On deep roots of Iranian hunter-gatherers, and possible scenarios on their formation
The Iranian hunter-gatherers are among the more enigmatic lineages, with unclarified deeper roots.
Although they fall broadly within the West Eurasian cluster, they are placed in an extreme position, displaying no strong genetic affilation with nearby Anatolian or Levant groups. – This distinct position is primarily attributed to them deriving a significant amount of their ancestry from a deeply diverged local West Eurasian branch (dubbed WEC2 by Vallini et al. 2024), which stayed in the supposed population hub on the Persian plateau, after the divergence of 'Ancient East Eurasian;s' (IUP = Initial Upper Paleolithic wave; c. 48–46kya), and after the deepest split within West Eurasian lineages, with the remainder WEC lineages expanding elsewhere (WEC; UP = Upper Paleolithic wave, such as Kostenki14 or Sunghir in Europe; >38kya). – Earlier proposals associated the distinct position to high amounts of Basal Eurasian ancestry, but this seems not accurate anymore. – For a more detailed explanation on the early peopling, refer to Vallini et al. 2022 and 2024; "Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa", "The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal".
For clarification, we will first look at the old model arguing for a high Basal Eurasian legacy among Iran_N:
Old models using solely Kostenki14 (or Goyet) as deepest West Eurasian source, needed significantly higher non-West Eurasian ancestry to model Iran_N. Specifically a higher frequency of Basal Eurasian ancestry is needed in such scenario. This scenario still cited quite often, although we already know it to be wrong. – For this, see Allentoft et al. 2024 for example:
This view is most likely obsolete:
E.g. UP Europeans had admixture from preexisting IUP groups; when using those UP Europeans as unadmixed West Eurasian source, all West Asian groups will need more basal ancestry by default, to counter the missing IUP/East Eurasian affinity. – This obviously screws our picture on Mesolithic and Neolithic West Asians, such as Iran_N.
Vallini et al. 2024 did take this into account, and presented a improved scenario on the peopling of Eurasia; a repetive population hub OoA on the Persian plateau, including IUP legacy among UP Europeans.
Vallini et al. 2024 described the origin of Iran_N as follows:
"We simulated two different West Eurasian populations: WEC and WEC2, with WEC2 staying in the Hub longer than WEC (and Kostenki14), and hence closer to it from a genetic point of view. [...] Our results showed that the genetic component closest to the Hub population is represented in ancient and modern populations in the Persian Plateau. Such a component, after mixing with Basal and East Eurasian ancestries, resurfaced in the palaeogenetic record, previously referred to as the Iranian Neolithic, the Iranian Hunter Gatherer’ or the East Meta49. [...] We found that after accounting for East and Basal Eurasian confounders, the populations that harbour the WEC component closer to the Hub population (WEC2) are the ones whose West Eurasian ancestry is related to the hunter gatherers and early farmers from Iran48. This is a genetic ancestry commonly referred to as the Iran Neolithic30 or the East Meta49, here named Iran HG for clarity. The Iran HG ancestry is widespread not only in modern-day Iran but also across ancient and modern samples from the Caucasus (in particular in the Mesolithic hunter gatherers of that region) and in the northwestern part of South Asia50."
-> The legacy of the UP Hub, the Hub_remnant (=WEC2) ancestry, peaks among ancient Iranian groups, especially Iran_HGs and Iran_N, representing a previously unknown deep West Eurasian lineage, deeper than the lineage leading to Kostenki14 & co:
In regards to the related Caucasus hunter-gatherers (CHG), they emerged by the expansion of Iranian hunter-gatherers and absorbed UP Caucasus and EHG-like groups:
This results fit quite well with the qpAdm results by Vallini et al. 2024 (supplementary data 11), with a total WEC/WEC2 amount of '0.765' = 76,5%. – E.g. a combination of WEC2 and WEC ancestry, with additional Basal, and EEC influences. – The EEC component seems primarily to be affilated with ANE-like geneflow, although some early mutual contacts with the AASI sublineage can not be excluded. – At least later, minor AASI geneflow reached Neolithic Iran, specifically via IVC mediated geneflow. – For comparison the Anatolia_Epipaleolithic had a total WEC/WEC2 amount of '0.968' = 96,8%; the Natufian_Epipaleolithic had a total WEC/WEC2 amount of '0.848' =84,8%; the Gravettian_Krems_UP had a total WEC/WEC2 amount of '0.946' = 94,6%. The reason for why ancient West Eurasian groups have some admixture is because of their relative later expansion (UP wave), after the expansion of the EEC/IUP wave and the Crown/MUP wave.
