Any info on haplogroup L4b2a2?

[Ayen224]

Beyond what 23AndMe says lol. But everything I’ve found does suggest that it originated in the Kenya/Tanzania region. Unless I’m misunderstanding. Also, 23AndMe mentions Ethiopia, would that likely be among both the Nilotic and Omotic people of Ethiopia? I imagine it should be both or either.

 

[Ayen224]

Nvm I’ve gotten something lol

 

[The alchemist]

@Ayen224

I think the L4 mtDNA is Ancestral East African related as Cushites carry it, it exists in the Nile Valley with modern Egyptian individuals, other Saharan peoples included, not to forget other Sudanese.

The relationship between L4a Cushites and L4b as well is tough. I think it is safe to say that L4 is evidence that Ancestral East Africans were several groups at some point that were probably genetically high in the AEA component.

I think Hadza and Zandawe got it from northeast Africans. Hadza seems to have it gotten from Cushitic expansion:

We observe very little HVRI/HVRII nucleotide diversity within the L4g haplogroup in the Hadza sample, consistent with previous studies of this population (fig. 5d; Vigilant et al. 1991; Knight et al. 2003). The “star-like” pattern of variation in the Hadza (with identical HVRI/HVRII haplotypes in 36 of 46 individuals) is consistent with an expansion of this subhaplogroup ∼4 kya.

I am open to correction but it seems that what they did here was merely compute how far back the Hadza and Sandawe lineages meet. We have Cushites in L4 that coalesced deeper. I think this was purely brought from Cushitics, not something that spread from Southeastern Africa and northward, at least, for these particular ones. I'm not talking about the ultimate origin some 90-80ky but how these lineages arrived and from where they expanded -- the consistent thing is the Cushtic mediation.

Our sample of the Sandawe also reveals a high frequency of L4g but with somewhat greater HVRI/HVRII nucleotide variation than in the Hadza. The most common Sandawe and Hadza L4g lineages differ by 3 mutations (fig. 5d), and the estimated TMRCA for this lineage in these populations is 24.5 kya (95% CI of 11.2–47.6 kya). The Hadza and Datog share several L4g haplotypes (after removal of hypervariable sites); the Sandawe, Turu, and Burunge share other L4g haplotypes

Examining the populations listed to have carried diversity within the broader lineage cluster, all are either Cushitic mixed or straight-up South Cushites. That list includes, Datog, Turu, and Burunge. Hadza, and Sandawe we already know have Cushitic admixture. If we check the evidence on YFull, what appears is a very concordant system. Southern African populations from South Africa appear on the tree out of an ancient Cushitic mixture with the hunter-gatherers that migrated southward.

 

[Ayen224]

@Ayen224

I think the L4 mtDNA is Ancestral East African related as Cushites carry it, it exists in the Nile Valley with modern Egyptian individuals, other Saharan peoples included, not to forget other Sudanese.

The relationship between L4a Cushites and L4b as well is tough. I think it is safe to say that L4 is evidence that Ancestral East Africans were several groups at some point that were probably genetically high in the AEA component.

I think Hadza and Zandawe got it from northeast Africans. Hadza seems to have it gotten from Cushitic expansion:

We observe very little HVRI/HVRII nucleotide diversity within the L4g haplogroup in the Hadza sample, consistent with previous studies of this population (fig. 5d; Vigilant et al. 1991; Knight et al. 2003). The “star-like” pattern of variation in the Hadza (with identical HVRI/HVRII haplotypes in 36 of 46 individuals) is consistent with an expansion of this subhaplogroup ∼4 kya.

I am open to correction but it seems that what they did here was merely compute how far back the Hadza and Sandawe lineages meet. We have Cushites in L4 that coalesced deeper. I think this was purely brought from Cushitics, not something that spread from Southeastern Africa and northward, at least, for these particular ones. I'm not talking about the ultimate origin some 90-80ky but how these lineages arrived and from where they expanded -- the consistent thing is the Cushtic mediation.

Our sample of the Sandawe also reveals a high frequency of L4g but with somewhat greater HVRI/HVRII nucleotide variation than in the Hadza. The most common Sandawe and Hadza L4g lineages differ by 3 mutations (fig. 5d), and the estimated TMRCA for this lineage in these populations is 24.5 kya (95% CI of 11.2–47.6 kya). The Hadza and Datog share several L4g haplotypes (after removal of hypervariable sites); the Sandawe, Turu, and Burunge share other L4g haplotypes

Examining the populations listed to have carried diversity within the broader lineage cluster, all are either Cushitic mixed or straight-up South Cushites. That list includes, Datog, Turu, and Burunge. Hadza, and Sandawe we already know have Cushitic admixture. If we check the evidence on YFull, what appears is a very concordant system. Southern African populations from South Africa appear on the tree out of an ancient Cushitic mixture with the hunter-gatherers that migrated southward.

