Ancient East Eurasians and their genetic legacy
This post will deal with the ‘Ancient East Eurasian’ meta-lineage, which is ancestral to all modern Asia-Pacific populations, such as Ancient South Asians (AASI), East/Southeast Asians, and Australasians, as well as certain ancient but largely extinct lineages associated with IUP remains such as the Ust’Ishim man or Bacho Kiro IUP. It is an up-to-date summary on the recent findings of Paleolithic and modern Eurasian archaeogenetic history, and also deals with the archaeologic data and distribution of IUP-affilated material culture(s).
Ancient East Eurasians are associated with the Initial Upper Paleolithic (IUP) wave, following the Out of Africa migration (>60kya). They are also occasionally known as “eastern non-Africans” (ENA) or, especially the modern Asia-Pacific lineages, as “East Eurasian Core” (EEC).
Humans of the Initial Upper Paleolithic wave (IUP) are suggested to have expanded from a population hub through a star-like expansion pattern (c. 48kya), and are linked to the “East Eurasian” genealogical lineage, broadly ancestral to modern populations in Eastern Eurasia, Oceania, and the Americas, notably East Asians, Southeast Asians, Indigenous Siberians, Aboriginal Australians, Papuans, Pacific Islanders, and mostly in Indigenous Americans, as well as partly modern South Asians and Central Asians.
While certain Initial Upper Paleolithic populations represented by specimens found in Central Asia and Europe, such as the Ust’-Ishim man, Bacho Kiro IUP or Oase 2, are inferred to have diverged early and used inland routes, the ancestors of all modern East Eurasian populations are inferred to have used a Southern dispersal route through South Asia, where they subsequently diverged rapidly, also explaining their closer relationship with each other than with the deep IUP Ust’Ishim or Bacho Kiro IUP remains.
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.
The Initial Upper Paleolithic (IUP) wave (>45kya) is “ascribed to a population movement with uniform genetic features and material culture” (Ancient East Eurasians), ancestral to modern East Eurasians (AASI, Australasians, and East/Southeast Asians). They diverged from West Eurasians and Basal Eurasians in a time frame of 50–60kya. Deep IUP-ancestry is represented by the Ust’Ishim man (c. 45kya), the Bacho Kiro man (c. 45kya) and the Oase remains (c. 45kya), while the Tianyuan man (c. 40kya) is representing a deep branch of Basal East Asians (ESEA). This shows us that the Ancient East Eurasians started to internally diversify by around 40kya; eg. AASI, Australasians, and ESEA lineages diverged from the main branch of Ancient East Eurasians, most likely somewhere in Southern Asia, after having diverged from the other deep IUP lineages, and after the divergence of their common ancestor with Ancient West Eurasians (c. 50kya).
The main East Eurasian ancestry lineages which contributed to modern human populations include the following:
- The indigenous South Asians or “Ancient Ancestral South Indian lineage” (AASI) — refers to an ancestral population that primarily contributed to modern South Asians. Partially represented by 5,000–1,500 year old Indus Periphery individuals as well as modern South Asians. Highest presence among tribal groups of southern India like the Paniya and Irula. While the lineage is occasionally represented by the distantly related Andamanese peoples, serving as an imperfect proxy, the Andamanese groups are genetically closer to the ‘Basal East Asian’ Tianyuan specimen.
- The Australasian lineage — refers to an ancestral population that primarily contributed to human populations in a region consisting of Australia, Papua, New Zealand, neighboring islands in the South Pacific Ocean and parts of the Philippines. Represented by present-day Australasians, e.g. Papuans and Aboriginal Australians, as well as the Philippine Negritos.
- The East and Southeast Asian lineage (ESEA) — refers to an ancestral population that primarily contributed to humans living in East and Southeast Asia, much of Remote Oceania, as well as Siberia and the Americas. Represented by ancient Tianyuan and Hoabinhian specimens and present-day East and Southeast Asians.
