(03-24-2024, 02:01 AM)Megalophias Wrote: Thanks TanTin, that is helpful. Does seem like ANA has a bit of West African affinity, but doesn't tell us what causes this.
f4(Chimp, South_Africa_1900BP; Israel_Natufian, Morocco_Iberomaurusian) would be good, to replicate the findings in the previous paper.
Do you have the ancient Malawi foragers (Hora and Fingira)? If you do then f4(Malawi, South_Africa_1900BP; Israel_Natufian, Morocco_Iberomaurusian) and f4(Chimp, Malawi; Israel_Natufian, Morocco_Iberomaurusian) would be nice.
If I understand it correctly, we can run these tests:
f4(Chimp, TEST ; Israel_Natufian, Morocco_Iberomaurusian)
Or we can run also:
f4( South_Africa_1900BP , TEST; Israel_Natufian, Morocco_Iberomaurusian)
f4( Malawi , TEST; Israel_Natufian, Morocco_Iberomaurusian)
Where TEST will be all the other groups that I will include for the test .
If we run only the first (3), that is not very informative, because we need to compare these F-stats for all other groups.
03-24-2024, 04:46 AM (This post was last modified: 03-24-2024, 04:50 AM by Megalophias.)
Huh, this is hard to interpret.
With Mota and most of the Malawi samples it is not significant (though positive leaning), so it could be that Natufian and Iberomaurusian form a clade relative to them. That would fit if ANA is basically on the Out-of-Africa branch, and did not contribute to early East/Southeast Africans. This goes against the idea of ANA coming from East Africa originally. Iberomaurusians would have to be considerably more Basal Eurasian than Natufians in that case, because all Eurasians have strongly positive scores.
The West Africans have negative scores, which is consistent either with gene flow from North Africa to West Africa, or shared ancestry between West Africans and ANA. They do share haplogroup E1b1 in a post-Out-of-Africa time frame, but then so does Mota.
With Chimp as outgroup South African 1900BP is significantly closer to Taforalt than to Natufian, which goes against the idea of ANA being on the Out-of-Africa branch, and suggests it does have actual Sub-Saharan affinity. Unless the Neanderthal in Natufians is enough to turn this stat significant?
If Malawi Hora is actually significantly closer to Natufian though (and it's not the contamination or something)? The heck would that mean? Some East-West divide that transcends the Sahara?
(03-24-2024, 04:46 AM)Megalophias Wrote: Huh, this is hard to interpret.
With Mota and most of the Malawi samples it is not significant (though positive leaning), so it could be that Natufian and Iberomaurusian form a clade relative to them. That would fit if ANA is basically on the Out-of-Africa branch, and did not contribute to early East/Southeast Africans. This goes against the idea of ANA coming from East Africa originally. Iberomaurusians would have to be considerably more Basal Eurasian than Natufians in that case, because all Eurasians have strongly positive scores.
The West Africans have negative scores, which is consistent either with gene flow from North Africa to West Africa, or shared ancestry between West Africans and ANA. They do share haplogroup E1b1 in a post-Out-of-Africa time frame, but then so does Mota.
With Chimp as outgroup South African 1900BP is significantly closer to Taforalt than to Natufian, which goes against the idea of ANA being on the Out-of-Africa branch, and suggests it does have actual Sub-Saharan affinity. Unless the Neanderthal in Natufians is enough to turn this stat significant?
If Malawi Hora is actually significantly closer to Natufian though (and it's not the contamination or something)? The heck would that mean? Some East-West divide that transcends the Sahara?
Yes, it is something like what you describe.
There is a new or better to say Unknown population in NorthAfrica, which contributed a lot for all Africa (South and East) and Europe as well. I call this new group Basal-mixed. In general they seems to mix with Neanderthal and from them we get the most of the Neanderthal components , for all the world. As the name suggest - they are Basal, mixed with some Neanderthals.
I am not sure what is the exact definition for ANA. For my Basal-Mixed I was able to isolate them and I am doing all kind of F4 and PCA tests with them. One of their branches is going to Caucasus, as I have a very good representative of this group there. I guess that all hg DE originated from this Basal-Mixed group.