Wow, thanks so much. This was beyond helpful. I really couldn’t find much about it at all. Most of what I found was pretty much saying that it was restricted to East and Northeast Africa, sparingly in the Near East, […] Ethiopia, […] Hadza and Sandawe.

But great, this helps a ton. So I’m gathering that L4 is one of the earliest haplogroups in East Africa and maybe the whole continent then? Also because of this schematic tree I saw. It seems it predates the L3 that populated the rest of the world by a good maybe 15 thousand years? If I guessed correctly.

Also do you have any ideas on why L4b2 seems to be so overwhelmingly present in the Hadza and Sandawe in particular? I think I read in the 43-58% range, if I read the attachment correctly. Do you think that alone could point to it having derived from a group ancestral to them? Could they be the reason it’s present in those other groups at lower frequencies?

Please correct me if I’m misunderstanding anything lol, which I’m sure I am. I’m just now learning about all this so I really have no real idea what I’m talking about lmao. I’m just throwing out probably really surface level ideas.

 

[Ayen224]

You know what, maybe the fact that there’s only about 1,300 Hazda members today skews the data somehow. Maybe there was more diversity long ago when they were larger in number, if they were larger in number. Otherwise yeah, I’m not exactly sure what the implications would be but surely their small number affects the data somehow?

 

[Garaad Awal]

It’s a really old haplogroup (20k yrs old) that probably originated somewhere on the Eastern regions of Africa (Eastern Sahel,Nile Valley, Horn etc).

You would need to deep test to find out which subclade you belong too

 

[Ayen224]

It’s a really old haplogroup (20k yrs old) that probably originated somewhere on the Eastern regions of Africa (Eastern Sahel,Nile Valley, Horn etc).

You would need to deep test to find out which subclade you belong too

Oh, does it go even further than that?
I figured mine just ends at L4b2a2.
L4 > L4b > L4b2 > L4b2a2

But cool, I wasn’t aware it can go farther.

Also, these lengths of times are outrageous. I can’t even imagine what people were up to 20k years ago lmao. Do you know if this haplogroup predates the ethnogenesis of the major groups that exist in East Africa today?

 

[The alchemist]

Wow, thanks so much. This was beyond helpful. I really couldn’t find much about it at all. Most of what I found was pretty much saying that it was restricted to East and Northeast Africa, sparingly in the Near East, […] Ethiopia, […] Hadza and Sandawe.

But great, this helps a ton. So I’m gathering that L4 is one of the earliest haplogroups in East Africa and maybe the whole continent then? Also because of this schematic tree I saw. It seems it predates the L3 that populated the rest of the world by a good maybe 15 thousand years? If I guessed correctly.

Also do you have any ideas on why L4b2 seems to be so overwhelmingly present in the Hadza and Sandawe in particular? I think I read in the 43-58% range, if I read the attachment correctly. Do you think that alone could point to it having derived from a group ancestral to them? Could they be the reason it’s present in those other groups at lower frequencies?

Please correct me if I’m misunderstanding anything lol, which I’m sure I am. I’m just now learning about all this so I really have no real idea what I’m talking about lmao. I’m just throwing out probably really surface level ideas.

It came to those groups in southeast Africa through Cushitic contact. It is in West Africa through Sudanic groups unrelated to the Cushitic expansion toward southeast Africa. Both of those events happened within the food-producing age. And we can probably assume it was somewhere in the Nile Valley region up to over 25 kya. Beyond that, probably, a broader region. The L4 and L3 go back to the same co-HG parent mutation. I think it is safe to assume L4 is from the Sudan region given that L3 was northeast Africa and is where non-African mtDNA diversity shot out, placing it somewhere aforementioned close to a place with southwest Asian access.

The frequency of it does not mean much to be honest, as one observes with those Hadza and Sandawe since they were small groups that can drive up frequencies quickly. A haplogroup could have origins in a place where it has 0% frequency today while having 90% in a place it was introduced 1000 years ago. All that makes sense is depth and frequency distribution related to people and geography -- my assessment is that it is from northeast Africa and I mean where Ancestral East Africa is from somewhere in the broader Nile Valley region/Eastern Sudanic belt, Eastern Sahara, etc.

 

[Ayen224]

It came to those groups in southeast Africa through Cushitic contact. It is in West Africa through Sudanic groups unrelated to the Cushitic expansion toward southeast Africa. Both of those events happened within the food-producing age. And we can probably assume it was somewhere in the Nile Valley region up to over 25 kya. Beyond that, probably, a broader region. The L4 and L3 go back to the same co-HG parent mutation. I think it is safe to assume L4 is from the Sudan region given that L3 was northeast Africa and is where non-African mtDNA diversity shot out, placing it somewhere aforementioned close to a place with southwest Asian access.