While going back to look at d-stats between some of these groups, I noticed some oddities that were produced when using African populations and modern East Asians, with other ancient Eurasians. Modern Africans show a preference for more recent than ancient Eurasians. There’s even a significant preference for Chalcolithic Iranians in 10,000 year old samples from Malawi, which makes no sense. This is probably some type of artifact in the data. This, to me, was creating the impression of a Basal Eurasian branch where none need be found. When you compare ancient Eurasians to each other, it does disappear.
For instance, the Z-scores using Chimp as an outgroup, and even Altai or Denisovan, were completely different than using Mbuti, Mota, or any other African individual or population. The significance of these stats vanished when comparing the first Anatolians versus ancient European hunters.
Not only that, it also disappeared when using ancient East Asians and Native Americans such as Tianyuan, Vietnam_N, Vanuatu_2900BP and Brazil_LapaDoSanto_9600BP. Sure enough, when you compare modern East Asians versus these samples, the modern groups end up being significantly closer to Ust_Ishim and Africans. So, instead of all ancient East Asians having Basal Eurasian, or all modern East Asians having ancestry from Ust_Ishim or some special relationship with Africans, this may also be an artifact. The second is possible, but probably minimally so.
So, what we have is Dstats in the order of (Chimp/Altai/Denisovan, Ust_Ishim; Anatolia_HG/Boncuklu_N, SunghirIV/Kostenki14/Vestonice16/Tianyuan/Vietnam_N/Brazil_LapaDoSanto_9600BP) all being quite insignificant. This had me look into creating some more graphs to look at the issue and deciding to stay away from using modern East Asians and Africans in analysis of ancient Eurasians.
The graph that I ended up with combined Natufians, Iranian farmers from Ganj Dareh, both the Anatolian hunter-gatherer from Pinarbasi and early farmers from Boncuklu, Upper Paleolithic European SunghirIV, Iberomaurusians, and Upper Paleolithic samples from Siberia and China, Ust-Ishim, Yana, and Tianyuan, respectively.
With this graph, it brings up the interesting prospect that deep ancestry [Basal/ANA] did not reach Anatolia, or the Caucasus with Dzudzuana, but later in the Levant, Caucasus, and Zagros region:
With the very minimal excess sharing between Boncuklu and Iran, I chose to use Boncuklu as the population that donates the Anatolian, or Dzudzuana-like stuff to Iran, while the Natufians preferred a source more like Pinarbasi (Anatolia_HG).
Without samples covering a range of time between 30,000-10,000 years ago across all of West Asia, it is hard to say if this will pan out. For now, this is the best that I can do. [...]
Iberomaurusians fit best as a mix of the so-called Basal Eurasian or Ancient North African and something coming from the same [WEC] branch as, but before the split of Boncuklu and Anatolia_HG.
The Iranian farmers first wanted to be grouped with Boncuklu, then onto Yana and Iberomaurusians. Afterwards, there was a Z-score between 2-3 that asked for more ancestry related to Tianyuan, but deep than the branch to Yana, going into Iranians. I had noticed this long ago and included it in previous posts. It does keep the graph together much better as more populations are added as well.
As previously mentioned, I avoided the use of any African or modern East Asian population. I did not want to have any artifacts create unnecessary admixture events or ghost populations. [...]
Villabruna, a 14,000 year old hunter-gatherer from Italy and the reason behind the name “Villabruna cluster”, actually shares significantly more drift with ancient Anatolians than Vestonice does, but also significantly more with Ancient North Eurasians (ANE) like Yana and MA1, than the Anatolians do.
For this reason, I chose to make Villabruna, the much younger sample, a mix of Gravettian, Anatolian, and ANE [...] the fact that R1b is present among them and significant relationships with Native Americans are there, it makes sense that ANE would also be in there. [E.g. WHG similarly must not be used as pure unadmixed West Eurasian proxy]. [...]
The major part of the reason I think that this Basal Eurasian or North African was needed in Anatolians, was making them have significant ancestry from Villabruna, who has that relationship with ANE and East Asians over Anatolia. This means that you then must compensate for that relationship not in Anatolia by giving them deeper ancestry that is probably not there. They share enough drift that these tools allow you to branch them together, but then you get caught up in a catch 22 by having to add all of these extra admixture events. For instance, having to make Anatolia a mix of Natufians/Levant, Iran, and WHG, rather than just another branch of West Eurasians that contributes to North Africans, Mesolithic Europeans, and into the Iranian plateau and maybe as far as India before the Neolithic. [...]
In this last graph, Villabruna is a mix of 77% Vestonice and Anatolia_HG (51% and 49% respectively) and 23% from a lineage related to Yana:
Just to make things a little more clear, I will show in more detail what I am talking about. It is the use of Africans and modern East Asians that gets in the way of robust analysis of ancient Eurasians. For whatever reason, there is an artifact that draws modern Asians and ancient West Asians much closer to Africans than UP samples from Europe and Asia.
Here are a few d-stats to show what I am talking about..
Chimp Malawi_Ho IBM Ganj_Dareh -0.00011 -0.321 580681
Chimp Malawi_Holocene IBM SunghirIV -0.001876 -4.17 584427
Chimp Malawi_Holocene IBM AnatoliaHG -0.000176 -0.411 507596
Chimp Malawi_Holocene IBM Iran_ChL 0.000235 0.654 569410
Chimp Malawi_Holocene IBM Yana -0.002173 -5.98 589155
Chimp Malawi_Holocene Ganj_Dareh SunghirIV -0.001849 -4.311 581183
Chimp Malawi_Holocene Ganj_Dareh AnatoliaHG -0.000137 -0.33 506101
Chimp Malawi_Holocene Ganj_Dareh Iran_ChL 0.00042 1.45 567512
Chimp Malawi_Holocene Ganj_Dareh Yana -0.002128 -6.497 585873
Chimp Malawi_Holocene SunghirIV AnatoliaHG 0.001456 2.912 507356
Chimp Malawi_Holocene SunghirIV Iran_ChL 0.002128 5.01 569380
Chimp Malawi_Holocene SunghirIV Yana -0.000277 -0.64 591351
Chimp Malawi_Holocene Anatolia_HG Iran_ChL 0.000391 0.959 497265
Chimp Malawi_Holocene Anatolia_HG Yana -0.001986 -4.528 511289
Chimp Malawi_Holocene Iran_ChL Yana -0.002501 -7.398 573952
Chimp MbutiSGDP IBM SunghirIV -0.001592 -4.869 1037166
Chimp MbutiSGDP IBM AnatoliaHG -0.000818 -2.706 836965
Chimp MbutiSGDP Ganj_Dareh SunghirIV -0.001268 -4.134 1003826
Chimp MbutiSGDP Ganj_Dareh AnatoliaHG -0.000363 -1.268 823271
Chimp Mbuti.SGDP SunghirIV AnatoliaHG 0.000712 2.001 847590
Chimp Ust_Ishim SunghirIV AnatoliaHG 0.000044 0.062 845798
MbutiSGDP Ust_Ishim SunghirIV AnatoliaHG -0.000853 -1.281 882870
Tianyuan Ust_Ishim SunghirIV AnatoliaHG 0.000254 0.312 705443
As you can see, there are some things here that seem a little off. It is even worse when you use samples like Ust_Ishim, Yana, and Tianyuan. I can say that it isn’t about there being some type of ancient attraction to Chimp either. The attraction is with Africans. This isn’t only the case for Mbuti, but even ancient Africans like Malawi_Hora_Holocene. Stats are even more significant for the Chalcolithic Iranians, which makes zero sense for 10,000 year old samples from SE Africa.
Etc.
To sum up:
- it is wrong to use UP Europeans (Goyet or Sunghir) as unadmixed West Eurasians (WEC), and thus consider Caucasus_UP or Dzudzuana as admixed with a more basal source – the same applies for WHG vs Anatolia_N -> all those European groups do have at least some East Eurasian/IUP admixture, either IUP or via ANE/EHG geneflow, or both. – The only real evidence for deeper admixture is present among Natufians and less among Iran Neolithic groups; e.g. ANA-like geneflow (*holds true when using Mota as proxy for ANA as well!!!*)
- Basal Eurasians are probably identical with Ancient North Africans, and left only some influence among ancient and modern West Asians, primarily via North African geneflow, either Iberomaurusian-like or directly ANA-rich geneflow (Emiran culture from Egypt to Levant and beyond etc.). – This fits the archaeologic record on material culture spread. – In the case of another Basal/Crown Eurasian-like lienage in the Gulf region, that lineage would have left traces among Iranian groups, absent from Anatolian ones.
- The repetive population hub expansion waves; e.g. IUP and UP, can plausibly explain the peopling of Eurasia, with UP groups replacing and partly absorbing IUP groups in Europe and Siberia, while those in West Asia remain unadmixed. – Later geneflow from Northern Africa diffused into the Levant and less to the Iranian plateau (partially paralleling the spread of chrY E). This North African influence was either mediated with a Iberomaurusian-like source or another ANA-rich group from Egypt etc.; e.g. Emiran material culture, possibly along a cline.
- 7% ANA/Basal + 16% IUP/EEC + 77% WEC/WEC2
As such, it is possible to model the remainder deep ancestry needed among Iran_N and Natufians via 'Ancient North Africans' (ANA); a sister lineage to the OoA exit group which stayed in Northern Africa; being defined as "more basal than Basal Eurasians". E.g. technically "basal Eurasian". This may either be via a IBM-like wave (geneflow), or independently from an ANA-rich source, represented for example by the Emiran material culture in the Levant, with roots in Northern Africa, e.g. ANA geneflow independently from Iberomaurusians along a cline (Egypt?). E.g. ANA takes the place of the originally defined "Basal Eurasian" lineage. While ANA is an African lienage, it is distinct from more deeper African lineages ancestral to West Africans, Central or South African HGs etc. Close but not as basal as Mota_HG (also cladal to OoA).
Finally, a Basal Eurasian lienage in the Gulf region which did not underwent archaic introgression, may well have existed, and contributed some ancestry to Iran_N, yet not to Caucasus_UP or Anatolian_HGs (not needed for them). This can however also explained by just ANA-like geneflow. – The previous models in which Iran_N derived between 48–62% Basal Eurasian ancestry are most likely wrong, rather this can be reduced via taking the IUP admixture among UP Europeans into account, as well as allowing Iran_N to derive ancestry from the WEC2 source, which stayed on the Persian plateau after the expansion of proper West Eurasians (WEC; see Vallini et al. 2024). – The remainder includes geneflow from surrounding groups: e.g. Caucasus_UP-like, ANE, and possibly EEC/AASI. Finally some ANA-like input, or alternatively a Basal Gulf lineage.
WEC2; the local deepest split of West Eurasian ancestry on the Persian plateau contributed significantly to Iran_N. By not including this component, they will need deep admixture to counter the absence.
Remainder need of Basal may than well be explained by minor ANA-like geneflow from Northern Africa. (Proxy may be Mota_HG as long as we have no ANA proxy).
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ReplyDeleteHi, interesting post, although I am curious as to what makes you think AASI has this "Hub" ancestry? As far as I know there are no AASI individuals sampled. Is it an exploratory model or based on f4 stats etc? Furthermore, why would this have taken place between 40 and 30kya specifically?
ReplyDeleteThanks for reading, looking forward to more posts on your blog
Hi Tatsuya -- are you interested in leading collaborative archaeogenetics research? We have a customized wiki that is invite only with a project focused on human origins called the Observatory, focused on bringing together talented independent researchers.
ReplyDeleteWe're about to publish a few template examples of how we want to engage in collaborative research -- you can see some of our published work here: https://observatory.wiki/Human_Bridges
Early Iranian plateau is mostly just Dzudzuana + some ANE-like + some Onge-like iirc. (Lazaridis et al 2018)
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