A working model on the peopling of Eurasia

This post will deal with the peopling of Eurasia by modern humans and their subsequent Paleolithic movements and divergence patterns. – Part I of our "in development" series on the question to 'who we are and where we came from': Paleolithic to Epipaleolithic period.

Overview

Modern humans have a "recent African" origin, having evolved within the African continent, and diversified there; one of those branches became isolated in Northeast Africa and would subsequently became ancestral to all modern living 'non-African populations': Eurasians. This branch would carry out the "Out of Africa" migration, – but they were not the first humans to leave Africa; they were preceded by earlier extinct waves of modern humans, possibly distantly related to those of the later main OoA wave – as well as deeper archaic groups which would have become ancestral to the Neanderthals or Denisovans.

Shortly after the Out of Africa migration of modern humans (c. 90–60kya), Basal Eurasians diverged and stayed in the Arab peninsula. – The majority of the OoA wave settled in a region streching from the Levant to northern Mesopotamia and the Persian plateau. It was in the Levant and northern Mesopotamian/Anatolia region (and later further in Europe, Central Asia and South/SoutheastAsia), where archaic introgression, e.g. Neanderthal (and in part Denisovan admixture events) took place. – The Persian plateau most likely acted as "population Hub" for the OoA movements (Vallini et al. 2022/2024); alternatively the Hub location has also been proposed to be located in Europe or Central Asia.

Subsequently, the Hub population started to develop internal differentiation into a broadly Western Eurasian clade (UP wave) and a broadly Eastern Eurasian clade (IUP wave), among some earlier extinct groups (ZlatyKun/Ranis):

The dispersal of these deep lineages may have happened either via repetive expansions, or more simultaneously but in different directions, largely isolated from each other.

The first and deepest split among "Common Eurasians" can be associated with the Zlaty Kun and Ranis lineage in Europe, which is basal to all other Eurasians, and can be described as Crown-like. This lineage headed into Europe, but became extinct without contributing ancestry to later populations. These samples displayed additional Neanderthal admixture. Another early pioneer group may have headed into the Sahul region of Oceania, being affilated with the archaeologic sites as early as 65kya. This pioneer group (Sahul Ghost) may have contributed between 3–24% ancestry to present-day Australasians.

Around 55–50kya, the major split between 'Ancient West Eurasians' and 'Ancient East Eurasians' was completed, although there still existed some mutual contact events within the Hub; – at least until around 48kya, when Ancient East Eurasians started to expand, in tandem with the affilated 'Initial Upper Paleolithic' material culture. -> IUP wave.

Below an edited schematic from Vallini et al. 2022, showing the inferred migration patterns according to the repetive wave model from a population Hub on the Persian plateau:

IUP period:

This IUP wave (c. 48kya) is ancestral to all ancient and modern East Eurasian populations. – A northern IUP route gave rise to the IUP microblade-based tool cultures, represented by the BachoKiro_IUP and Oase_IUP specimens in Europe, as well as multiple remains found in Central Asia, Siberia and Northwest China, such as Kara Bom etc., who are all forming a substructured basal sister clade to modern East Eurasians; those IUP lineages largely went extinct, but contributed to the formation of succeeding UP Europeans, as well as to the Tianyuan lineage in Northern China; also evident through the unusual genetic affinity between the European GoyetQ116-1 and the Chinese Tianyuan specimens.

A southern IUP route wave with a coherent genetic makeup ('East Eurasian Core'; "EEC") headed into Southern Asia, where they accumulated shared drift (EEC-drift). After some time, they rapidly diverged into the AASI lineage (ancient South Asian), the Önge lineage (Southeast Asian), the ESEA lineage (broadly Eastern Asian), and the Australasian lineage (Oceanian); ancestral to all modern East Eurasian populations of the Asia-Pacific region; Australasians may harbor an additional pre-EEC component (Oceania_IUP):

The northern and southern route dispersals for the deep East Eurasian branches (IUP_North and EEC_South) are also evident in terms of IUP-affilated material culture:

The IUP and Core & Flake based cultures encountered each other in Northern China, fitting the observed geneflow between IUP and ESEA/Tianyuan lineages:

Both archaeogenetic and archaeologic data support a single southern route dispersal for the EEC, and subsequently rapid divergence in the South–Southeast Asia region:

A single major migration of modern humans into the continents of Asia and Sahul was strongly supported by earlier studies using mitochondrial DNA, the non-recombining portion of Y chromosomes, and autosomal SNP data [42–45]. Ancestral Ancient South Indians with no West Eurasian relatedness, East Asians, Onge (Andamanese hunter–gatherers) and Papuans all derive in a short evolutionary time from the eastward dispersal of an out-of-Africa population [46,47]. The HUGO (Human Genome Organization) Pan-Asian SNP consortium [44] investigated haplotype diversity within present-day Asian populations and found a strong correlation with latitude, with diversity decreasing from south to north. The correlation continues to hold when only mainland Southeast Asian and East Asian populations are considered, and is perhaps attributable to a serial founder effect [50]. These observations are consistent with the view that soon after the single eastward migration of modern humans, East Asians diverged in southern East Asia and dispersed northward across the continent.

