Somali & Horner Genetic Models

[Shimbiris]

Feel like we should have a thread for sharing genetic models for Somalis and other Horners like other Cushites, Ethiosemites, Omotics and even Horner Nilotes and the minority Bantus in Koonfur.

I'll start by sharing this model:

Made it using PCA positions from the Global25 PCA from Eurogenes. A very pristine, 25 dimensional PCA (Principal Component Analysis / genetic cluster) based on hundreds of thousands of autosomal SNPs that has proven very informative for creating ancestry composition models for populations, provided you know what you're doing and understand the limitations. The results often come very close to formal stat data (like qpAdm) from peer-reviewed papers and the author of Eurogenes, David Wesolowski, has been running all these genomics tools for like a decade and consistently rubs shoulders with academics from institutions like HarvardMed who comment on the results posted on his blog from time to time so the saaxiib knows what he's doing:

Getting the most out of the Global25

The first thing you need to know about the Global25 is that I update the relevant datasheets regularly, usually every few weeks, but they'r...

eurogenes.blogspot.com

@Apollo The model I ran is basically close to what I think we'll see once we have "pure" early Cushite samples that lack Mota-related (Horn Hunter-Gatherer) ancestry. These Kenyan-Pastoral-Neolithic samples have a lot of Horn to Southeast African HG ancestry with its substantial San/Southern HG type admixture so they eat up the "Mota" scores of all Horners except for the Oromos and Wolaytas who have the most:

Hmm, but I'm still surprised by these lower numbers. I've been out of the modeling game for a while since I lacked a laptop for months and had personal issues (long story) but I'll see if I can't get higher numbers. Anyway, point is I think the general gist of the Horn Cushites and Ethiosemites' genetic story will turn out:

• Neolithic Cushites enter the Horn around 3000 BCE bringing with them cattle, goat, sheep, donkey and dog domestication, grain-collecting, pottery, bows & arrows, stelae, dolmens, burial mounds, rock-carvings and rock-paintings while being mix between proto-Nilotes and Neolithic Egyptians. More the latter than the former probably like the "Ethio-Somali" component at a 60:40 to 70:30 ratio. This is the bulk of all Cushites and Ethiosemites' ancestry (~60-70%+).
• Varying degrees of admixing with local Horn HGs similar to the Mota Hunter-Gatherer from Southwest Ethiopia occur. Anything from 1-20% ancestry depending on the Cushitic and Ethiosemitic group.
• Ancient Yemenis hit the scene around 1000 BCE and after bringing with them metallurgy, writing, monumental architecture, camel domestication, asiatic admixture into other local livestock, Proto-Ethiosemitic (PES) and about 10-30% of the ancestry in most Cushites and Ethiosemites overtime as Horners have internal migrations and spread this admixture across the region from northern Eritrea and Ethiopia.

The only wildcard is this weird "Nilo-Saharan" stuff that keeps showing up like above and in old studies like Hodgson et al. 2014 that exists outside of the Kenyan-Pastoral-Neolithic in the model I shared, and the old "Ethio-Somali" ADMIXTURE components:

Spoiler

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I've seen people theorize that maybe it's something real and there was a real early Nilotic related migration into the Horn probably between 0 CE and 3000 BCE given that Horners lack West-African ancestry but I doubt it. We'll see, I guess.

Anyway, guys, feel free to share your own models when you get the hang of it and models from loads of other tools like formal stats (qpAdm) or even Gedmatch and old admix calculators if you feel they're relevant. Go ham!

 

[Shimbiris]

Is there any internal diversity within the canfar? Pretty surprising their profile looks like identical to northern Abyssinians.

I'm not 100% sure these samples are even Canfars. They originally clearly mislabeled what were supposed to be Xamtanga speaking Agaws as "Afars" which made good sense. But when I spoke to Pagani via email he seemed to think the mislabeling in their paper's supplementary info was the other way around and removed the info saying they were Agaws. I was perplexed after that. But the thing is, walaal, Afars' Y-DNA weirdly correlates with these autosomal results:



They have about as much J1 as Xabashis if not more. In fact, their Y-DNA profile looks very Northern Highlander with their elevated E-V6 being their only unique trait which is probably the early Afars' equivalent to our E-V32 and Sahos' E-V22 (those saaxiibs are about as fixed for V22 as reer Dir are for T1a; like 90%+ keep turning up V22, last I checked)

I also think I saw some new Canfar samples from another study and they looked like these samples so I'm starting to think these are just Canfars and there was just some misunderstanding with the Pagani paper's supplementary information years ago claiming they were Agaws.

 

[Karaboga]

Somalis seem to always have the largest genetic distance of the HOA groups.

 

[tariq moses]

I think Natufian + Taforalt works a little bit better, I may be wrong doe, but I recall Taforalt making the fit better for the Pastoral Neolithic genomes.