The frequency of it does not mean much to be honest, as one observes with those Hadza and Sandawe since they were small groups that can drive up frequencies quickly. A haplogroup could have origins in a place where it has 0% frequency today while having 90% in a place it was introduced 1000 years ago. All that makes sense is depth and frequency distribution related to people and geography -- my assessment is that it is from northeast Africa and I mean where Ancestral East Africa is from somewhere in the broader Nile Valley region/Eastern Sudanic belt, Eastern Sahara, etc.

That was super informative, thank you. I assume then that my maternal line has Eastern Nilotic origins somewhere along the way, since according to that first attachment, all presence in Western Nilotic speakers can be attributed to that. Which is understandable given there’s plenty of them around us where we are, in both countries. I found a few other people with my same exact subgroup on random message boards. Think two were Kalenjin, the other was Rwandan. From what ethnic group I don’t know though.

I think I’m still trying to wrap my head around the implications of mtDNA and Y-DNA. As far as how they move around and are passed on to different populations and things. But cool, thanks for all that! Super informative.

 

[The alchemist]

That was super informative, thank you. I assume then that my maternal line has Eastern Nilotic origins somewhere along the way, since according to that first attachment, all presence in Western Nilotic speakers can be attributed to that. Which is understandable given there’s plenty of them around us where we are, in both countries. I found a few other people with my same exact subgroup on random message boards. Think two were Kalenjin, the other was Rwandan. From what ethnic group I don’t know though.

I think I’m still trying to wrap my head around the implications of mtDNA and Y-DNA. As far as how they move around and are passed on to different populations and things. But cool, thanks for all that! Super informative.

The clade is way older than Eastern Nilotic -- I'm not making the Nilotic association but the deeper genetic variations that would have existed in the region of which Nilotic also source ancestry. I only mean it was carried by whatever diversity existed in the region. Whether the L4 you have was introduced to the region you're from by Eastern Nilotics is a different matter.

And also, I recognize L4 is one of the Ancestral East African clades, not the one. I have to clarify since autosomal lineages and haplogroups can have strong links especially due to older events although not always.

 

[Ayen224]

The clade is way older than Eastern Nilotic -- I'm not making the Nilotic association but the deeper genetic variations that would have existed in the region of which Nilotic also source ancestry. I only mean it was carried by whatever diversity existed in the region. Whether the L4 you have was introduced to the region you're from by Eastern Nilotics is a different matter.

And also, I recognize L4 is one of the Ancestral East African clades, not the one. I have to clarify since autosomal lineages and haplogroups can have strong links especially due to older events although not always.

Ahh okay, that makes sense then. It just doesn’t seem to be all that common so there’s hardly any info on it from what I’ve seen. Think from a graph I saw, the more common one for Western Nilotes tends to be L2a and some other few I can’t remember. A distant cousin of mine on 23andMe was actually that also. Like a distant relative that some of my family know. But I think I’ve learned enough, so basically it tends to exist in pastoral communities throughout in East Africa is what I’ve gathered. And ofc the Hadza and Sandawe. Also found that my subclade (think that’s what it’s called?) is L4b2a2c… Whatever that even means tbh

But yeah, seems it existed in a couple random samples in Kenya https://haplotree.info/maps/ancient...DNA_haplogroup&searchfor=L4b2a2c&ybp=500000,0
And the TMRCA is 10k years ago or something. If I’m understanding that Y-full site correctly. Also L4b2a2 is apparently found in the Nama and Khomani San, but in low frequencies. But yeah, I wonder what that original L4 woman looked like and how they lived. Super interesting. I imagine that the global population was around that had to be insanely small as well, compared to now at least. So maybe they lived in very small communities. It’s so insane to think there were humans roaming the Earth tens of thousands of years ago lol. That is brain melting.

But in any case, thanks for all that! Super helpful as always.

 

[The alchemist]

Ahh okay, that makes sense then. It just doesn’t seem to be all that common so there’s hardly any info on it from what I’ve seen. Think from a graph I saw, the more common one for Western Nilotes tends to be L2a and some other few I can’t remember. A distant cousin of mine on 23andMe was actually that also. Like a distant relative that some of my family know. But I think I’ve learned enough, so basically it tends to exist in pastoral communities throughout in East Africa is what I’ve gathered. And ofc the Hadza and Sandawe. Also found that my subclade (think that’s what it’s called?) is L4b2a2c… Whatever that even means tbh

But yeah, seems it existed in a couple random samples in Kenya https://haplotree.info/maps/ancient...DNA_haplogroup&searchfor=L4b2a2c&ybp=500000,0
And the TMRCA is 10k years ago or something. If I’m understanding that Y-full site correctly. Also L4b2a2 is apparently found in the Nama and Khomani San, but in low frequencies. But yeah, I wonder what that original L4 woman looked like and how they lived. Super interesting. I imagine that the global population was around that had to be insanely small as well, compared to now at least. So maybe they lived in very small communities. It’s so insane to think there were humans roaming the Earth tens of thousands of years ago lol. That is brain melting.