03-24-2024, 05:36 AM (This post was last modified: 03-24-2024, 05:37 AM by Desdonas.)
If all y-hg DE (rather than CF) originated from the Basal-mixed group, then D1-M174 in some East Eurasian populations may be only a y-hg movement, leaving the autosomal influence very small and we can regard Jomon and Hoabinhian totally on the ENA meta branch?
Also, until now, all IUP specimens in North Eurasia belong to y-hg C, K2 and F2, lacking D, G, IJ, K1 and H. I guess that G, K1 and H2 do leave significant autosomal influence in Near Eastern populations, which is the Basal Eurasian effect.
03-24-2024, 06:03 AM (This post was last modified: 03-24-2024, 06:22 AM by TanTin.)
(03-24-2024, 05:36 AM)Desdonas Wrote: If all y-hg DE (rather than CF) originated from the Basal-mixed group, then D1-M174 in some East Eurasian populations may be only a y-hg movement, leaving the autosomal influence very small and we can regard Jomon and Hoabinhian totally on the ENA meta branch?
Also, until now, all IUP specimens in North Eurasia belong to y-hg C, K2 and F2, lacking D, G, IJ, K1 and H. I guess that G, K1 and H2 do leave significant autosomal influence in Near Eastern populations, which is the Basal Eurasian effect.
Yes, this is a very good comment.
There were some processes of interaction between all these 3 groups:
Africans, Basal and Basal-Mixed.
The Pure Basal (hg CF) or similar were the first to spread and they went very far.
You may be surprised, but we have their traces in America... We have them in Taiwan and in North-East Asia.
So the Arabian peninsula was such zone for huge admixture. But because of some climate changes and instability, these populations came from somewhere, mix, then they had to go somewhere else or disappear. From Arabian peninsula we may track some migrations in all directions: Middle East, Europe, Central Asia, Iran, India and Australia.
I guess at some time: there was a combination of some population that included both C and D hg .
Another direction where we see such migration is Caucasus and CHG.
It was also a puzzle how IUP people migrated from Europe and Balkans to China. But if we consider some initial location on Arabian Peninsula and then migration in all directions, then the picture for this OOA become more logical.
(03-19-2024, 10:19 AM)Norfern-Ostrobothnian Wrote: An actual "African" genotype doesn't actually exist, the grouping is entirely geographical and paraphyletic in regards to Eurasians. South Sudanese Nilo-Saharans without any additional admixture from West Asia are more related to Eurasians than they are to West Africans, and both are more related to Eurasians than either are to Central African Hunter-Gatherers or South Africans. Eurasians are not the first split among human clades on a Middle Paleolithic scale in regards to Homo Sapiens, they are one of the last ones of the big clades to be still extant. Arguably there's also the internal North and South divide of South Africans but according to some models that also predated Eurasian East African split. So by definition Ancient North African is African but also not since the term doesn't actually refer to any single monophyletic clade. Now if they had any West or East African ancestry or contributed to them that's a different question, but even so at some point there has to have been a clade more related to Eurasians than to East or West Africans that became the bulk of the ancestry in Ancient North African and subsequently the non-Anatolian part of Iberomaurusian and partially Natufian.
I have some doubts about the phylogenetic position of ANA. Especially E1b1b is deeply nested in the diversity of E2, E1a, and E1b1a. In this situation, could the following three situations be considered?
1. ANA is a mixture of an East/West African related lineage and an unknown para-Eurasian lineage.
2. Some ANA-related populations contributed to East/West Africans.
3. Some lineages like A00 indicates a more ancient layer in West Africans.
An alternative view that makes room for complexity is that ANA was largely composed of a population that split off from the West and East African lineages in the very early days, and then stayed in North Africa. There the population mixed minorly with some North African basal groups probably descendants of the Jebel Irhoud successors, Aterian, whatever existed there that was very drifted. Later you had a proto-Basal OOA population coming back to Africa and going into North Africa mixing with the population aforementioned. These people were likely very African-like since this was the early days but shared OOA drift where it took an intermediate stage. Stabilize that concoction through many thousands of years with even more drift, then you have what we call Ancient North African. Later you had the southwest Asian paleolithic population coming into North Africa going to the ANA population and thus you have the Iberomaurusians some 25 kya.