The Australasian, Ancient Ancestral South Indian, and East and Southeast Asian lineages display a closer genetic relationship to each other than to any non-Asian lineages, and together represent the main branches of “Asian-related ancestry”, which diverged from each other >40kya (Yang 2022, Zhang et al. 2023).
The Australasian lineage however received higher archaic admixture in the Oceania region, and may also harbor some small amounts of “xOoA” admixture (3%) from an earlier human dispersal, which did not contribute to any other human population. Furthermore, Australasians, specifically Papuans, may also carry some ancestry from a deeper East Eurasian lineage, closer to deep IUP branches, such as the Ust’Ishim specimen (closer in a phylogenetic sense), which is absent from the AASI or the ESEA branches.
Traces of another unsampled deeply diverged East Eurasian lineage can be observed in the genome of ancient and modern inhabitants of the Tibetan Plateau; the Tibetan Ghost lineage. While modern Tibetans mostly derive their ancestry from a mostly “northern East Asian” source (specifically Yellow River farmers), a minor, but significant contribution stems from a deeply diverged East Eurasian local “Ghost population” that was distinct from other deeply diverged lineages such as Ust’Ishim, Hoabinhian/Onge or Tianyuan, representing the local Paleolithic population of the Tibetan Plateau.
Deeper IUP-associated East Eurasian lineages have been associated with the remains of the Ust’-Ishim man from northern Central Asia, and the Oase 2 and Bacho Kiro IUP cave specimens in southeastern Europe, and represent early inland migrations, deeply diverged from all other East Eurasian populations (eg. being basal to them, but not directly ancestral).
The phylogenetic structure of Ancient East Eurasians:
A slightly adapted and simplified tree I made for this post:
We currently lack a sequenced AASI specimen, thus it is technically speaking still a “ghost population” often simulated via an “imperfect proxy”, generally Andamanese, but Tianyuan or Hoabinhian work equally well.
The ESEA lineage includes as most basal sub-lineages the Hoabinhian/Andamanese followed by the Tianyuan lineage, both being considered as “Basal East Asian. The derived sub-lineage of Ancient East Asians again diverged into the Jomon and Longlin as well as the ancestral population of Northern and Southern East Asians. ANEA and ASEA are the dominant components for modern Neo-East Asians.
…the ESEA lineage differentiated into at least three distinct ancestries: Tianyuan ancestry which can be found 40,000–33,000 years ago in northern East Asia, ancestry found today across present-day populations of East Asia, Southeast Asia, and Siberia, but whose origins are unknown, and Hòabìnhian ancestry found 8,000–4,000 years ago in Southeast Asia, but whose origins in the Upper Paleolithic are unknown.
The Australasian branch diverged first into an ancestral Aeta sub-lineage, and an Australo-Papuan sub-lineage, which again diverged after arriving in the Sahul region. There they received geneflow from an earlier wave (deep Papuan ghost). Later on, Hoabinhian-affilated geneflow merged with a Papuan-like group to give rise to the Leang Panninge hunter-gatherer population on Sulawesi, being a nearly 50/50 admixture between Onge/Tianyuan and Papuan-like ancestry.
Models on Australasians simulating the “deep Papuan ghost” via Ust’Ishim as proxy:
Possible scenario is that during the initial divergence of Ancient East Eurasians into deep IUP, Tibetan Ghost and EEC (East Eurasian Core), a fourth branch diverged, rapidly heading into Oceania: the deep Papuan ghost. This branch did only leave ancestry among later Australasians (except Aeta as far as I can model). The EEC stayed some time in a “secondary hub” in South Asia, before diverging into AASI, ESEA, and proper Australasian, with Australasians later absorbing the earlier deep East Eurasian lineage in the Sahul region:
A similar scenario was also modeled by Vallini et al. 2022; they however decided to describe Papuans “just as a simple sister lineage to Tianyuan”, noting that this parasimous model is 1 out of 6 equally fitting scenarios in which they derive variable amounts from an earlier East Eurasian lineage, and or low amounts of an pre-OOA (xOOA) wave, recently suggested to make up 3%. In either case, Australasians do carry some amounts of ancestry absent from other East Eurasian Core groups (AASI & ESEA), but are primarily derived from the same EEC source.