But in any case, thanks for all that! Super helpful as always.

The L2b2a2 is way older than 20,000 years old. The L4b2a2c (how did you arrive at this subclade?) is correct to be around 10,000 years old. As I said earlier, southern African hunter-gatherers, of which the Nama and Khomani San descend had mixed with Cushites thousands of years ago. That is why they have this mtDNA which is a northeast African variation.

But as you probably noticed in YFull the L4b2a2c has an Ancestral East African spread since that clade also has a very Cushitic heavy presence. Even the Kenyan non-Cushitic ones are definitely Cushitic mediated, IMO, than Nilo Saharan. What I mean by Anecstal East African is that DNA type spread among different populations in the northeast African Nile Valley region.

The population size could vary. It was more like wide extensions of people fragmented into groups that had high contact so even how we think of populations today is not how hunter-gatherers did. Because you could have extreme migration of females from one group to another with a patrilocal system to avoid inbreeding. This was one system that one observes; that people went from one group to another with high between-group migration. Now, the people that they mixed were possibly more often than not in a given time more similar to them than distinct, but we see throughout a very long time transect there were layers of distinct genetic substructure, meaning that genetically differentiated peoples did mix at certain junctures. One of them is how the Cushitic people came about in the Nile Valley region. But the same can be said about Nilotic peoples as well. Since what we today call "pure" this or that is really a layman's terms of saying certain genetic profiles have been stable over long periods of time rather than them being forever unmixed.

I don't subscribe to the notion that Dinka-like peoples were the only types of people that existed in the region. I believe some of the samples we've seen in Kenya that resemble Cushites with more Eurasian ancestry probably were not mixed with hunter-gatherers of Kenya, at least not entirely, but likely sourced their non-Eurasian side from some old Nile Valley population that had qualities that showed both Ancestral African and Mota like qualities in ways that we probably have not captured and certainly does not exist today in the region. It is the same reason I am very skeptical of attributing any minor Mota-like property in Somalis to post horn of African admixture rather than an expression of an older process.

 

[Ayen224]

The L2b2a2 is way older than 20,000 years old. The L4b2a2c (how did you arrive at this subclade?) is correct to be around 10,000 years old. As I said earlier, southern African hunter-gatherers, of which the Nama and Khomani San descend had mixed with Cushites thousands of years ago. That is why they have this mtDNA which is a northeast African variation.

But as you probably noticed in YFull the L4b2a2c has an Ancestral East African spread since that clade also has a very Cushitic heavy presence. Even the Kenyan non-Cushitic ones are definitely Cushitic mediated, IMO, than Nilo Saharan. What I mean by Anecstal East African is that DNA type spread among different populations in the northeast African Nile Valley region.

The population size could vary. It was more like wide extensions of people fragmented into groups that had high contact so even how we think of populations today is not how hunter-gatherers did. Because you could have extreme migration of females from one group to another with a patrilocal system to avoid inbreeding. This was one system that one observes; that people went from one group to another with high between-group migration. Now, the people that they mixed were possibly more often than not in a given time more similar to them than distinct, but we see throughout a very long time transect there were layers of distinct genetic substructure, meaning that genetically differentiated peoples did mix at certain junctures. One of them is how the Cushitic people came about in the Nile Valley region. But the same can be said about Nilotic peoples as well. Since what we today call "pure" this or that is really a layman's terms of saying certain genetic profiles have been stable over long periods of time rather than them being forever unmixed.

I don't subscribe to the notion that Dinka-like peoples were the only types of people that existed in the region. I believe some of the samples we've seen in Kenya that resemble Cushites with more Eurasian ancestry probably were not mixed with hunter-gatherers of Kenya, at least not entirely, but likely sourced their non-Eurasian side from some old Nile Valley population that had qualities that showed both Ancestral African and Mota like qualities in ways that we probably have not captured and certainly does not exist today in the region. It is the same reason I am very skeptical of attributing any minor Mota-like property in Somalis to post horn of African admixture rather than an expression of an older process.

I uploaded my 23AndMe results onto Genomelink way back, and I remembered them giving me a slightly more specific haplogroup. But awesome, that pretty much sums it up, and also basically what I've found online.

And yeah, I find it hard to believe that as well, that Nilotic-type people were the only inhabitants of the Nile Valley region. Also just read up on the Bottleneck and Founder effects. Really interesting. Do you have any examples of either that are believed to have occurred within Africa?

Also, totally random, but do you know if Nilotic people are thought to have been residing in the Sahara region ever, whilst it was already a desert? I know the 'Saharan' in Nilo-Saharan is totally unrelated to us and refers to Sahelian groups instead. But yeah, just wondering. As far as if it were in fairly recent history, I imagine that would be especially unlikely considering the animals we herd today. I don't imagine cattle could survive in the complete desert lol, unlike the Sahel or something.