(03-18-2024, 06:19 PM)Woz Wrote: The affinity for Zlaty Kun in Iranian HG's is likely from their Baradostian ancestry, which we don't have samples of, and which is not Zlaty Kun, just some early branch of Eurasians. Perhaps this is what those early researchers called "Basal Eurasian": a mixture of Baradostian (admixture calculators go for Zlaty Kun as a proxy in the absence of actual Baradostian samples) and "ANA" (quite possibly Emiran). Zlaty Kun had Neanderthal ancestry though, and probably so did Baradostian.
If I recall, even Iberomaurusians had higher than average Neanderthal ancestry, which doesn't make a lot of sense if operating under the assumption that ANA is really some sort of genuinely African type ancestry. I'm skeptical that the ANA-side of IBM is really some deeply rooted local Aterian relict and not just some very old Egyptian or Levantine (Emiran as you mentioned) reflux.
They clearly have European HG ancestry, maybe all of their non-ANA is simply WHG-like, so that's where their Neanderthal comes from. I also think Aterian is too old, haplogroup E probably came from East Africa less than 40 thousand years ago, and that should be most of the African part.
(03-19-2024, 05:12 PM)Kale Wrote: Aren't Nilote's y-hg A mostly/all A-M13? Y-full and FtDNA both have the TRMCA of M13 at ~10KBC. Probably a later incursion from the South.
Y-hg B seems to have most of it's diversity in Central Africa.
At some point in the past, it is possible East Africa may not have had y-hg A or B, just E (and D0).
Could be just a bottleneck? I used to think CT is Eurasian because it would be unlikely that C and F (and D?) all went extinct in Africa, but there really isn't all that much diversity in Africa, something like 10 branches at the OoA time depth with E and D0 both there from CT. So likely a lot went extinct, plus sampling is also way behind, maybe something could turn up eventually.
(03-19-2024, 08:15 PM)Kale Wrote:
(03-19-2024, 06:57 PM)kolompar Wrote: What kind of lame Basal Eurasian is that if it's not more related to populations with Basal Eurasian?
What I was trying to illustrate regarding point 3 was this.
Congo_Mbuti.DG Sunghir.SG ZlatyKun.SG Ust_Ishim.DG 0.00278 4.44 1127764
Congo_Mbuti.DG MA1.SG ZlatyKun.SG Ust_Ishim.DG 0.00285 3.89 791393
Congo_Mbuti.DG Andaman_100BP.SG ZlatyKun.SG Ust_Ishim.DG 0.00289 4.22 1111692
Congo_Mbuti.DG Iran_Wezmeh_N.SG ZlatyKun.SG Ust_Ishim.DG -0.00048 -0.75 1126449
If Iran_N is ~60% of it's ancestry from something in the neighborhood of Sunghir/MA1/Andaman, and there is no connection between ZlatyKun and Iran_N, shouldn't that last stat have 60% of the d-value of the first 3?
It might be something in Ust-Ishim, the same thing that also makes him less related to East Eurasians than he should be.
The other option is this is proof there was Iran/Basal gene flow into West Eurasians.
(03-19-2024, 07:32 PM)TanTin Wrote: Let me add something about this Z- requirement.
It is valid only when we do statistics for some group of individuals or for some population.
However we can run F-statistics for individuals only.
In our case: ZK - is one individual only.
BK are 4 or 5, but we may run Fstats for for whichever we like.
Laos_Hoabinhian.SG - is pretty much the same..
So to avoid this inconvenience with Z-requirement - the simple step to bypass it: just select one individual and run the F-test with it.
In such case F-stats will just count the number of shared alleles between these 4 individuals and it will provide results in the form of simple count and percentage..