 

[Karaboga]

Alright here is my model. I've noticed that the typical model (Dinka, Natufian, Yemeni, Taforalt) doesn't fit well with Cushitic samples and produces results with very high genetic distances.

I'm not an expert but there's definitely something in the more Cushitic samples that's unaccounted for.

 

[tariq moses]

Alright here is my model. I've noticed that the typical model (Dinka, Natufian, Yemeni, Taforalt) doesn't fit well with Cushitic samples and produces results with very high genetic distances.

View attachment 212967
I'm not an expert but there's definitely something in the more Cushitic samples that's unaccounted for.

Natufian+Taforalt largely represent native Egyptian ancestry IMO

Natufians and Taforalt both have a common paternal ancestor represented by their E3b lineages, in the case of the Natufians it was E1b1b1b2 and the Neolithic Levantines also had some E3b.
In the case of Taforalt, it's E-M78, both of those lineages are native to Egypt but E3b came from the Horn of Africa. So we know Taforalt and the Natufians were both affected by a paleolithic Egyptian population.

We also see cultural ties between these people, such as the removal of incisors which was practised by the Taforalt culture and some of the Natufians, we also see some burial customs where they would bury their dead in a prone and elongated position. This has been found in Egypt 24,000 years ago, and Sudan 13,000 years ago. The removal of incisors was also practised by these 13,000 year old Sudanese remains.

"Nearly 70 graves (at Al-Khiday) belong to a pre-Mesolithic phase, showing an unusal ritual of body deposition. The individual was buried in a prone and elongated position, a rare ritual only attested to in Africa at Wadi Kubbaniya [Egypt] and Jebel Moya [Sudan], as well as in the Near East at several Natufian sites and in Europe at Dolni Vestonice [24,000 BC]. ... in contrast the Neolithic burials are all in a flexed contracted position."

"Tooth avulsion was observed in the majority of the 94 pre-Mesolithic Al Khiday individuals, involving the maxillary central incisors."

It was also practised recently by the Beja people in the 9th century
The second kingdom of the Beja is that of Baqlīn, which has many towns and is very large. Their religion is similar to that of the Magians and the Dualists; they call the Almighty God by the name "az-zabhīr" and the devil by the name "sahāy harāqa". They pull out the hair of their chin and remove their central incisors.


So we have cultural ties between the Natufians, Taforalt and paleolithic Egypt/Sudan, and a genetic tie, as we see with the common Y-dna ancestor which points to the direction of Egypt. (Recall E-M78 and other E3b lineages in the Middle East and Taforalt)

There is a physical study on the al khiday remains which represent a native egyptian population which contributed to the middle east,

"Al Khiday Late Palaeolithic (AKH) is close to Hierakonpolis C-Group (MMD=0.04), Al Khiday Neolithic (0.01), Neolithic Ghaba (0.06), Kerma Ancien/Moyen (0.02), Kerma Classique (0.01), and Napatan Tombos (0.04); these distances do not differ significantly (Supplementary Table S6). Of all samples, Late Palaeolithic Al Khiday is farthest from Final Neolithic Gebel Ramlah (MMD=0.19), Meroitic (0.17), and Gebel Sahaba (0.17)."

This is very important because it shows paleolithic Egyptians were already clustering with strongly "Eurasian" related Lower Nubians, Kermans were said to have a "caucasoid" morphology and they cluster very close to early ancient Upper Egyptians, so that means paleolithic Egyptians cluster close to early Upper Egypt/Lower Nubia, which is were the Cushitic/Pastoral Neolithic component comes from.


So I think paleolithic Egyptians were partly ancestral to the Natufians and Taforalt, and because we don't have their dna, the best models will be "Natufian + Taforalt" once we get their DNA, they will be modelled as being natufian + taforalt, but it will be quickly realised thats its the other way around, buts thats just what it will look like on the surface.

 

[Genie]

this stuff is so fascinating where can i go if i want to build a foundation for learning it?

 

[tariq moses]

The fact that Kenyan pastoralists show Yemeni ancestry which they obviously don't have is likely an indication that its compansating for a lack of Neolithic/Chalcolithic samples...
Yemeni ancestry in the Horn may be overestimated and may drop a little when a Neolithic Levantine/Chalcolithic Israeli sample is included, I could be wrong doe.

 

[tariq moses]

this stuff is so fascinating where can i go if i want to build a foundation for learning it?

I think getting your DNA tested is a good start, 23andme is pretty good for this, having your DNA analysis infront of you will push you to learn about your haplogroups, autosomal ancestry etc... in an organic manner and you'll naturally learn about these things pretty quick, you could buy some population genetics books if you want, it's not what i did but it should help.