Also, as far as the combination of groups that made Cushitic people, I always found that pretty interesting, even kind of odd. But I think cause I was thinking of two entirely unrelated groups, in every way. Like on the level of a Dutchman and a Hamer person for example. But thinking about it again, I imagine that the group that was heavily Eurasian also had some *fairly* recent 'SSA' ancestry as well? It's weird talking about these ancient groups using modern-day terms and understandings of sociology and populations lol. Or I could be totally wrong on that. But yeah, I imagine they were at least semi-familiar with each other for some time prior to their blending and the subsequent ethnogenesis of Cushitic people. And even that blending probably happened over a prolonged period of time.
But regardless, I guess any populations of people existing in close proximity to each other for an extended period of time are bound to mingle and blend at some point, no matter how long.

 

[The alchemist]

I uploaded my 23AndMe results onto Genomelink way back, and I remembered them giving me a slightly more specific haplogroup. But awesome, that pretty much sums it up, and also basically what I've found online.

Is the feature still there on Genomelink?

And yeah, I find it hard to believe that as well, that Nilotic-type people were the only inhabitants of the Nile Valley region. Also just read up on the Bottleneck and Founder effects. Really interesting. Do you have any examples of either that are believed to have occurred within Africa?

If I understood you correctly with whether bottlenecks and founder effects ever occurred in Africa, the answer is yes, everywhere at different times. We see it in the uniparental diversity, inbreeding levels, effective population size, etc.

Also, totally random, but do you know if Nilotic people are thought to have been residing in the Sahara region ever, whilst it was already a desert? I know the 'Saharan' in Nilo-Saharan is totally unrelated to us and refers to Sahelian groups instead. But yeah, just wondering. As far as if it were in fairly recent history, I imagine that would be especially unlikely considering the animals we herd today. I don't imagine cattle could survive in the complete desert lol, unlike the Sahel or something.

This is a complex topic. I mean Sahara as in the Eastern Sahel which would be within the reach of the Nile Valley as a corridor. You had many types of refugia that existed in the entire Saharan region at different times, even in drying periods, with several (now dry) tributaries on the West of the Nile. The cattle could survive in those limited areas.

Saharans and Nilotic groups are related. But you are right, Dinka types that lack the obvious Iberomarusian-like DNA probably always stayed on the Eastern side away from the central Sahara and would have been influenced genetically as you see with the Saharan groups there by the non-Nilo-Saharan groups.

There was a mix of a complex demic and cultural diffusion of pottery that should have at least passed on some minor genetics but that does not necessarily need to be genetically hard impact.

Also, as far as the combination of groups that made Cushitic people, I always found that pretty interesting, even kind of odd. But I think cause I was thinking of two entirely unrelated groups, in every way. Like on the level of a Dutchman and a Hamer person for example. But thinking about it again, I imagine that the group that was heavily Eurasian also had some *fairly* recent 'SSA' ancestry as well? It's weird talking about these ancient groups using modern-day terms and understandings of sociology and populations lol. Or I could be totally wrong on that. But yeah, I imagine they were at least semi-familiar with each other for some time prior to their blending and the subsequent ethnogenesis of Cushitic people. And even that blending probably happened over a prolonged period of time.
But regardless, I guess any populations of people existing in close proximity to each other for an extended period of time are bound to mingle and blend at some point, no matter how long.

All the components had lived in the broader region for 20-plus millennia. I don't think those North Africans without the East African DNA had recent East African for two reasons. The East African DNA in Somalis, as an example, lacks the Green Saharan influence we see the Nilo-Saharan received. Old Kingdom leaks of an Upper Egyptian had no noteworthy East African genetics.

I scribled this together some time ago. It should give you the general gist:

It could be that those people formed some form of confederacy and proto-state, some form of terminal Paleolithic survival strategy. The reason I say this is that it was implied that things could have been hectic between the Pleistocene and Neolihitc transition, and those components in Cushitic are Paleolithic in kind not Neolithic emerging population assortments.

The Cushitic component wherever you find it is very stable as well so it had to either be a very rapid mixing to standardize that genetics, or we have to broaden the population size if one wants to lengthen the time of this geneflow interaction. You also have to push back the upper bound of the earliest mixtures beyond the accepted 8000-year time period where we think the ethnogenesis of the Cushiitc DNA profile came together. For this, one has to increase the effective population size of those types of DNA to the point where no other diversity exists wherever they live.

We have potential fossils that could serve as the genetic stand-in for this interaction found contemporaneously ~14000 years ago - hypothetically convenient, the descendants of those would be the Cushitic mixtures.

 

[Ayen224]

Ngl, I forgot my password and then wasn't receiving any of the password reset emails for a minute lol, so, sorry for responding 5000 years late.

Is the feature still there on Genomelink?

