East Eurasian phylogeny – Nov. 2024

While the phylogeny of East Eurasians is still not entirely clear, we have made significant improvements on our knowledge of Ancient East Eurasians and their diverging patterns. In this article we will try to summarize the availabe data as future reference for other posts.

Basically, we have a deep clade of an Initial Upper Paleolithic (IUP) lineage or lineages affilated with the Ust'Ishim specimen in Northern Central Asia, the Bacho Kiro and Oase specimens in southeastern Europe, and the Kara Bom site in the Altai and Baikal region, which diverged from "proper East Eurasians" (c. 48kya to 46kya) shortly after their divergence from "Ancient West Eurasians" (c.50kya to up to 55kya), thus sharing minimal drift with modern East Eurasians. – The four major modern East Eurasian branches, which have been termed as "East Eurasian Core" (EEC), are:

1. Australasians (Australo-Papuans)
2. Paleolithic Tibetans (ghost)
3. AASI/SAHG (Ancient South Asians)
4. East/Southeast Asians ("ESEA"; including the basal Asian Onge/Hoabinhians and the Tianyuan lineage)

The EEC is inferred to have used a "southern dispersal route" via South Asia into Southeastern Asia, and subsequently into Oceania, Siberia, and the Americas; giving rise to modern East Eurasian via a rapid dispersal and divergence. – In contrast, the IUP lineage(s) have used a "northern dispersal route", but went largely extinct, except some contributions to later Paleolithic Europeans and Northern Asian specimens.

While the northern "IUP" route is to a large extent associated with the distribution of "microblade" material culture, such as in the Ust'Ishim or Oase sites, the southern "EEC" route is mostly associated with core & flake material culture, next to some other regional microlith types. – A contact zone between microblades and core & flakes is evident in Northwestern China and the Mongolia region. The 40kya Tianyuan specimen was found in a core & flake site, representing one of its most northern extension. Core & flakes are also commonly found in East/Southeast Asia, South Asia, and Australia. Microblades later reappeared among Mesolithic Siberians and Americans, also entering northern Japan.

Below, the supposed migration patterns of Basal East Eurasians and derived groups:

The Northern IUP route:

The northern IUP lineage(s) represent the most basal East Eurasians, sharing only minimal evolutionary drift with contemporary East Eurasians. They used an inland route northwards and subsequently into Europe and Northern Asia/Siberia.

The northern IUP lienage(s) are represented by the Ust'Ishim, Oase, and Bacho Kiro specimens, as well as sites in Uzbekistan and Siberia.

After adding Kostenki14 as a key ancient European sample, we found that the 45 kyr old Ust’Ishim would fit better as a basal split along the branch leading to Tianyuan and Bacho Kiro (Supplementary Section 3.3, Supplementary Material online) (Supplementary fig. S2, Supplementary Material online). As noted in Supplementary Section 3.3, Supplementary Material online, however, alternative configurations are compatible with a trifurcation between Kostenki14, Ust’Ishim and the branch leading to Tianyuan and Bacho Kiro, despite the total score obtained when placing Ust’Ishim together with Tianyuan and Bacho Kiro seems to point to a small albeit nonnegligible evolutionary path shared among these three samples. ...the total score obtained when placing Ust’Ishim together with Tianyuan and Bacho Kiro seems to point to a small albeit nonnegligible evolutionary path shared among these three samples. ...the tree where Ust’Ishim is a sister of Tianyuan/Bacho Kiro (Figure S2.B), has the lowest final score and so is the most supported. ~Vallini et al. 2022/24 & Allentoft et al. 2024

Reconstruction of the Oase 2 specimen:

This northern IUP lineage went extinct, but contributed around 23–26% ancestry to the later GoyetQ116-1 specimen in Europe, as well as 10–30% ancestry to the Tianyuan specimen in Northern China. This is also evident in excess-affinity between the GoyetQ116-1 and the Tianyuan specimens, as well as the close proximity between northern IUP affilated microblade material culture and southern EEC core & flakes material culture.

The Southern EEC route:

The Southern EEC lineages populated, via a secondary hub in South Asia, the Asia-Pacific region, diversifying rapidly into the Australasian, AASI/SAHG, UP Tibetan, and ESEA lineages (Onge, Tianyuan, Ancient East Asian):

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. ~Aoki et al. 2023

The internal phylogenetic structure of the EEC lineages is not entirely clear. Based on genetic distance and inferred diverging patterns, it is reasonable to consider Australasians (Australo-Papuans) as deepest split within the EEC, which headed rapidly into Oceania. – The "residual EEC" subsequently diversified into the AASI/SAHG lineage which stayed in Southern Asia; the UP Tibetan ghost lineage which populated the Himalayan plateau; and the ESEA lineage which populated Southeast and Eastern Asia, with its deepest branches being Onge and Tianyuan. Ancient and modern East Asians form either a trifurication between Onge and Tianyuan, or can be modeled as roughly 79% Onge-like +21% Tianyuan, Tianyuan being accordingly 75% Onge-like + 25% northern IUP ancestry, fitting the close geographic position between the Tianyuan site and nearby IUP sites. One alternative model estimated roughly 49% Onge (Southern Basal East Asian) + 51% Tianyuan (Northern Basal East Asian) for modern East Asians (ANEA/ASEA).