 

[Genie]

I think getting your DNA tested is a good start, 23andme is pretty good for this, having your DNA analysis infront of you will push you to learn about your haplogroups, autosomal ancestry etc... in an organic manner and you'll naturally learn about these things pretty quick, you could buy some population genetics books if you want, it's not what i did but it should help.

I'm far too suspicious of those DNA companies can't lie , but might have to bite the bullet and just do it .

 

[Mutombo]

Here are my results.

 

[Shimbiris]

Here are my results.

@Sophisticate

I found you a prospective suitor, walaashay. 100% Somali like you like them. I hope his qabiil, career prospects and temperament pan out too.

 

[Sophisticate]

@Sophisticate

I found you a prospective suitor, walaashay. 100% Somali like you like them. I hope his qabiil, career prospects and temperament pan out too.

I don't consider someone a prospect unless I know their details and gauge their mind. To the rest, it's...

 

[Som]

I'm not 100% sure these samples are even Canfars. They originally clearly mislabeled what were supposed to be Xamtanga speaking Agaws as "Afars" which made good sense. But when I spoke to Pagani via email he seemed to think the mislabeling in their paper's supplementary info was the other way around and removed the info saying they were Agaws. I was perplexed after that. But the thing is, walaal, Afars' Y-DNA weirdly correlates with these autosomal results:



They have about as much J1 as Xabashis if not more. In fact, their Y-DNA profile looks very Northern Highlander with their elevated E-V6 being their only unique trait which is probably the early Afars' equivalent to our E-V32 and Sahos' E-V22 (those saaxiibs are about as fixed for V22 as reer Dir are for T1a; like 90%+ keep turning up V22, last I checked)

I also think I saw some new Canfar samples from another study and they looked like these samples so I'm starting to think these are just Canfars and there was just some misunderstanding with the Pagani paper's supplementary information years ago claiming they were Agaws.

Tbh though Canfars look almost identical to somalis, I'm surprised they are so close to habeshas.

 

[Shimbiris]

Tbh though Canfars look almost identical to somalis, I'm surprised they are so close to habeshas.

There maybe some diversity with them. I suspect, based on what people often say about Jabuutian Canfars and what I've seen with my own eyes, that Jabuutian Canfars probably look very Somaloid genetically. These samples are likely more representative of the Eritrean and some of the Ethiopian ones.

 

[tariq moses]

There maybe some diversity with them. I suspect, based on what people often say about Jabuutian Canfars and what I've seen with my own eyes, that Jabuutian Canfars probably look very Somaloid genetically. These samples are likely more representative of the Eritrean and some of the Ethiopian ones.

Eritrean/Ethiopian Afars look very Somali aswell, its not just the Djibouti Afars, i think its mainly due to the Danakil being a similar enviroment to Somalia. I think Djibouti Afars will be mostly the same as Eritrean/Ethiopian Afars just slightly Somali shifted, Afar clans were said to be fluid and sometimes included Issa Somalis so who knows tbh.

 

[Shimbiris]

Eritrean/Ethiopian Afars look very Somali aswell, its not just the Djibouti Afars, i think its mainly due to the Danakil being a similar enviroment to Somalia. I think Djibouti Afars will be mostly the same as Eritrean/Ethiopian Afars just slightly Somali shifted, Afar clans were said to be fluid and sometimes included Issa Somalis so who knows tbh.

To be honest, I dunno. I did see some folks in Jabuuti who gave me pause but Afars overall do look distinct to me. There's a lot of Somali looking people then some do actually give me Highland Ethiopian vibes and others just look... unique. I've noticed they're often shorter than Somalis too. But this is all subjective. Let's not derail the thread down a phenotype tangent.

 

[wheel]

My Puntdnal k12 modern results.

Spoiler: puntdnal k7

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What was your puntdnal k7 modern result? @Shimbiris

 

[Som]

There maybe some diversity with them. I suspect, based on what people often say about Jabuutian Canfars and what I've seen with my own eyes, that Jabuutian Canfars probably look very Somaloid genetically. These samples are likely more representative of the Eritrean and some of the Ethiopian ones.

Saho and afar are almost the same, there's a community called Irob in Ethiopia which is christian and probably mixed with habeshas. Irobs are basically Christian saho-afars.
I think we should be very careful about samples. Are Somali samples collected all across Somalia? What about Ethiopian samples, Amhara and Oromo is mostly a linguistic cultural identity

 

[Som]

My Puntdnal k12 modern results.

Spoiler: puntdnal k7

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What was your puntdnal k7 modern result? @Shimbiris

Interesting. The subsaharan competent is significantly lower than what it should be according to studies. If we add south African hunter gatherers + sub Saharan you get just a little bit more than 50% subsaharan African ancestry while it should be slightly above 60% according to most studies.
@Shimbiris