It must have been like 3am or something when I sent that last reply because it actually wasn't Genomelink, my bad. It was DNA Genics. It seems it's a paid feature, though I don't recall paying for it. But I guess I must have. It's pretty neat though. Also gives you a confidence level for the assignment, and a list of ancient samples that share that same clade.

But, if you don't want to pay for that, there is https://dna.jameslick.com/mthap/. You can upload your raw data and it'll give you a list of your 3 best haplogroup matches, along with the markers you share, any markers you don't have that are required for it to be the correct assignment, etc.

Honestly, if anyone in my family ever decides to become a criminal, and leave some DNA somewhere, it's a wrap for them

But yeah, they also gave me L4b2a2c, followed by L4b2a2 and L4b2a2a. I had no mismatched markers with L4b2a2c and L4b2a2 (of course), but I had two with L4b2a2a, so safe to say L4b2a2c is correct.

I scribled this together some time ago. It should give you the general gist:

This is so neat. I imagine it took tons of reading and corroborating information to put this together.

The Cushitic component wherever you find it is very stable as well so it had to either be a very rapid mixing to standardize that genetics, or we have to broaden the population size if one wants to lengthen the time of this geneflow interaction.

So which of these two possibilities do you find the most likely given the information you've collected over the years? I assume the general consensus is the first one? Or maybe that it's been a combination where the mixing was very rapid, but then the resulting population remained very stable and insular for a long time also. Which seems very likely, I mean I'm pretty sure Somalia is one of the most homogenous nations in the world, no?

And just know, I've read everything else you've said also. I'm just not at all knowledgeable enough to even provide any useful further commentary or questions on much of it lol. But it's all really interesting and insightful info, thank you.

And actually, I was wondering, the Ancestral East African population that both Cushitic and Nilotic groups attribute ancestry to, would they have had no West African ancestry whatsoever? I ask because of that dialogue that's gained traction recently about the supposed ghost hominin signal detected in (some?) West Africans. Even though I've also read that the study it stems from is somewhat dubious and may be full of misrepresentations. But regardless, do you know if this same DNA would have been present in this Ancestral East African population?

 

[Ayen224]

Hello @The alchemist, super long time, I know. I hope you're doing well. I was wondering if you have any new hypotheses regarding this haplogroup at all? Or any in the region whatsoever. I read a paper from 2021 about mtDNA distribution in East Africa last night, just randomly as it was recommended to me via email, and it just brought the topic to the forefront of my mind again.

 

[The alchemist]

I had to remove the quotes given that my post exceeds the limits on words, so just figure out what I am answering from the two of your posts. @Ayen224

I have mtDNA L2a1, I wrote down my long result from there on to Google and I seem to have L2a1+143, which makes sense:

I belong to any of those. Most likely in those concentrated with Somalis or northeast Africans, which would be L2a1j.

The screenshots of those samples are of one individual who was Pastoral Neolithic, and one is a hunter-gatherer individual who had clear pastoral admixture. Such evidence is outlined in Lipson et all 2022:

The other one (Jawuoyo) was a hunter-gatherer with E-V22 (Nile Valley clade), accompanying considerable Hadza-like qualities, being similar to just more southern African hunter-gatherer and central African hunter-gatherer shift. This sort of falls in line with why the mtDNA is similar to what I showed with the Cushitic-influenced foragers in past comments.

The most ancient ancestor (TMCRA) of L4b2a2c was 10,000 years ago old. This means that you were probably of an ancestral East African maternal stock if your clade split between the initial millennium like 10,000-9000, however, from then on, it is highly likely that your maternal ancestor was actually from a Cushitic population, given that what we observe in the data is dominated by northeast Africans that are Cushitic dominated.

There are two Luhya samples that are in the basal section. From my assessment, those people are not pure Bantus and usually have noticeable Cushitic substructure within aspects of their ethnic demographics, the reason why you have E-V32 popping up among them:

One would see some results here and there of various Nilo-Saharan people if it was comprehensively represented among Nilotic peoples and Saharans. So it looks like you might be of a Cushitic maternal origin. We cannot completely rule out that you could have mtDNA from the first or so thousand years before those Ancestral East African people mixed with the desert Afro Asiatics, however, seeing how the earliest samples look nothing like pure Nilo-Saharans, the most reasonable assumption is that you come from a maternal Cushitic origin.

You might wonder, well, why don't you have any Eurasian or Cushitic DNA to prove that? The answer to that is that we're talking about an ancient Cushitic introduction. It only takes a couple of generations before autosomal ancestry is burried in layers of geneflow of where the assimilation happened until it is not noticeable.

One introduction could have come through the migration of Cushites through a southern Sudanese path, and then moving in towards northwestern Kenya. That is how the pastoral neolithic came to Kenya thousands of years ago. It is possible that your Nilo-Saharan ancestors intermarried with some as they moved down.