Australasians (Australo-Papuan):

Australasians represent the deepest diverged lineage within the EEC, and split from orther EEC lineages (AASI/SAHG, UP Tibetan, and ESEA (Onge/Tianyuan) in South Asia or in-between South‐Southeast Asia. – Alternatively, Australasians can also be modeled as a lineage slightly basal to the EEC (43%) + proper EEC (57%); --> eg. 43% 'Basal East Eurasian' (sort of Proto-Australasian which trifuricated from the northern IUP and actuall EEC within the East Eurasian hub on the Persian plateau) + 57% EEC (presumably Onge/Tianyuan-like), see also Vallini et al. 2022 and 2024.

In 2017, the Reich laboratory already noted:

We also compared the quality of fit of full graph models (using the SGDP data) in which we added an extra admixture event between Ust’-Ishim and Australasians in either direction, with the hypothesis that if one of these models is correct, it should score better than the other. In both cases, the score improved by more than 11, but the two models had similar residual lists, and their log-likelihood scores only differed by ∼0.3. This would seem to indicate either that 1) the shared drift signal does not reflect a true admixture, 2) there was very evenly bidirectional gene flow, or 3) our model is not sufficiently powered to detect the true mixture source. Moreover, both graphs still had numerous other residuals involving Ust’-Ishim with Z-scores above 2 (up to Z  =  2.48 with Australasians admixed and Z  =  2.89 with Ust’-Ishim admixed).

Based on the rapid divergence model along the southern route, it is reasonable to describe Australasians as just a sister lineage to "residual EEC" lineages (with or without minimal geneflow from deeper sources as well as extra Denisovan input.

The Australasian lineage is primarily ancestral to modern Papuans, Melanesians and Aboriginal Australians. Aboriginal Australians and Papuans diverged from each other between 40–33kya, shortly after the peopling of Oceania/Sahul.

A deep Australasian component is also observed among the Aeta/Agta, a Philippines "Negrito" group. Australasian/Papuan-like ancestry also contributed (51%) to the genetic makeup of a Sulawesi hunter-gatherer specimen (Leang Panninge), with the remainder (49%) being made up by Basal Asian (Onge/Tianyuan-like) ancestry.

Modern Polynesians also derived around 20% ancestry from the Papuan genepool, with remainder being Ami/ASEA derived.

AASI/SAHG:

The AASI/SAHG lineage, which represents the ancestry of the first stable/long-term hunter-gatherers and peoples of the Indian subcontinent, formed around ~40,000 years BCe. It was found that the AASI/SAHG are distinct from Western Eurasian groups and have a closer genetic affinity with Ancient East Eurasians (such as Andamanese Onge or East Asian peoples). Based on this, it has been inferred that the AASI/SAHG lineage diverged from other Eastern Eurasian lineages, such as 'Australasians', 'Onge', and 'East/Southeast Asian people', during their southern route dispersal.

While Onge (Andamanese HG) or Eastern Siberian Paleolithic remains (Amur33K; a Tianyuan-like specimen) can be used as imperfect proxy for the AASI/SAHG as both have the same phylogenetic relationship to the non-West Eurasian-related ancestry of South Asians, likely due to shared EEC ancestry deeply in time, a better option is the non-West Eurasian ancestry extracted from South Indian tribal groups, such as the Paniya, Irula and Pulliyar tribes. ~Yelmen et al. 2019

The AASI/SAHG lineage represents a primary EEC lineage, next to Onge/Tianyuan.

UP Tibetan ghost:

The UP Tibetan ghost describes an East Eurasian/EEC lineage observed among modern inhabidants of the Himalayan plateau in low amounts. This lineage is inferred to be distinct from Ust'Ishim, Australasians, AASI, Onge and Tianyuan, thus representing a regional variation of Paleolithic East Eurasians.

...our results reject previously suggested sources of gene flow into the Tibetan lineage13,35,36, including deeply branching Eastern Eurasian lineages, such as the 45,000-year-old Ust'-Ishim individual from southern Siberia, the 40,000-year-old Tianyuan individual from northern China, and Hoabinhian/Onge-related lineages in southeast Asia (Supplementary Fig. 10), suggesting instead that it represents yet another unsampled lineage within early [East] Eurasian genetic diversity. This deep [East] Eurasian lineage is likely to represent the Paleolithic genetic substratum of the Plateau populations. ~Chi-Chun Liu et al. 2022 & Hongru Wang et al. 2023

ESEA (East Asian, Onge, Tianyuan):

The ESEA lineage represent a primary branch of the EEC, with its two most basal clades being Onge/Hoabinhian and Tianyuan. Ancient and modern East Asians fit either as trifurication from Onge and Tianyuan, or as admixture between both. Furthermore, Tianyuan displays evidence for geneflow from a Northern IUP lineage (BK_IUP-like) absent from Onge.