One possible qpGraph model for Ancient East Eurasians based on McColl et al. 2018::

Note: ASEA describes “Ancient Southern East Asians”, while ANEA describes “Ancient Northern East Asians”.

Compare with a graph including archaic introgression events:

Australasians (specifically Papuans and Australians) may have a deeper early wave ancestry (Sahul Ghost or xOoA); this would also explain the earlier archaeologic remains (65–55kya):

Note: it is also possible to model Australasians as just a single distinct EEC branch with extra Denisovan/archaic inputs, next to Önge, AASI and ESEA; e.g. an admixture between 'residual EEC' and an Oceanian IUP or basal EEC:

– We decided to use the scenario with deeper Ghost admixture, also in regards to the earlier archaeologic findings in Australasia, which contrast the later genetic divergence date estimation (c. 40kya for EEC).

Our qpAdm models on North China UP (Tianyuan), East Asians (ANEA and ASEA), as well as Papuans; with Önge as unadmixed EEC proxy:

UP period:

During the IUP expansion, ancestral West Eurasians stayed in the Hub region, accumulating shared genetic drift. At around 40kya, ancestral West Eurasians started to expanded out of the Hub, being affilated with Upper Paleolithic material culture (Aurignacian and Gravettian like tools, as well as Baradostian types). These West Eurasian lineages which expansed out of the Hub became known as the 'West Eurasian Core' ("WEC"), those who stayed in the Hub may have became the "WEC2":

Those heading into Europe would encounter remnants of the East Eurasian-affilated IUP populations, which whom they would replace and partially absorb, subsequently giving rise to the Aurignacian culture(s) represented by GoyetQ116‐1 (with 17–23% IUP admixture) and Kostenki14 (with no or only marginally relevant IUP admixture) and the Gravettian culture(s) represented by Sunghir and the Vestonice clusters (e.g. GoyetQ116-1 + Kostenki14 like).

In Siberia, the UP wave (Kostenki14-like type) would merge with a local EEC group (a Tianyuan-like lineage; primarily of the Önge/ESEA-like type, but also with an IUP component) to give rise to the Ancient North Siberians and derived Ancient North Eurasians (ANS/ANE).

The ANS/ANE have previously been described as "Paleolithic admixture event between WEC and EEC lineages". The ANE/ANS lineage expanded massively throughout Eurasia, mostly via an East to West expansion, contributing to multiple groups such as the Mesolithic "Eastern hunter-gatherers" (EHG) in Europe, the "West Siberian hunter-gatherers" (WSHG), as well as towards populations of the Persian plateau and Southwest Asia, and finally also to the formation of Native Americans (in tandem with a derived ESEA component).

The WEC lineages which populated Anatolia and the Caucasus received geneflow from the WEC2 group and Basal Eurasians to their South, from the Persian Gulf region and Arab peninsula, and would give rise to several of the most important West Eurasian lineages: namely contributing to the WHG cluster (which also derived parts of their ancestry from UP Europeans as well as some ANE-like geneflow), the Anatolian_HGs (which would give rise to later Anatolian and European Farmers and also contributed significantly to other nearby groups), and the Caucasus_UP as well as Levant_UP groups.

Those related to the Levant_UP groups would later (c. 30kya) also expand into Northern Africa, resulting in the formation of the Iberomaurusian culture cline, by merging with the local 'Ancient North African' (ANA) lineage. The ANA represents a near trifurication between the OoA group and Mota_HG ( – the deep SAHG-like admixture), after their divergence from other African lineages. ANA may also have contributed in variable amounts to ancestral Niger-Congo and Nilo-Saharan groups, but their exact phylogenetic relationships remain elusive.

Subsequent geneflow from groups from Northeast Africa (Egypt Paleolithic) would have left some genetic influences onto the Levantine groups (and beyond), resulting in the formation of the Epipaleolothic Natufians, who would later again expand throughout the Arab peninsula and Northeast Africa.

The ancestral West Eurasians who stayed in the Hub (WEC2), would later, after contact events with Basal Eurasian, Caucasus_UP and Ancient North Eurasian (ANE) components, re-emerge as the Iranian Mesolithic hunter-gatherers and Neolithic Iranians.

The existence of the WEC2 Ghost is hypothetical, and based on the setup of Vallini et al. 2022/2024. It may or may not have existed.

Summary on Hub model (Persian plateau)

The first successful major expansion was the IUP/EEC wave (Ancient East Eurasians), which populated most of Eurasia; with the EEC heading into the South–Southeast Asia region, diversifying there, and the main source of ancestry for all modern East Eurasians.

The second successful major expansion was the UP/WEC wave (Ancient West Eurasians), which expanded after the IUP wave. The UP wave replaced and partly absorbed the previous IUP groups.