Their movement in simplified form walked down this path and not through the Eritrean corridor that my ancestors underwent:

On Google Maps, you can actually spot the Cushitic burials peripheral towards the southern Sudanic lands:

I went and checked the map to see such ring-form burials because they were easy to spot in the northern Somali peninsula. Turns out one can say the same for northwestern Kenya. The point is, that the L4b2a2c could have been introduced through such migration. It looks to me that mtDNA was common among those Cushitics.

It looks like a Somali goes back around the time the genesis of Cushitic formed:

Some Cushites arrived in Kenya around 4200 ybp, and you see that samples from South Africa have sub-clades that go back to that common ancestor date, which is again, beneath timewise the more basal Somali sibling branch:

I think there was a complex and gradual mixing of Ancestral East Africans and proto-Cushitic speakers, and then once you had some even mix on a gradient on an upper and lower bound, there was a rapid spread of founder effects (basically family units that migrated to different parts and formed respective tribes) that established a stabilized tribal distribution. Later those tribes mixed across again stabilizing what already was similar genetically but tightening the upper and lower bound elements since the model was mobile seasonal pastoralism. This is why the Cushitic component, no matter where, is similar. But this happened in ways that confirm a paternal. Some of those very early Cushites probably went in other directions and were assimilated by overwhelmingly numerous Chadic Saharans or other Sudanics as well.

The proto-Cushitic speakers were patrilineal and mixed with Ancestral East African women, who might have been matrilineal.

Regarding the thing, Ancestral East African is a very specific term I coined to describe the Cushitic East African ancestors. But I changed it in the drawing to highlight deep lineages. In this case, when I say Ancestral East African, I only mean ANE2 since Nilo-Saharan is a respective branch that I describe as such.

In truth, I should perhaps coin it Ancient East African for the Cushitic ancestry and Ancestral East African being the common ancestral line people conflate with, being the parental lineage to the respective lineages ANE and Nilo-Sharans.

But to the question of Nilo-Saharan West African affinity, well, I think it is some Green Saharan West African hunter-gatherer DNA that probably looked more like forager with increased central African ancestry rather than modern Yoruba. But since it also probably accompanied very early divergent East African ancestry as well, the percentage of West African-like ancestry increased to somewhere between 28-30% Yoruba-like because Yorubas already contain such ancestry. ANE in Cushites lacked that ancestry which tells us it came later and that ANE and Nilo-Saharan proper divergent much earlier than we thought. But again, I think pre-Cushitic (meaning before Cushitc was a thing, before animal husbandry and farming) offshoot ANE mixed with Nilo-Saharans that did not introduce geneflow back to Cushitics after. I think the ANE of Cushites was a small isolated ban of hunter-gatherers.

Take note that some of what I say here is liable to change and also falls into speculative realms within quite rational conditions of what we know, the room for re-interpretation is wide but what I am saying is quite reasonable and not out of bounds given the conditions.

The question of the archaic ancestry in West Africans and if the West African type ancestry in Nilo-Saharans contains such ancestry. The "archaic" ancestry in West Africans contains a "Ghost" modern, really just another lineage that went extinct but was akin to perhaps Ancestral North African, East African, or the older Central and Southern African hunter-gatherer, not "archaic" in the sense of old humans. That ancestry is the large bulk. But then you did have an older lineage that seemed to be the same age as Neanderthals; that ancestry was ~2%. What people do is conflate "modern" with the very old stuff, and add the two numbers to inflate, and frame it as if it is all from the very old ancestry that has Neanderthal time-depth.

I think Ghost modern is a north African lineage relatively close or distantly related to Ancient North African.

To the question of if Nilo-Saharans got it. I think not above 1% if they do have such ancestry at all.

Sorry for not responding right away. Don't think my lack of answer is dismissive. I often take mental footnotes of things I am mentioned on to answer later for whatever reason I don't delve into the topics as I read them first. Just ask away if you feel curious. It's cool to have people who want to engage with it.

 

[Ayen224]

@The alchemist
Wow! Thanks so much for this, so much to delve into. Sorry I'm only just now replying, it's the first time I've logged into the site again since before your reply. I think some of this will take multiple readings to fully grasp, as I'm only familiar with the most absolute surface-level terminology and concepts when it comes to this field. Enjoyable and super duper helpful reading nonetheless, but I'll probably research some of these things elsewhere and then return here so I can understand them in context. I really appreciate the time and effort you've put into giving such a thorough and informative response, that is not lost on me.