Z-number doesn't matter in such case. More especially in the case where est is near 0 .
Dividing near 0 value with some small number is not much recommended.
If our test populations are a group with significant numbers, then we must take into account Z-value. however when working with individuals we may just ignore this.
Z is only a requirement to show there was gene flow. Maybe you can't prove a negative but if Z is close to zero you have no evidence of gene flow, that's how f-stats are usually used.
Don't really know about bias but f4 should be less affected by it if I go by this. https://uqrmaie1.github.io/admixtools/ar...stats.html
For Africans that will be positive because Japan and Loschbour are both OoA bottlenecked. Will a simple PCA not work? First component should separate modern and archaic.
(03-21-2024, 07:52 AM)Desdonas Wrote: In fact, until now I still believe that BE split from other Eurasians before 55-60 kya. But if there is not much Neanderthal in Oceanians and Onge, then the Neanderthal pulse shared by all Eurasians at around 55 kya may be the similar size. The extra Neanderthal in Oase, Bacho Kiro and East Asians is secondary. Furthermore, BE may not be very basal, while Crown Eurasian may be more derived than expected.
It was Hoabinhian, Jomon, and maybe Longlin and AASI. For Oceanians I don't know because I can't really calculate their Neanderthal from just f-stats because of their Denisovan. For East Asians it might also be that their extra archaic affinity comes from the Denisovan that the Salkhit paper detected. I don't know how much the European ancients are considered for the usual suggestion that there was only one Neanderthal admixture event. Maybe all admixing Neanderthal was very similar, I think around the Altai they also got replaced by Vindija ones?
1. IBM's non-ANA ancestry, except the Near Eastern Pinarbasi like component, there may also be some Goyet-like geneflow. Mtdna-M1 has an epicenter in Africa/IBM-like genepool, which makes some people even consider that M1 is ANA, while MxM1 is OoA. In fact, M1 could be associated with an unsampled Goyet-related population from Europe. (Migrated through the Mediterranean?)
2. Y-hg E has a TMRCA of about 52kya rather than 40kya. But during 52-40kya, E may diversified in East Africa, and then expanded to North Africa and West Africa.
3. The Altai-like Neanderthal lineage was indeed replaced by a new Neanderthal lineage (Chagyrskaya). From the graph below we can infer that Chagyrskaya is significantly Vindija-related.
Some of this reminded me of a random run I did with a simulated coordinate from Anthrogenica of "ANA." I placed several old samples to see different things, and something peculiar surfaced on the Taforalt samples. The result might not mean much as the ANA sim could be the issue. But it is interesting regardless.
(03-22-2024, 01:50 AM)Desdonas Wrote: 1. IBM's non-ANA ancestry, except the Near Eastern Pinarbasi like component, there may also be some Goyet-like geneflow. Mtdna-M1 has an epicenter in Africa/IBM-like genepool, which makes some people even consider that M1 is ANA, while MxM1 is OoA. In fact, M1 could be associated with an unsampled Goyet-related population from Europe. (Migrated through the Mediterranean?)
2. Y-hg E has a TMRCA of about 52kya rather than 40kya. But during 52-40kya, E may diversified in East Africa, and then expanded to North Africa and West Africa.
3. The Altai-like Neanderthal lineage was indeed replaced by a new Neanderthal lineage (Chagyrskaya). From the graph below we can infer that Chagyrskaya is significantly Vindija-related.
Yes, exactly what I was thinking.
1. I've checked Ostuni's bam but there doesn't seem to be much if any mtDNA, maybe it was removed? Closest relatives of M1 are in Southeast Asia, so are the relatives of other European M haplogroups.
2. E-V38 is less than 40 thousand years old and includes the West African E-M2 and Mota's E-M329. And I think the few West African E haplogroups all have TMRCA less than 20 thousand years so E might have stayed in East Africa for a long time.
3. I was thinking about that graph, that maybe Ust'-Ishim has special Neanderthal ancestry and that's what makes him less related to other Eurasians.
(03-23-2024, 04:15 PM)Horatio McCallister Wrote: 1. The point isn't that IBM had any Neanderthal ancestry at all, it's that their Neanderthal levels were higher than you would expect being a half/half West Eurasian + ANA mix. I went back to the original IBM paper's supplements ( Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations | Science) to see what they had to say about this - "Considering the dual ancestry of the Taforalt individuals, we can explain the Altai affinity in Taforalt as a dilution of its Natufian-related ancestry with its significant proportion (~36.5%) of sub-Saharan African ancestry." However, when looking at the f4s they used to determine this, some things stood out as unusual:
IBM has comparable Z scores to Natufians and Levant_N, even though the latter obviously have proportionately much less ANA than IBM does, although to be fair they do have lowish SNP counts. Also Iran_N has lowest Neanderthal out of all the Eurasians in that test and even lower than some of the Africans. There are some other odd results too like the high scores for Mozabites and Ju_Huan North, I would be interested in seeing if someone here could possibly re-run these or similar tests as a sanity check.
2. There have been lots of papers over the last few years showing that the divergence between Eurasians and Africans is very deep, going back 100k years. I don't think there's any real reason to assume that this proto-Eurasian coalescence (CT and L3) needed to have taken place in Africa. The below paper makes the case that the proto-Eurasian population spent an extended period of time coalescing in the neighborhood of Arabia for tens of thousands of years before disseminating across Eurasia as a whole, which sounds a lot more likely to me than the conventional OoA scenario whereby a branch of humans leaves East Africa 55,000-60,000 years ago and rapidly colonizes and replaces Neanderthals and Denisovans from all parts of Eurasia.
The Z score for Natufian is lower simply because less SNPs, less certain result. The f4 estimates itself look correct. But what's going on in South Africa?
I find it much less likely that OoA humans stopped and contemplated for thousands of years in Eurasia. I think they must have had some huge technological advantage that allowed them to overtake other humans very quickly, and the conditions for OoA were a short, rare one-off event.
03-25-2024, 12:48 AM (This post was last modified: 03-25-2024, 03:58 AM by Desdonas.)
(03-24-2024, 10:25 PM)kolompar Wrote: The Z score for Natufian is lower simply because less SNPs, less certain result. The f4 estimates itself look correct. But what's going on in South Africa?
I find it much less likely that OoA humans stopped and contemplated for thousands of years in Eurasia. I think they must have had some huge technological advantage that allowed them to overtake other humans very quickly, and the conditions for OoA were a short, rare one-off event.
The linked pnas paper (graph is shown below) mentions that OoA occurs at about 80kya, followed by "Arabian Standstill". This clearly requires the back migration of E and D2 (D0) into Africa, and if it is true, we may see the genetic adaptation/related alleles in Africans significantly. So then it may become conflictive. Anyway, a single OoA without back migration is more parsimonious.
However, if a single OoA occured at 50kya (even not 55-60kya), there would be no time left for the genetic adaptation mentioned in the paper. So, either there is a bias in the research of the paper, or the ages of CT, DE, and D may be older than expected. I remember that some studies and graphs suggest that the ages of DE (Yap) and D (CTS3946 level) may reach 73-71 kya, and if the initial OoA population size is smaller, then 10,000 to 20,000 years may be enough for the "Arabian Standstill".
Finally, I believe that the replacement of Neanderthals and Denisovans was largely due to the diseases carried by the OoA population. It is known to all that the migration route of Oceanians is through South Asia and Southeast Asia, but the entire southern route region lacks IUP tools. Southeast Asia and Southern China maintain the ancient pebble-tool industry.
A combination of evidence, based on genetic, fossil and archaeological findings, indicates that Homo sapiens spread out of Africa between ~70-60 thousand years ago (kya). However, it appears that once outside of Africa, human populations did not expand across all of Eurasia until ~45 kya. The geographic whereabouts of these early settlers in the timeframe between ~70-60 to 45 kya has been difficult to reconcile. Here we combine genetic evidence and palaeoecological models to infer the geographic location that acted as the Hub for our species during the early phases of colonisation of Eurasia. Leveraging on available genomic evidence we show that populations from the Persian Plateau carry an ancestry component that closely matches the population that settled the Hub outside Africa. With the paleoclimatic data available to date, we built ecological models showing that the Persian Plateau was suitable for human occupation and that it could sustain a larger population compared to other West Asian regions, strengthening this claim.
Note: there are no new data in this paper, they analyze already published data.
(03-18-2024, 06:19 PM)Woz Wrote: The affinity for Zlaty Kun in Iranian HG's is likely from their Baradostian ancestry, which we don't have samples of, and which is not Zlaty Kun, just some early branch of Eurasians. Perhaps this is what those early researchers called "Basal Eurasian": a mixture of Baradostian (admixture calculators go for Zlaty Kun as a proxy in the absence of actual Baradostian samples) and "ANA" (quite possibly Emiran). Zlaty Kun had Neanderthal ancestry though, and probably so did Baradostian.
"Basal" is generally the accumulation of certain markers . There is a huge difference between the average profile of African, European and Asian populations.
By running some F4 statistics we may see some are negative other are positive, compared to Ust-Ishim.
This difference can not be explained by Coalescent theory so they introduced hypothetical "Basal" population which is supposed to be the source for these "opposite" markers.
However in my opinion this "Basal" group is not related to the time of Zlaty Kun or near that.. My search for "Basal" is for very archaic species.
(03-24-2024, 02:01 AM)Megalophias Wrote: Thanks TanTin, that is helpful. Does seem like ANA has a bit of West African affinity, but doesn't tell us what causes this.
f4(Chimp, South_Africa_1900BP; Israel_Natufian, Morocco_Iberomaurusian) would be good, to replicate the findings in the previous paper.
Do you have the ancient Malawi foragers (Hora and Fingira)? If you do then f4(Malawi, South_Africa_1900BP; Israel_Natufian, Morocco_Iberomaurusian) and f4(Chimp, Malawi; Israel_Natufian, Morocco_Iberomaurusian) would be nice.
It's been suggested that ANA phylogenically actually branches off from a common node with West Africans rather than East Afris, although I was always skeptical of this.
(03-19-2024, 04:38 PM)Hammas Wrote: I know this is kind of unrelated but is it really true that Iran N has 20% Onge related ancestry? I’ve seen other models with Zlaty Kun and the Onge admixture isn’t present. Which model is more accurate?
I'm pretty sure Iran_N has Tianyuan, apart from any ANE DNA it has.
I agree with people saying that Basal is something Baradostian. Iran_N is just as "deep" as Natufians if not even more deep, and yet as far as I know it lacks an affinity to ANA. Natufian clearly has a basal component other than ANA as it's usually modeled as ANA + Dzudzu/AHG or something like that.
(03-25-2024, 12:48 AM)Desdonas Wrote: Finally, I believe that the replacement of Neanderthals and Denisovans was largely due to the diseases carried by the OoA population. It is known to all that the migration route of Oceanians is through South Asia and Southeast Asia, but the entire southern route region lacks IUP tools. Southeast Asia and Southern China maintain the ancient pebble-tool industry.
Is there any evidence of this? The great plagues of the Bronze Age and later the colonial period happened because of difference in lifestyles between the interacting groups made one of those groups especially less resistant to the other group's disease. Why would this happen for Neanderthals and Humans? I guess Neanderthals lived in smaller groups, but humans at this time also lived in very small groups up until the mesolithic.
![[Image: South-Africa.png]](https://i.postimg.cc/85Bb2SVM/South-Africa.png)
![[Image: Basal-Mixed.png]](https://i.postimg.cc/tRZr8m57/Basal-Mixed.png)
![[Image: 41586_2020_1929_Fig9_ESM.jpg]](https://media.springernature.com/full/springer-static/esm/art%3A10.1038%2Fs41586-020-1929-1/MediaObjects/41586_2020_1929_Fig9_ESM.jpg)