The phylogenetic patters show that the IUP expansion gave rise to the northern route IUP lineage(s) and the southern route EEC lineage(s); the Ust'Ishim lineage similarly expanded during the IUP wave, but shares only minimal evolutionary drift with the rest of the IUP/EEC lineage, pointing to a slightly early divergence than the main wave ancestral to BachoKiro_IUP,  Oase_IUP or the EEC (see also Vallini et al. 2022 or Allentoft et al. 2024 supplementary informationen).

"The Ust’Ishim lineage is described as "near trifurcation" between West and East Eurasians, but sharing a short period of evolutionary drift with Eastern Eurasians, having diverged from their ancestor shortly after the divergence from Ancient Western Eurasians."

The UP wave gave rise to the WEC lineage(s) expanding from the Hub, and the WEC2 lineage which stayed within the Hub.

These complex patterns of expansions, migration and contact events shaped the Paleolithic to Epipaleolithic Eurasian demographic makeup. Outgoing from these newly emerged genetic lineages and further migration and contact events, but also isolation events, modern Eurasian sub-populations formed.

Plausible alternative scenarios (Hub in Europe/Central Asia)

Alternative scenarios with a Crown Eurasian Hub in Europe or Central Asia, and without the WEC2 Ghost, work equally well, and include a more dominant "Basal Eurasian" legacy for West Asian lineages.

There are two variants of this scenario:

1. Using Kostenki14 as baseline for the UP/WEC lineage; with GoyetQ116-1/Fournol needing extra IUP admixture (fitting its affinities to Tianyuan and BachoKiro_IUP), while Caucasus_UP/Dzudzuana as well as Iran_N (Ganj_Dareh_Neolithic) need significant extra Basal admixture; compare Allentoft et al. 2024 etc.; e.g. similar to the Vallini scenario, but without a WEC2 Ghost and repetive expansions: pre-IUP, IUP, and UP waves.

2. Using GoyetQ116-1 as baseline for the UP/WEC branch, with Kostenki14 having some Basal and ZlatyKun-like admixture, and Caucasus_UP/Dzudzuana as well as Iran_N (Ganj_Dareh_Neolithic) having significant Basal Eurasian admixture. – This way, GoyetQ116-1 still has an indirect higher affinity to Tianyuan/BachoKiro_IUP through the absence of a Basal component, compared to Kostenki14 etc., and does not need IUP admixture; representing the deepest branch of West Eurasians, via a population Hub in Europe:

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:

This model also differes in regards to the used route of the ENA/EEC wave: instead of a single southern route dispersal of the IUP/EEC wave into South-Southeast Asia and subsequently northwards, – here (variant 2.), the ENA/EEC branch expanded along a northern route into East Asia and diversified in southern East Asia, subsequently expanding further into South Asia, Southeast Asia, and Oceania, as well as back northwards to northern East Asia.

I caution that the same phylogenetic pattern would also work for a southern route entry (down the Tian Shan route into South Asia), but the Kale 2025 model specifically preferred a northern route via the Altai IUP sites, and in the above setup also looks quite plausible.

Based on this scenario, the autosomal profiles of major West Eurasian lineages (compare the above qpGraph) – as per before, here GoyetQ116-1 and the Fournol cluster represent the base of West Eurasian ancestry; significant Basal Eurasian ancestry for West Asian/Middle Eastern groups:

This scenario indeed can explain all the observed genetic affinities, uniparentals and archaeologic record, and represents a valid alternative to the Hub model as per Vallini et al. 2022/2024 etc.

E.g. the main differences are in regards to the migratory patterns, and the used baseline for early West Eurasian ancestry (GoyetQ116-1 vs Kostenki14 [vs the WEC2 Ghost]), as well as an significantly higher legacy of Basal Eurasians in Western Asia. For ENA/EEC, less changed; one notable point is EA forming a deep clade with Önge, while Tianyuan=EA+IUP (rather than Tianyuan=Önge+IUP -> EA=Önge+Tianyuan).

The higher frequency of Basal Eurasian ancestry also fits with observed lower archaic allele sharing for West Asian lineages – note, this may also be correct for certain groups in the K14/Vallini scenario when excluding the WEC2 lineage:

Conclusion

The exact patterns on the peopling of Eurasia remains disputed, but we have a good idea on the overall happenings and affinities.

A major question remains on whether there were repetive waves spreading pre-IUP, IUP and UP ancestries, as well as if Kostenki14/WEC2 or GoyetQ116-1 can be regarded as base for West Eurasian ancestry.

These options accordingly affect the amount of needed Basal Eurasian and or IUP admixture for UP-affilated lineages, and to an extent, the plausible migration patterns.

We hope our summary on the Paleolithic patterns of the peopling of Eurasia help to get a more compact overview, and provide future directions for entangling the genetic and demographic history of Eurasia and beyond.