Contribution to other ancient lineages:
The deep IUP East Eurasian lineage(s) did not contribute to modern Eurasian populations, but left some ancestry among the mostly West Eurasian Goyet Caves specimen (GoyetQ116–1) of Europe (c. 23%), who in turn contributed to some later European hunter-gatherers in variable amounts, most evident in some East Eurasian affinity (proxied by Tianyuan) in later Iberian hunter-gatherers).
The Tianyuan lineage directly contributed around 29–47% ancestry to the Ancient North Eurasians (ANE/ANS), which in turn significantly contributed to Eastern European hunter-gatherers, evident in an increased affinity of them to the Basal East Asian Tianyuan specimen.
Currently, the strongest affinity to Tianyuan in Holocene European HGs was reported for Eastern European HGs (EHG). This is because the ancestry found in Mal’ta and Afontova Gora individuals (Ancient North Eurasian ancestry) received ancestry from UP East Asian/Southeast Asian populations54, who then contributed substantially to EHG55. However, observing early Asian ancestry in Mesolithic Portugal and EHGs from Russia, at geographically opposite corners of west Eurasia, but not in central Europe, rules out the possibility that ancestry similar to Tianyuan was transmitted through the EHG–WHG admixture cline observed in Mesolithic Europe56 (Fig. (Fig.5b).5b). On the contrary, this result supports the idea of genetic continuity from (at least) the LGM to the Mesolithic in southern Iberia, while other pre- and post-LGM population expansions diluted much of the subtle signal in most other parts of Europe.
The East Eurasian/Tianyuan component among the Ancient North Eurasians also correlates with the presence of haplogroup P-M45, which in turn gave rise to R (and Q) among the ANE and Paleo-Siberians. P-M45 became dominant through a founder effect during the formation of the ANE, and later R clades spreaded via drift and via ANE geneflow to other West Eurasians. Its parent clade, P* as well as sister clades P2 and P3 are confined primarily to Southeast Asia, specifically Basal East Asian groups correlating with Hoabinhian-like geneflow. The direct ancestral clade to P-M45, P-295 was found among an Andamanese individual, while the oldest P clade (P-PF5850 or P*) was found among a Hoabinhian-rich Jehai individual. Other P clades are found among the Aeta and various Southeast Asian groups in low to medium amounts, with a peak in the Philippines. Up-stream clade K2b was found among the Tianyuan specimen.
ANE-mediated Tianyuan-like ancestry as well as additional deep East Eurasian ancestry is also evident among the Mesolithic and Neolithic Iranians (Iran_N & Iran_Meso).
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.
While older models needed quite high East Eurasian input for Iran_N:
The improved model (including a deep local West Eurasian source; WEC2), results in a lower East Eurasian component, mainly via ANE, but also via a remainder IUP/EEC source:
Based on the availabe data, and the specific Y chromosome variation among Iran_N and later populations, it is reasonable to link both J and G clades to WEC/WEC2-like ancestry, the major contributor for all modern West Eurasians. R2 can be attributed to the ANE component, while clades such as K1 (LT) or H2 may have been introduced by their deep East Eurasian component (deep IUP or even AASI-like). This is evident in that all other K clades, K2a, K2b, K2c, K2d and K2e are nested within East Eurasian lineages. R2 correlates with the ANE-ancestry among Iran_N and is also found among WSHG-like groups.
Basics about the IUP aka “East Eurasian” wave(s) based on archaeologic and material culture data:
The Initial Upper Paleolithic (also IUP, c. 50,000–40,000 BP) covers the first stage of the Upper Paleolithic, during which modern human populations expanded throughout Eurasia.