…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. ~Melinda A. Yang 2022 (also Boer et al. 2021, Tianyi Wang et al. 2021 etc.)

In 2017, the Reich laboratory already noted that Onge fit as a near-trifurcation with the Australasian and East Asian lineages (than excluding Tianyuan). The best-fitting arrangement features Onge and East Asians as a weak clade (⁠p~0.02). As the model reaches a second, only slightly inferior local optimum with Onge and Australasians as sister groups instead, a possibly admixture between two of the three lineages has been proposed. An admixture event in either Onge (between the Australasian and East Asian lineages) or Australasians (between the Onge and deep eastern Eurasian lineages) is likewise weakly significant. – By adding the basal Asian Tianyuan specimen, as well as the hypothetical Tibetan ghost and AASI/SAHG, the Onge form a clade with Tianyuan and East Asians, with the Tibetan ghost, AASI/SAHG, and Australasians being independent East Eurasian branches.

The ESEA lineage therefor includes Onge/Hoabinhians and Tianyuan/AR33k as the two most basal clades (dubbed "Basal Asian" or "Basal East Asian"), with AEA (Ancient East Asians) as derived lineage. The AEA further diversified into the Jomon lineage, the Longlin lineage, the ASEA (Ancient Southern East Asian) and the ANEA (Ancient Northern East Asian) lineages.

While AEA can be described as trifurication from Onge and Tianyuan, they alternatively can be modeled as admixture between those two.

Possible admixture models for ASEA/AEA:

right: 'Cameroon_SMA','Georgia_Kotias_UP.SG','China_AmurRiver_Paleolithic','Russia_UstIshim_IUP.DG','Papuan.DG','Irula.SG','Onge.SG'

target: China_Fujian_Qihe_Epipaleolithic.SG
left weight se z
Laos_Hoabinhian.SG 0.79 0.057 13.818
China_Tianyuan 0.21 0.057 3.665
p_value: 0.0149770443094482

ANEA could be modeled as ASEA+Tianyuan, fitting the replacement of Tianyuan/AR33k ancestry by ANEA ancestry, evident in the AR19k specimen and genetic continuity since than. (ANEA = 90% ASEA + 10% Tianyuan):

right: 'Cameroon_SMA','Georgia_Kotias_UP.SG','China_AmurRiver_Paleolithic','Russia_UstIshim_IUP.DG','Papuan.DG','Irula.SG','Onge.SG'

target: China_AmurRiver_LPaleolithic
left weight se z
Laos_Hoabinhian.SG 0.684 0.045 15.257
China_Tianyuan 0.316 0.045 7.053
p_value: 0.015745816005512

Subsequently, ASEA and ANEA ancestries expanded massively during the early to late Neolithic, becoming the dominant ancestries in Southeast Asia and Northeast Asia/Siberia respectively. – In East Asia itself, an admixture between roughly 2/3 ANEA and 1/3 ASEA gave rise to the Yellow River Neolithic ancestry, which became the dominant ancestry in Eastern Asia, including the Tibetan plateau.

"Basal Asian" Tianyuan-like ancestry became largely replaced, but contributed roughly or slightly more than 1/3 (29–36% or 34–47%) ancestry to "Ancient North Eurasians" (ANE/ANS), with the remainder being West Eurasian (UP European), who than significantly contributed to the formation of Native Americans (in tandem with a basal ANEA ancestry), to various ANE-rich West Siberian groups and to Eastern European hunter-gatherers (EHG or EEHG). This Tianyuan-affinity was still evident in excess affinity shared with EHG:

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. ~Villalba-Mouco et al. 2023

"Basal Asian" Onge/Hoabinhian-like ancestry is maximized among modern Andamanese peoples as well as Semang/Maniq tribals on the Malaysian peninsula. Hoabinhian-like ancestry also contributed around 30% to Laos/Vietnam Neolithic farmers associated with the dispersal of Austroasiatic languages.

Onge/Tianyuan-like ancestry contributed around 49% ancestry to the Leang Panninge hunter-gatherer specimen in southern Sulawesi, with the remainder being Papuan-related.

Conclusion

Our knowledge on the phylogenetic structure of East Eurasian significantly improved, granting us a better view on the peopling of the Asia-Pacific region.

So far, we know there are four major East Eurasian lineages (EEC) which rapidly diverged along the southern route into South–Southeast Asia: Australasian, UP Tibetan, AASI/SAHG, and ESEA (Onge/Tianyuan). Modern East Asians fit either as trifurication between Onge and Tianyuan, or as admixture between both, nested within the two deep ESEA branches.

A similar phylogenetic tree fitting with the above data has already been published by Mondal et al. 2019, also including archaic introgression events:

OOA origin of modern humans, with a Eurasian split between Europeans and the group comprising two subgroups, East Asians, Indian and Andamanese on one hand, and Papuans and Australians on the other.

Accordingly, our knowledge on the genetic history of the Asia-Pacific region has improved significantly. We are looking forward for further genetic data to improve the presented model.

One possible qpGraph model: