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.

They fall broadly within the West Eurasian cluster, but are placed in an "extreme" position, displaying no strong genetic affilation with nearby Anatolian or Levant groups, pointing to deep divergence and or partial distinct ancestries.

Their genetic makeup and formation remains unclear, but it has been agreed that they are primarily derived from a deep local, presumably Basal Eurasian source, and can broadly be modeled via either a three- or four-way admixture, including a Caucasus_UP component, an Ancient North Eurasian (ANE) component, and Önge-like component, and an Basal Eurasian component (Amjadi et al. 2025, Allentoft et. al. 2024, Lazaridis 2018 etc.). A hypothetical WEC2* component may make up a significant amount of ancestry for them, instead of the extra Basal+Önge input (Vallini et al. 2024); although WEC2 may be phylogenetically similar to K14, thus likely not covering the Basal ancestry.

The inferred Basal Eurasian lineage is assumed to have split from other Eurasians after the OoA exit, but before the archaic introgression event and the divergence between West and East Eurasians, having been largely isolated in the Arab peninsula. 

*The WEC2 lineage is hypothetical, but plausible, representing the deepest split on the West Eurasian branch (e.g. split from K14/WEC), after the divergence from the IUP/East Eurasian lineage. To clarify its nature, as well as the legacy and extent of the supposed Basal Eurasian lineage, real Paleolithic samples from Arabia and the Persian plateau are needed. WEC2 may alternatively just turn out as Basal+ENA.

Overview

The term Iranian hunter-gatherers or Neolithic Iranians, is primarily used to refer to a genetic lineage representing the Mesolithic to early Neolithic population of the Iranian plateau, South-Central Asia and the Caucasus.

Iranian hunter-gatherers descend primarily from the local Upper Paleolithic population of the Persian plateau. Their exact nature remains elusive, with proposals of them ranging from being Basal Eurasian-rich, WEC2-rich, or Crown/ZlatyKun-like. – The Persian plateau likely acted as Hub for the early peopling of Eurasia after the OoA exit (Vallini et al. 2022 and 2024), although the Hub may also have been in Europe or Central Asia.

Repetive waves from the inferred Hub contributed in variable degrees to present-day Eurasian and Oceanian populations: The first wave (represented by ZlatyKun and Ranis) went extinct, except maybe being affilated with the supposed Sahul Ghost admixture among Australasians. The second wave was primarily ancestral to all present-day East Eurasians and Oceanians, as well as Initial Upper Paleolithic (IUP) groups in Eastern Europe, Central Asia and Siberia. The third wave became the major ancestral source for all present-day West Eurasian populations.

The Iranian hunter-gatherer lineage is represented by Mesolithic hunter-gatherers and later Neolithic herders and early farmers in present-day Iran, such as remains excavated from the Hotu and Kamarband Caves and Ganj Dareh, as well as Wezmeh. They formed the main ancestral source for later Neolithic and Calcholithic Iranians and nearby Mesopotamian groups, also contributing indirectly to later Levant and Arabian groups.

A deeply diverged sister branch (> 12kya) best represented by remains from Shahr-i-Sokhta, formed the dominant ancestry component of the Indus Valley Civilisation in Northwestern India, which was mixed with a local East Eurasian Core (EEC) component (c. 15–34%) termed Ancient Ancestral South Indian (AASI). IVC-like ancestry forms the major ancestral source for most present-day Indian groups.

Another close sister lineage of Iran_N forms the main ancestral source (c. 70%) for Caucasus hunter-gatherers (CHG) who replaced the previous Upper Paleolithic Caucasus groups (Dzudzuana-like) and also contributed to later European populations, both via indirect geneflow via Anatolia (e.g. admixed with Anatolian HG or farmers ancestry) or via the Proto-Indo-Europeans/Yamnaya (e.g. admixed with the local Eastern European hunter-gatherers [EHG -> CLV cline]).

While the Elamite language is a plausible candidate for a derived linguistic heritage of Neolithic Iranians, or earlier hunter-gatherers, the link to Dravidian or Sumerian is less clear. – It is likely that they habor deep linguistic ties, e.g. Sumero- Elamo-Dravidian, or Zagrosian.

