egyptian/Northeast-African-like proxy, and a small Caucasus/Upper-Paleolithic West-Eurasian-like correction.

I would not take the labels literally as exact ancestry percentages. These are formal qpAdm proxies, not proof that the ancestry is literally “Swahili,” “Ptolemaic Egyptian,” or “Satsurblia.” The Satsurblia-like component is also small and imprecise, so I would interpret it cautiously.

The right-set diagnostics were interesting: the model improved a lot when Han was removed, and then passed strongly when Morocco_Iberomaurusian was also removed. That suggests the original rejection was not just because of the source model, but also because the right set was exposing tension around East Asian-related and Iberomaurusian/North-African-related contrasts.

Would be interested in feedback from people who work with Horn/East African qpAdm models: does this look like a reasonable reduced-right exploratory model, or would you recommend a stricter/better right set or better Horn/Northeast African proxies?

I ran a qpAdm grid for my target, labeled Eurasiatic, using an AADR-based PLINK dataset plus my target sample.

The full initial grid ran 160/160 models, but none of the feasible models passed with the original right set. The best “least bad” direction was repeatedly around:

Tanzania_Swahili-oNearEast / Tanzania_Swahili / Kenya_Swahili + Egyptian / Northeast African / Levant-like sources

The strongest reduced-right result I found was:

Target: Eurasiatic
Left/source model:

• Tanzania_Swahili-oNearEast
• Egypt_AbusirelMeleq_Ptolemaic
• Georgia_Satsurblia_LateUP

Right set:

• Mbuti
• Russia_UstIshim_IUP
• Russia_Kostenki_UP
• Georgia_KotiasKlde_Mesolithic
• Iran_GanjDareh_N
• Israel_Natufian
• Papuan
• Karitiana
• Mixe

This model excludes Han and Morocco_Iberomaurusian from the earlier right set.

qpAdm result:

• p = 0.555
• chisq = 4.91
• dof = 6
• feasible = TRUE

Weights:

• Tanzania_Swahili-oNearEast = 47.1% ± 2.8%
• Egypt_AbusirelMeleq_Ptolemaic = 45.9% ± 6.5%
• Georgia_Satsurblia_LateUP = 7.0% ± 5.1%

My interpretation is that the target is being modeled best as a mix of an East African / Swahili-oNearEast-like proxy, an Egyptian/Northeast-African-like proxy, and a small Caucasus/Upper-Paleolithic West-Eurasian-like correction.

I would not take the labels literally as exact ancestry percentages. These are formal qpAdm proxies, not proof that the ancestry is literally “Swahili,” “Ptolemaic Egyptian,” or “Satsurblia.” The Satsurblia-like component is also small and imprecise, so I would interpret it cautiously.

The right-set diagnostics were interesting: the model improved a lot when Han was removed, and then passed strongly when Morocco_Iberomaurusian was also removed. That suggests the original rejection was not just because of the source model, but also because the right set was exposing tension around East Asian-related and Iberomaurusian/North-African-related contrasts.

Would be interested in feedback from people who work with Horn/East African qpAdm models: does this look like a reasonable reduced-right exploratory model, or would you recommend a stricter/better right set or better Horn/Northeast African proxies?

Does anyone have the Pagani 2012 Ethiopia dataset? The link appears to be dysfunctional now. Looking to download the data to improve my sampling for my Amhara side.

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool - PMC

mega.bioanth.cam.ac.uk

I wanted to share three exploratory results and get feedback from people who understand Horn African ancestry modeling, especially the behavior of Levantine / North African proxies in mixed Horn-related models.

For context, I am not treating any of this as a formal ancestry claim. I know G25 distances are not proof of descent, and my qpAdm model was formally rejected. I am mainly trying to understand why the same broad pattern keeps appearing.

My qpAdm exploratory run used public AADR references. Across several rounds, no tested model formally passed:

• Round 2: 24 tested, 0 accepted
• Round 3: 96 tested, 0 accepted
• Round 4: 64 tested, 0 accepted
• Round 5: 64 tested, 0 accepted

The least-bad cleaned model was:

CEU + Tanzania_Swahili-oNearEast + Lebanon_IA3

With approximate weights:

• CEU: 41.2% ± 9.2
• Tanzania_Swahili-oNearEast: 38.8% ± 2.6
• Lebanon_IA3: 20.0% ± 9.5

But the p-value was around:

p ≈ 4.0e-168

So this is clearly not a valid qpAdm ancestry model. I am reading Lebanon_IA3 only as a possible stand-in for some broader ancient Levantine / Red Sea / Near Eastern-related affinity that is not being captured well by the public reference set.

What makes it interesting is that my G25 “Eurasiatic_Array_Scaled” distances seem to pull in two related directions.

First, when compared to modern-ish populations, my closest results are heavily North African:

• Tunisia: Kef_Sousse — 0.0837
• Algerian: Algerian43A22 — 0.0871
• Tunisia: Tunisois — 0.0875
• Tunisia: Beja — 0.0883
• Algerian: ALG100 — 0.0893
• Tunisia: Msaken — 0.0895
• Berber_Tunisia_Sen: BerSF8 — 0.0898
• Berber_Tunisia_Sen: BerSF5 — 0.0897
• Tunisian: Tunisian20D4 — 0.0903
• Tunisian: Tunisian20F4 — 0.0926

Then, when compared to ancient samples, the closest hits include a lot of African-shifted Mediterranean, Punic, Guanche, and Islamic-period Iberian / North African-like references:

• Austria_Ovilava_Roman_oAfrica.SG:R10667.SG — 0.0992
• CanaryIslands_Guanche.SG:gun005_noUDG.SG — 0.1003
• England_Saxon_oAfrica.SG:EA503.SG — 0.1050
• Spain_NazariPeriod_LateMuslim:I8146 — 0.1052
• Punic:I24215 — 0.1080
• Punic:I1735 — 0.1118
• Punic:I24673 — 0.1128
• Italy_Imperial_oAfrica.SG:R132.SG — 0.1131
• Portugal_Miroico_LateRoman_oAfrica.SG:R10503.SG — 0.1140
• Punic:I3528 — 0.1168
• CanaryIslands_Guanche.SG:gun008_noUDG.SG — 0.1167
• Punic:I2200 — 0.1208
• CanaryIslands_Guanche.SG:gun011_noUDG.SG — 0.1209
• CanaryIslands_Guanche.SG:gun012_noUDG.SG — 0.1222
• Spain_BellBeaker_oAfrica:I4246 — 0.1240
• Punic:I2405 — 0.1235
• Spain_NazariPeriod_Muslim:I7425 — 0.1263
• Turkey_Byzantine_oAfrica:I8372 — 0.1270
• Italy_Sardinia_IA_Punic_1:VIL011 — 0.1287
• Tunisia_Punic_oAfrica2.SG:R1778.SG — 0.1289
• Punic:I24039 — 0.1299

My current interpretation is:

The qpAdm result does not prove Lebanon_IA3 ancestry, and the G25 results do not prove Punic, Guanche, Tunisian, or North African ancestry. But the repeated pattern may be showing that my “Eurasiatic” side is best approximated by a combination of Northwest European-like ancestry plus Horn/East African-like ancestry plus a Levantine / North African / Red Sea-related component.

In other words, I am wondering whether Lebanon_IA3 is simply functioning as a generic ancient Near Eastern proxy for something closer to Horn African / Red Sea admixture that is missing from the reference set.

Questions for the subreddit:

1. In Horn African qpAdm modeling, does Lebanon_IA3 often appear as a stand-in when closer ancient Ethiopian / Eritrean / Red Sea / Sudanese references are missing?
2. Do close G25 distances to Tunisian, Algerian, Punic, Guanche, and oAfrica Mediterranean samples usually indicate real North African-like affinity, or can they appear because those samples are themselves mixtures of African + Mediterranean + Levantine-like ancestry?
3. Would a better qpAdm model probably need ancient or more specific references from Ethiopia, Eritrea, Sudan/Nubia, the Red Sea corridor, or Arabia?
4. Is it reasonable to interpret this as a broad Horn/East African + West Eurasian + Levantine/North African-like proxy effect, rather than a literal Punic or Lebanese signal?

Again, I am treating this as exploratory only. I am mainly looking for methodological feedback on proxy behavior, not trying to make a literal ethnic claim from rejected qpAdm or G25 distances.

I wanted to share an exploratory result and get feedback from people who understand Horn/East African + Near Eastern proxy behavior in qpAdm and G25.

I ran an exploratory qpAdm setup using public AADR references. None of the tested models formally passed. In fact, the best cleaned model was still strongly rejected:

CEU + Tanzania_Swahili-oNearEast + Lebanon_IA3

Estimated weights:

• CEU: 41.2% ± 9.2
• Tanzania_Swahili-oNearEast: 38.8% ± 2.6
• Lebanon_IA3: 20.0% ± 9.5
• p ≈ 4.0e-168, so this is clearly not a formally accepted qpAdm model

I am not interpreting Lebanon_IA3 literally as “Lebanese ancestry.” My read is that, in this setup, Lebanon_IA3 is probably acting as a broad ancient Levantine / Near Eastern stand-in for ancestry not well captured by the available public AADR Horn/Ethiopian references. The same applies to Tanzania_Swahili-oNearEast: I am treating it as a proxy for an East African/Horn-adjacent component with some Near Eastern affinity, not as a literal Swahili ancestry claim.

What makes it interesting is that my G25 distance results for the same “Eurasiatic” side are repeatedly pulling toward North African / Punic / Guanche / Mediterranean outlier references. Some of the closest distances include:

• Austria_Ovilava_Roman_oAfrica.SG:R10667.SG — 0.0992
• CanaryIslands_Guanche.SG:gun005_noUDG.SG — 0.1003
• England_Saxon_oAfrica.SG:EA503.SG — 0.1050
• Spain_NazariPeriod_LateMuslim — 0.1052
• Punic:I24215 — 0.1080
• Punic:I1735 — 0.1118
• Punic:I24673 — 0.1128
• Italy_Imperial_oAfrica.SG:R132.SG — 0.1131
• Portugal_Miroico_LateRoman_oAfrica.SG:R10503.SG — 0.1140
• Punic:I3528 — 0.1168
• CanaryIslands_Guanche.SG:gun008_noUDG.SG — 0.1167
• Punic:I2200 — 0.1208
• CanaryIslands_Guanche.SG:gun011_noUDG.SG — 0.1209
• CanaryIslands_Guanche.SG:gun012_noUDG.SG — 0.1222
• Spain_BellBeaker_oAfrica:I4246 — 0.1240
• Punic:I2405 — 0.1235
• Spain_NazariPeriod_Muslim:I7425 — 0.1263
• Turkey_Byzantine_oAfrica:I8372 — 0.1270
• Italy_Sardinia_IA_Punic_1:VIL011 — 0.1287
• Tunisia_Punic_oAfrica2.SG:R1778.SG — 0.1289
• Punic:I24039 — 0.1299

So my current interpretation is:

The qpAdm result does not prove a literal Lebanon_IA3 source, and the Punic/Guanche G25 distances do not prove that I am Punic, Guanche, or North African. But both analyses seem to point in the same general direction: my non-Horn/non-European side may be expressing some kind of older Northeast African / Red Sea / Levantine / North African-related affinity that is not being modeled cleanly with the available public references.

I would be interested in feedback on whether this is a reasonable interpretation, or whether Lebanon_IA3 is simply acting as a generic West Eurasian / Levantine “catch-all” proxy in a rejected qpAdm model.

In particular, I am wondering:

1. In Horn African qpAdm models, how often does Lebanon_IA3 or a similar Levantine ancient proxy appear as a stand-in when closer Ethiopian/Eritrean ancient references are missing?
2. Do Punic/Guanche/North African G25 distances usually reflect real North African-like affinity, or can they simply appear because those samples themselves are mixed African + Mediterranean + Levantine-like proxies?
3. Would a better model require ancient Ethiopian/Eritrean, Sudanese/Nubian, or Red Sea references that are not available in the public AADR set?

I am treating all of this as exploratory only. I am mainly trying to understand the pattern rather than make a literal ancestry claim.

Hi everyone,

I’ve been working through an exploratory qpAdm analysis using public AADR references for my target sample, labeled Eurasiatic. My known background is broadly maternal NW European / Anglo-American and paternal Ethiopian/Horn African, likely Amhara-related.

I tested several rounds of qpAdm models:

Round 2: 2-way models
Round 3: broad 3-way models
Round 4: Horn-core 3-way models
Round 5: cleaned right-pop sensitivity test

None of the models formally passed qpAdm. Even the best valid-weight model had a very low p-value, so I’m not treating this as a formally accepted ancestry model.

The best cleaned valid-weight proxy model was:

Eurasiatic = CEU + Tanzania_Swahili-oNearEast + Lebanon_IA3

Approximate weights:

CEU: ~41.2% ± 9.2%
Tanzania_Swahili-oNearEast: ~38.8% ± 2.6%
Lebanon_IA3: ~20.0% ± 9.5%

p ≈ 4.0e-168, so formally rejected.

My interpretation is that the broad signal is still directionally meaningful:

NW European-like + Horn/East African-like + Near Eastern/Levant-like

But the public AADR set does not seem to have a close enough Ethiopian/Amhara reference to produce a proper qpAdm pass. I’m treating labels like Tanzania_Swahili-oNearEast, Kenya_Somali, Lebanon_IA3, and Turkey_N as proxies only, not literal ancestral sources.

I’d be interested in feedback from people here, especially on better public proxies or right-pop setups for modeling Ethiopian/Horn ancestry in qpAdm.

Looking to refine my Amhara populations in qpAdm. Does anyone have the dataset from https://ega-archive.org/datasets/EGAD00010001047?

Merged my FTDNA data with AADR and ran qpAdm: broad NW European + East African/Horn-like signal, but no accepted model yet.

I finally got my FTDNA autosomal raw data converted and merged with the AADR 1240K dataset, then ran ADMIXTOOLS 2 / qpAdm models against ancient and modern proxy populations.

Basic workflow:

1. Converted FTDNA raw CSV into PLINK PED/MAP, then BED/BIM/FAM.
2. Converted AADR v66 1240K EIGENSTRAT/TGENO into PLINK using PLINK2.
3. Merged my sample with AADR.
4. Fixed the .fam population labels so ADMIXTOOLS could recognize the AADR groups.
5. Extracted precomputed f2 stats with ADMIXTOOLS 2.
6. Tested qpAdm models using different combinations of European, North African, Levantine, Punic, Horn/East African, Nile Valley, Swahili, and Pastoral Neolithic proxies.

The early North African / Levantine / Punic models failed badly. They produced impossible weights like huge positive North African ancestry paired with huge negative Levantine or Roman ancestry, so I treated those as invalid.

The models became more sensible once I added northwest European proxies like English, CEU, and GBR, plus East African / Horn / Nile-related proxies like Kenya_Somali, Sudan_Kulubnarti, Tanzania_Swahili, and Kenya_PastoralN_Nderit.

The best broad signal was consistently:

Northwest European + East African / Nile-Horn / Swahili-Pastoral-like

The most useful feasible proxy models were roughly:

• English + Tanzania_Swahili-oNearEast: ~47.5% English / ~52.5% Tanzania Swahili-oNearEast
• English + Kenya_PastoralN_Nderit: ~41.4% English / ~58.6% Kenya Pastoral Neolithic Nderit
• English + Kenya_Somali: ~57.4% English / ~42.6% Kenya Somali

Important caveat: none of these were formally accepted qpAdm models. The p-values were still extremely low, so I’m treating them as exploratory proxy positions rather than final ancestry proportions.

My takeaway is that with the AADR references I had available, qpAdm could place the broad axis pretty clearly, but it could not find a clean formally accepted source model for a modern mixed individual. Better Ethiopian/Eritrean/Somali/Afar/Oromo/Tigray/Amhara references would probably improve the modeling a lot.