The Initial Upper Paleolithic corresponds to the spread of a particular techno-complex in Eurasia, to which possibly relates the European Châtelperronian. It is associated with a specific type of stone blade technology:
[Their] … expansion (linked to IUP in Eurasia) can be dated earlier than 45 ka as proposed by Zwyns et al. (2019), and here we propose it to be a wider phenomenon that populated the broad geographic area between Mediterranean Levant (Marks and Kaufman 1983; Boëda and Bonilauri 2006; Kuhn et al. 2009; Leder 2017; Kadowaki et al. 2021), East Europe (Richter et al. 2008; Fewlass et al. 2020; Hublin et al. 2020), Siberia-Mongolia (Zwyns et al. 2012; Derevianko et al. 2013; Kuhn 2019; Zwyns and Lbova 2019; Zwyns et al. 2019; Rybin et al. 2020), and East Asia (Boëda et al. 2013; Morgan et al. 2014; Peng et al. 2020) in <5 kyr, reaching as far South as Papua New Guinea before 38 ka, and which eventually died out in Europe after repeated admixtures with Neanderthals (Bacho Kiro and Oase1 being two notable examples) (fig. 2B). In Western Europe, in the same timeframe, this interaction has been suggested as a trigger for the development of Chatelperronian material culture (Roussel et al. 2016). Among these features the most notable is the presence of rock art at ~40 kya in Sulawesi, Indonesia86, compatible in age with the oldest European art (41–35 kya)87,88; as well as the innovative usage of projectile weapons, recorded in Europe89,90,91, the Levant92, and South Asia93.
While Ancient East Eurasians spreaded the IUP material culture, it itself was not a homogenous static technology, but displayed regional differences, based on the divergence patterns and environmental conditions:
Currently, the IUP appears as a highly variable and, in some places, a long-lasting phenomenon. This raises questions regarding the definition of the IUP concept and the cultural unity of this phenomenon. More broadly, it forces us to consider whether the shared elements of material culture reflect common cultural descent (i.e. dispersal) or convergence.
Microlithic industry of pleistocene antiquity in South Asia, such as at Jurreru Valley at around 35000 years ago, Mehtakheri at around 44000 years ago, Patne before 25000 years ago, Buddha Pushkar at around 28000 years ago, Middle Son Valley beginning 47000 years ago, and Kana at around 42000 years ago, but also the one at Batadomba lena and microlithic industry found at different stratigraphic layers at the cave of Fa Hien Lena in Sri Lanka, represent IUP industies along the Southern route, relevant for modern East Eurasians (a possible secondary hub for the main EEC lineages).
the earliest microlith assemblage in South Asia (48,000–45,000 cal. years BP), located in tropical rainforest on the island of Sri Lanka. Between c. 48–45,000 to 4,000 cal. years BP, despite a long stratigraphic hiatus, technological processes of production and raw material choices show clear continuity, implying a long-term stable adaptation in this part of the world.
IUP material culture is also observed along a Northern route into Central Asia and Southern Siberia as well as southeastern Europe. Those may be in part linked to the dispersal of the deep IUP Ust’Ishim-like groups, and in the case of the Tibetan plateau, the Tibetan Ghost lineage. Contact between those and the Southern route are evident in Northern China and the Mongolia region since at least 30,000 years ago.
In East Asia, it was primarily Core and Flake tools, as found in the Tianyuan Cave, and widely distributed in East and Mainland Southeast Asia, together with a version of Hoabinhian tools. Those arose via adapted versions of the Southern route material culture.
The appearance of a large tool industry using quartz sandstone gravel in southern East China about 50–40 kaBP cal means that human groups in southern China employing this industry had moved north and spread into East China. This is thought to reflect the migration to FE Eurasia of basal East Eurasians, who were diffused via the southern route reconstructed by genomic analysis (Fig.1; Fig.2).