The same unclear affilation exists for Proto-Indo-European or Indo-Anatolian. While some argue for a link to the CHG cluster, others favor an EHG origin, or a hybrid origin within the Caucasus Lower-Volga cline (CLV), also including WHG, Anatolian, and WSHG influences.

Formation of the Iran Mesolithic/Neolithic genepool:

Iranian-hunter gatherers are inferred to have originated from the local Upper Paleolithic population of the Persian plateau. Those are suggested to have been, or were primarily so, of Basal Eurasian origin.

Mesolithic hunter-gatherer remains from the Alborz mountain range have been described to be derived from the local Paleolithic population, e.g. the Baradostian culture; and are ancestral to later Neolithic herders and farmers. Their estimated amount of Basal Eurasian ancestry was as high as 62–66%.

For context:

The local Zagros Upper Paleolithic (Pebdeh), Rostamian, and Baradostian material cultures (Mohammad Javad Shoaee et al. 2024 etc.):

The UP Iran group may have later came into contact with both a Caucasus_UP/Dzudzuana-like group and with Ancient North Eurasians (ANE), resulting in the formation of early Mesolithic and Neolithic Iranians, as represented by the Hotu HG and Ganj Dareh Neolithic remains.

E.g. the 'Iran_UP or HG' ancestry resurrfaced in the archaeogenetic record as the 'Iranian hunter-gatherers' or 'Neolithic Iranians' (Iran_HG/N), playing a crucial role in the demographic history of the region and beyond, specifically in Southern Asia. – For example, an early Iran_HG or Neolithic herders-like wave into South Asia initiated the formation of the Indus Valley Civilization (IVC), which consists the main ancestry of most modern South Asians. – There is also the possibility for multiple distinct Iran_N like waves into Southern Asia, contributing independently to the South Indian Neolithic tradition, as well as the IVC and other Neolithic areas.

Mesolithic and Neolithic Iranians are inferred to have lower archaic allele sharing. Although this can also be explained by purification (purifying selection), the correlation very much corresponds with the inferred high Basal Eurasian ancestry:

While early papers modeled the Neolithic Iranians as just a two-way admixture between a Basal Eurasian-rich lineage and a lineage closer to Ancient North Eurasians (ANE) or Eastern European Hunter-Gatherers (EHG), those are likely outdated, and better explained by three- or four-way models; specifically a Caucasus_UP/Dzudzuana-like component + an ANE component + an additional Basal component + either an Onge-like or local deep West Eurasian (WEC2) component.

This makeup stands in contrast to Neolithic Anatolian and Levant groups, who are primarily to exclusively of Caucasus_UP like ancestry. Natufians, despite sharing most of their ancestry with Neolithic Anatolian groups, have an additional "Ancient North African" (ANA) ancestry component. – The Caucasus_UP group itself has between 6–46% Basal Eurasian ancestry, depending on the used respective WEC baseline (Goyet vs Kostenki14 etc.).

Below the three- or four-way models. See e.g. Lazaridis et al. 2018 (Caucasus_UP/Dzudzuana+ANE+extra_Basal[Mbuti as imperfect proxy]).

Three-way:

Four-way:

Caucasus_UP/Dzudzuana itself has 6–46% Basal ancestry; remainder is Goyet or WHG-like (higher Basal need) or Kostenki14 / Vestonice16-like (UP European; lower Basal need).

The estimation for Basal Eurasian ancestry among Iran_N and Iran_HGs ranges usually from 36% to up to 68%, but as low as c. 7% (e.g. when allowing a WEC2 component). Furthermore, it plays a role if WHG or certain other UP Europeans (such as GoyetQ116-1) are defined as base for West Eurasians, as those may have evidently IUP-affilated admixture; similarly, Kostenki14 may have some Basal admixture. – This results in an increase/decrease of Basal ancestry respectively.

Vallini et al. 2024 specifically argues that Mesolithic and Neolithic Iranians carry such a deeply diverged West Eurasian ancestry (WEC2), that stayed close to the population Hub (the place of dispersal and divergence between West and East Eurasians on the Persian plateau). This type of ancestry, after mixing with surrounding groups, re-emerged as the Mesolithic and Neolithic Iranians:

E.g. Mesolithic and Neolithic Iranians may either be modeld as Basal+ANE (weak fit; does not explain the presence of yDNA J), Basal+Dzudzuana+ANE (good fit), Basal+Dzudzuana+Onge+ANE (good fit), or Basal+WEC2+Dzudzuana+ANE (hypothetical, best fit).

