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Ancient East Eurasians

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The term Ancient East Eurasian, alternatively also known as East Eurasian or Eastern Eurasian, is used in population genomics to describe the genetic ancestry and phylogenetic relationship of diverse populations primarily living in the Asia-Pacific region, belonging to the "Eastern Eurasian clade" of human genetic diversity,[1][2][3][4][5][6] and which can be associated with the Initial Upper Paleolithic (IUP) wave, following the Out of Africa migration (>60kya).[4][6]

Dispersal

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Repetitive expansions into Eurasia from a population Hub OoA. Representative samples dated between 45 and 40 ka across Eurasia can be ascribed to a population movement with uniform genetic features and material culture consistent with an IUP affiliation.

Modern humans of the Initial Upper Paleolithic wave (IUP) are suggested to have expanded from a population hub through a star-like expansion pattern (>45kya), and are linked to the "East Eurasian" 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, and partly in 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 or Oase 2, are inferred to have 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.[7][8][9][10][11][12][13]

Ancient East Eurasians diverged from Ancient West Eurasians around 46,000 years ago, and started to diversify themselves 45,000 years ago.[14] This divergence most likely occurred in the Persian Plateau.[15]

 
Inferred model for the phylogenetic substructure of Eastern Eurasian populations.

Lineages

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Major East Eurasian ancestry lineages which contributed to modern human populations include the following:[8]

  • 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.
  • Ancient Ancestral South Indian lineage — refers to an ancestral population that primarily contributed to Indigenous 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 man.[16][17]
  • East and Southeast Asian lineage — 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.
 
Estimated ancestry components among selected modern populations per Changmai et al. (2022).[18]

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.[8] The Australasian lineage however received higher archaic admixture in the Oceania region, and may also harbor some small amounts of "xOoA" admixture from an earlier human dispersal, which did not contribute to any other human population. Alternatively, Australasians can be described as nearly equally admixture between a "Basal East Asian" source (represented by Tianyuan) and a deeper East Eurasian lineage not sampled yet.[7][1][8]: 11 

Traces of an unsampled deeply diverged East Eurasian lineage can be observed in the genome of ancient and modern inhabitants of the Tibetan Plateau. While modern Tibetans mostly derive their ancestry from a 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.[19][20]

Deeper IUP-associated East Eurasian lineages have been associated with the remains of the Ust'-Ishim man from Siberia, and the Oase and Bacho Kiro cave specimens in southeastern Europe, and represent early inland migrations, deeply diverged from all other East Eurasian populations. These deep East Eurasian populations did not contribute to later Eurasian populations, except small contributions to the Goyet Caves specimen of Europe. The exact substructure and relationship between these deeper East Eurasian lineages is not well resolved yet.[7][21]