Those came into later contact to northern IUP types:
About 44–40 kaBP cal, along with the migration of human groups, an IUP industry spread from the west. However, in FE Eurasia, with the exception of the southern Korean Peninsula, the IUP industry remained rare. This IUP industry in the Korean Peninsula was not the one that diffused eastward and reached the Korean Peninsula directly. Rather, it is thought that it was the IUP industry which was accepted by the local human group inhabiting regions surrounding the Korean Peninsula such as NE China, the Russian Far East and eastern Siberia, and was transformed in this process. And it is thought that this industry diffused to the Korean Peninsula with the migration of human groups. Therefore, even assuming some human groups bearing an IUP industry had migrated from the west and entered FE Eurasia, such instances appear to have been extremely limited.
In the Early UP (40–28 kaBP cal), industries became increasingly regionalized, reflecting the establishment and regionalization of human groups bearing these industries in various regions of FE Eurasia. At the same time, technical and cultural elements such as small blade technology and personal ornamentation propagated and spread within FE Eurasia through contact with human groups in surrounding areas and between various regional groups within FE Eurasia. In addition, the oldest assemblages in the Japanese Archipelago appeared for the first time in southwestern Paleo-Honshu Island. Because those assemblages are identified with the denticulate tool industry, it is believed that human groups bearing this industry migrated from an area centering on East China and the southern Korean Peninsula to southwestern Paleo-Honshu Island via Kyushu, with the lithic industry disseminating accordingly. The movements of this industry and human groups in the Early UP reflect the colonization and regional grouping of basal East Eurasians who had moved north from southern China into various regions of FE Eurasia during the final Middle Paleolithic and Initial UP.
For that, see KATO Shinji “Upper Paleolithic human dispersals and cultural diffusions in Eastern Eurasia”.
The lack of IUP tools in Southeast Asia and Oceania may be partly explained by the environmental conditions, although IUP tools have been found in Queensland and New South Wales (Australia).
Long-term lithic technological stability from the Late Pleistocene to the Holocene in tropical contexts is also potentially seen in Southeast Asia. In the territories between Thailand, south China, Vietnam and northwest of Sumatra, the Hoabinhian techno-complex persisted from ~43 to 4 ka [107–110,112–115]. This industry is characterised by plain pebbles, with partially ground edges, choppers, chopping tools, unmodified flakes and the Sumatralith, an oval cobble unilaterally retouched, and short-axes made of transversally fractured tabular cobbles that are also unilaterally retouched [116]. Although the evidence is scarce, probably due to preservation bias, bone points were also documented in the Hoabinhian toolkit after 22 ka [22].
In Europe, IUP-affilated material culture can be found among the Oase and Bacho Kiro IUP remains. The Initial Upper Paleolithic corresponds to the spread of a particular techno-complex in Eurasia, to which possibly relates the European Châtelperronian. But the later Aurignacian complex (Protoaurignacian and Early Aurignacian) with its famous Cave art seems to correspond to another, later, human wave which spread through the Levant area (Ancient West Eurasians during the UP period).
That way, the spread of IUP-affilated and UP-affilated material cultures largelly fit the expansion waves of Ancient East Eurasians and Ancient West Eurasians respectively.
Possible phenotype characteristics:
Based on shared characteristics of the AASI and Basal East Asian groups, a “default” phenotype of Ancient East Eurasians, or at least of the East Eurasian Core (EEC) may have been close to that:
It is not a large step to get to the regional “Australoid” phenotypes among Australasians, nor to the regional “Mongoloid” phenotypes of Neo-East Asians. Just some drift, and for Neo-East Asians light skin and straight hair, evident in the selective pressure they underwent during their northwards dispersal, and finally among the ANEA branch in Northeast Asia.
In comparison, the forensic reconstruction of the (deep IUP) Oase 2 specimen:
I hope this up-to-date summary was an interesting read, and helped to clarify some open questions on East Eurasian phylogenetics and demographic history.
Thank you for reading. Jacob.