And okay that makes sense, so the most likely cause of my maternal haplogroup is a Cushitic woman somewhere deeeeep down in my maternal line. Certainly nothing in living memory of course, as my mum doesn't know of my grandmother having any non-Acholi ancestry, and more importantly, anyone recent enough to have been recounted in my family's oral history would have been recent enough to have made a mark on my autosomal makeup even slightly. I hope this isn't too taxing, but if you had to assign like actual percentages (in your opinion, of course - and even just guestimating) as far as the chances of this haplogroup being introduced into my genetic makeup 'pre-Cushitic' so to speak, in the alternative possibility that you gave, verusus, being introduced from a Cushitic woman somewhere down the line, I'm curious about what your figures might be? I don't take too much of the information on 23AndMe seriously, but I suppose this might explain the negligible 6 Neanderthal variants. Although, I feel like all but 10 people on the Earth are assigned those lol, and who knows which direction some of them go as far as introgression, at least when it comes to most Africans.

Also, I'm wondering, is it likely that virtually all East Africans have trace Cushitic admixture then? I had figured basically all do except for us (Western) Nilotes, but it seems that even we may? Maybe it's just bias and I've simply just seen all the instances where it is present, but I swear it seems as though it can be (and is) found in pretty much all East African groups. I really hope more genetic research is done in the region soon enough, I'm very keen to see what other things are uncovered about the populations over time.

 

[The alchemist]

Wow! Thanks so much for this, so much to delve into. Sorry I'm only just now replying, it's the first time I've logged into the site again since before your reply. I think some of this will take multiple readings to fully grasp, as I'm only familiar with the most absolute surface-level terminology and concepts when it comes to this field. Enjoyable and super duper helpful reading nonetheless, but I'll probably research some of these things elsewhere and then return here so I can understand them in context. I really appreciate the time and effort you've put into giving such a thorough and informative response, that is not lost on me.

Thank you.

And okay that makes sense, so the most likely cause of my maternal haplogroup is a Cushitic woman somewhere deeeeep down in my maternal line. Certainly nothing in living memory of course, as my mum doesn't know of my grandmother having any non-Acholi ancestry, and more importantly, anyone recent enough to have been recounted in my family's oral history would have been recent enough to have made a mark on my autosomal makeup even slightly. I hope this isn't too taxing, but if you had to assign like actual percentages (in your opinion, of course - and even just guestimating) as far as the chances of this haplogroup being introduced into my genetic makeup 'pre-Cushitic' so to speak, in the alternative possibility that you gave, verusus, being introduced from a Cushitic woman somewhere down the line, I'm curious about what your figures might be? I don't take too much of the information on 23AndMe seriously, but I suppose this might explain the negligible 6 Neanderthal variants. Although, I feel like all but 10 people on the Earth are assigned those lol, and who knows which direction some of them go as far as introgression, at least when it comes to most Africans.

Reviewing the initial topic entry and my claims, it seems that the chance for you to descend from a Cushitc female line is close to 100%. You have a sub-structure that is related to a broader structure that is very pastoral and Sahara-related. Sometimes it might go toward some IMB-related stuff in some of the Paleolithic temporal depth. In this sense, you could have gotten this from Neolithic mixed food producers.

Also, I'm wondering, is it likely that virtually all East Africans have trace Cushitic admixture then? I had figured basically all do except for us (Western) Nilotes, but it seems that even we may? Maybe it's just bias and I've simply just seen all the instances where it is present, but I swear it seems as though it can be (and is) found in pretty much all East African groups. I really hope more genetic research is done in the region soon enough, I'm very keen to see what other things are uncovered about the populations over time.

Evidence of frequencies of admixture do exist at low values among certain groups that relate to mobility, post-Neolithic. One usually sees other markers accompany. Typically, those people are mixed in more than one way as seen with Darfurians with differential substructures. However, I would not say this is widely spread. Mostly it is limited unless they have gotten it indirectly through mixed Arabs.

 

[Ayen224]

Thank you.

Reviewing the initial topic entry and my claims, it seems that the chance for you to descend from a Cushitc female line is close to 100%. You have a sub-structure that is related to a broader structure that is very pastoral and Sahara-related. Sometimes it might go toward some IMB-related stuff in some of the Paleolithic temporal depth. In this sense, you could have gotten this from Neolithic mixed food producers.

Woah, I was so certain I replied to this like last month, no wonder I didn't get any more alerts, my bad. But thank you so much! Your knowledge is always invaluable. I know it doesn't have any stake on our lives now, far from it, but it's always so fascinating to learn about the groups we descend from and the ways they lived, etc.

Evidence of frequencies of admixture do exist at low values among certain groups that relate to mobility, post-Neolithic. One usually sees other markers accompany. Typically, those people are mixed in more than one way as seen with Darfurians with differential substructures. However, I would not say this is widely spread. Mostly it is limited unless they have gotten it indirectly through mixed Arabs.

Oh okay, that definitely comes as a shock to me then. I figured pretty much everyone in the Great Lakes region - at least Uganda, Rwanda, Kenya and Tanzania has some level of Cushitic admixture, even if very minutely, barring groups like myself who are primarily/overwhelmingly Nilotic. But that's definitely interesting. I guess maybe it's just been overrepresented to me.