The above three- and four-way models also correlates with observed uniparental haplogroups, especially Y-DNA chromosome patterns: yDNA G and H may correlate with the Basal and East Eurasian components respectively, IJ and LT with the two West Eurasian (Caucasus_UP and WEC2) components, and R2 with the ANE component.

In regards to the related Caucasus hunter-gatherers (CHG), they emerged by the expansion of Iranian hunter-gatherers and additional UP Caucasus and EHG-like ancestries:

"In fact, the CHG genome can be modelled as a mixture of three populations: 72% Western Asia_UP (ancestors of Iran_N) + 18% Caucasus_UP + 10% EHG (Eastern European Hunter-Gatherers) (Allentoft et al., 2024)" as cited by Chataigner C. et al. 2024

Genetic makeup – qpAdm models:

To determine the genetic makup and affinities of Iranian hunter-gatherers, one can compare the different working models with attested demographic patterns and material cultures.

A four-way qpAdm run by Lezagacy came to similar results as Lazaridis et al. 2018, using Onge/EEC as component:

(Credits to Lezagacy for the above model.)

We tried to apply the approach of Vallini et al. 2024, using a second deeply diverged and local West Eurasian source (WEC2), proxied by Ust'Ishim who forms a near trifurication between West and East Eurasians:

The above results fit with Vallini et al. 2024. This way, we can successfully modeled Iran_N as four-way admixture of nearby sources, and explain their distinct position via the deep WEC2 component:

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. We found that after accounting for East and Basal Eurasian confounders, the populations that harbour the WEC component closer to the Hub population (grayscale gradient of population points in Fig. 2A, Supplementary Data 11) are the ones whose West Eurasian ancestry is related to the hunter gatherers and early farmers from Iran48.

 

The Vallini scenario migratory patterns:

Note that adding ZlatyKun instead of Ust'Ishim further improves the fit, this may suggest that the non-WEC component is indeed Basal to all of them; e.g. WEC2 is possibly not valid.

Addendum:

When excluding a hypothetical WEC2 lineage; or applying WEC2~K14 (e.g. inferring that K14/WEC expanded from the Hub, while WEC2 stayed but was phylogenetically similar to K14 rather than Ust'Ishim) – as well as including ZlatyKun and Ethiopia_4500BP as proxies for ancestries basal to the West/East Eurasian split, we got these results for Iran_N:

Previous qpGraph model on Iran_N:

Below a more novel scenario: using GoyetQ116-1 as baseline for West Eurasians ancestry instead of Kostenki14:

The respective genetic profilies for later West Eurasian lineages:

Using GoyetQ116-1 (Fournol cluster) as West Eurasian baseline, with Kostenki14 having some Basal and ZlatyKun-like admixture, allows for an alternative model to explain the observed affinity between GoyetQ116-1 and ENA groups, such as Tianyuan and BachoKiro_IUP, compared to Kostenki14.

This scenario can further be validated by taking uniparental, archaeologic and geologic data into account, such as the CI eruption. – It proposes a Crown Eurasian Hub in southeastern Europe, from which the different lineages diverged and subsequently expanded accordingly:

E.g. a significant Basal Eurasian component is likely for Neolithic Iranians in either case.

When using K14 as baseline, the results are broadly identical:

A different setup differentiating K14 (or CUP+ANE), EEC and ancestry "Basal" to them give us similar results:

In the above scenario CUP (Kotias_UP) has the following makeup:

Summary:

Mesolithic and Neolithic Iranian hunter-gatherers, herders, and farmers represent a distinct Western Eurasian population. – Their main ancestry is defined by a combination of WEC/WEC2 ancestry and significant amounts of Basal Eurasian ancestry, as well as ancestry affilated with Ancient North Eurasians (ANE).

Overall, Mesolithic and Neolithic Iranians fall into an extreme position of West Eurasian diversity; representing a "basal West Eurasian" group. – With regards to decreased Neanderthal ancestry, both Basal admixture and purifying selection must be considered.

We hope that our summary helps to entangle and better understand the formation of Iranian hunter-gatherers, and further helps in future investigation on the prehistory of Western Asia to can clarify open questions.