References

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  1. ^ a b Lipson, Mark; Reich, David (2017). "A working model of the deep relationships of diverse modern human genetic lineages outside of Africa". Molecular Biology and Evolution. 34 (4): 889–902. doi:10.1093/molbev/msw293. ISSN 0737-4038. PMC 5400393. PMID 28074030.
  2. ^ Skoglund, Pontus; Mathieson, Iain (31 August 2018). "Ancient Genomics of Modern Humans: The First Decade". Annual Review of Genomics and Human Genetics. 19 (1): 381–404. doi:10.1146/annurev-genom-083117-021749. ISSN 1527-8204. PMID 29709204. S2CID 19933330.
  3. ^ Zhang, Ming; Fu, Qiaomei (1 June 2020). "Human evolutionary history in Eastern Eurasia using insights from ancient DNA". Current Opinion in Genetics & Development. Genetics of Human Origin. 62: 78–84. doi:10.1016/j.gde.2020.06.009. ISSN 0959-437X. PMID 32688244. S2CID 220671047.
  4. ^ a b Vallini, Leonardo; Pagani, Luca (2022). "The future of the Eurasian past: highlighting plotholes and pillars of human population movements in the Late Pleistocene". Journal of Anthropological Sciences. 100 (100): 231–241. doi:10.4436/JASS.10013. ISSN 1827-4765. PMID 36565457.
  5. ^ Nägele, Kathrin; Rivollat, Maite; Yu, He; Wang, Ke (2022). "Ancient genomic research - From broad strokes to nuanced reconstructions of the past". Journal of Anthropological Sciences. 100 (100): 193–230. doi:10.4436/jass.10017. PMID 36576953.
  6. ^ a b Vallini, Leonardo; Zampieri, Carlo; Shoaee, Mohamed Javad; Bortolini, Eugenio; Marciani, Giulia; Aneli, Serena; Pievani, Telmo; Benazzi, Stefano; Barausse, Alberto; Mezzavilla, Massimo; Petraglia, Michael D.; Pagani, Luca (25 March 2024). "The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal". Nature Communications. 15 (1): 1882. Bibcode:2024NatCo..15.1882V. doi:10.1038/s41467-024-46161-7. ISSN 2041-1723. PMC 10963722. PMID 38528002. ... and the split between EEC and WEC, with the former leaving the Hub18, 46 kya (allowing the time for them to reach Ust'Ishim and Bacho Kiro by ~45 kya).
  7. ^ a b c Vallini et al. 2022 (4 July 2022). "Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa". Retrieved 16 April 2023.{{cite web}}: CS1 maint: numeric names: authors list (link)
  8. ^ a b c d Yang, Melinda A. (6 January 2022). "A genetic history of migration, diversification, and admixture in Asia". Human Population Genetics and Genomics. 2 (1): 1–32. doi:10.47248/hpgg2202010001. ISSN 2770-5005.
  9. ^ Sato, Takehiro; Adachi, Noboru; Kimura, Ryosuke; Hosomichi, Kazuyoshi; Yoneda, Minoru; Oota, Hiroki; Tajima, Atsushi; Toyoda, Atsushi; Kanzawa-Kiriyama, Hideaki; Matsumae, Hiromi; Koganebuchi, Kae (1 September 2021). "Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan". Genome Biology and Evolution. 13 (9): evab192. doi:10.1093/gbe/evab192. ISSN 1759-6653. PMC 8449830. PMID 34410389. the southern migration wave seems to have diversified into the local populations in East Asia (defined in this paper as a region including China, Japan, Korea, Mongolia, Taiwan and Southeast Asia), and the northern wave, which probably runs through the Siberian and Eurasian steppe regions and mixed with the southern wave, probably in Siberia.
  10. ^ Osada, Naoki; Kawai, Yosuke (2021). "Exploring models of human migration to the Japanese archipelago using genome-wide genetic data". Anthropological Science. 129 (1): 45–58. doi:10.1537/ase.201215. S2CID 234247309. Via the southern route, ancestors of current Asian populations reached Southeast Asia and a part of Oceania around 70000–50000 years ago, probably through a coastal dispersal route (Bae et al., 2017). The oldest samples providing the genetic evidence of the northern migration route come from a high-coverage genome sequence of individuals excavated from the Yana RHS site in northeastern Siberia (Figure 2), which is about 31600 years old (Sikora et al., 2019).
  11. ^ Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; Allentoft, Morten E.; Sato, Takehiro; Korneliussen, Thorfinn; Chuinneagáin, Blánaid Ní; Matsumae, Hiromi; Koganebuchi, Kae; Schmidt, Ryan; Mizushima, Souichiro; Kondo, Osamu; Shigehara, Nobuo; Yoneda, Minoru; Kimura, Ryosuke (25 August 2020). "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations". Communications Biology. 3 (1): 437. doi:10.1038/s42003-020-01162-2. ISSN 2399-3642. PMC 7447786. PMID 32843717. Population genomic studies on present-day humans7,8 have exclusively supported the southern route origin of East Asian populations.
  12. ^ Aoki, Kenichi; Takahata, Naoyuki; Oota, Hiroki; Wakano, Joe Yuichiro; Feldman, Marcus W. (30 August 2023). "Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia". Proceedings of the Royal Society B: Biological Sciences. 290 (2005). doi:10.1098/rspb.2023.1262. ISSN 0962-8452. PMC 10465978. PMID 37644833. 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.
  13. ^ Demeter, Fabrice; Shackelford, Laura L.; Bacon, Anne-Marie; Duringer, Philippe; Westaway, Kira; Sayavongkhamdy, Thongsa; Braga, José; Sichanthongtip, Phonephanh; Khamdalavong, Phimmasaeng; Ponche, Jean-Luc; Wang, Hong; Lundstrom, Craig; Patole-Edoumba, Elise; Karpoff, Anne-Marie (4 September 2012). "Anatomically modern human in Southeast Asia (Laos) by 46 ka". Proceedings of the National Academy of Sciences. 109 (36): 14375–14380. Bibcode:2012PNAS..10914375D. doi:10.1073/pnas.1208104109. ISSN 0027-8424. PMC 3437904. PMID 22908291. Inferences from nuclear (51), Y chromosome (52), and mitochondrial genome (53) data support an early migration of modern humans out of Africa and into Southeast Asia using a southern route by at least 60 ka. Patterns of genetic variation in recent human populations (11, 54, 55) recognize Southeast Asia as an important source for the peopling of East Asia and Australasia via a rapid, early settlement.
  14. ^ Vallini, Leonardo; Zampieri, Carlo; Shoaee, Mohamed Javad; Bortolini, Eugenio; Marciani, Giulia; Aneli, Serena; Pievani, Telmo; Benazzi, Stefano; Barausse, Alberto; Mezzavilla, Massimo; Petraglia, Michael D.; Pagani, Luca (25 March 2024). "The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal". Nature Communications. 15 (1): 1882. Bibcode:2024NatCo..15.1882V. doi:10.1038/s41467-024-46161-7. ISSN 2041-1723. PMC 10963722. PMID 38528002. ... and the split between EEC and WEC, with the former leaving the Hub18, 46 kya (allowing the time for them to reach Ust'Ishim and Bacho Kiro by ~45 kya).
  15. ^ Vallini, Leonardo; Zampieri, Carlo; Shoaee, Mohamed Javad; Bortolini, Eugenio; Marciani, Giulia; Aneli, Serena; Pievani, Telmo; Benazzi, Stefano; Barausse, Alberto; Mezzavilla, Massimo; Petraglia, Michael D.; Pagani, Luca (25 March 2024). "The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal". Nature Communications. 15 (1): 1882. Bibcode:2024NatCo..15.1882V. doi:10.1038/s41467-024-46161-7. ISSN 2041-1723. PMC 10963722. PMID 38528002.
  16. ^ Yelmen, Burak; Mondal, Mayukh; Marnetto, Davide; Pathak, Ajai K; Montinaro, Francesco; Gallego Romero, Irene; Kivisild, Toomas; Metspalu, Mait; Pagani, Luca (5 April 2019). "Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations". Molecular Biology and Evolution. 36 (8): 1628–1642. doi:10.1093/molbev/msz037. ISSN 0737-4038. PMC 6657728. PMID 30952160.
  17. ^ Kusuma, Pradiptajati; Cox, Murray P.; Barker, Graeme; Sudoyo, Herawati; Lansing, J. Stephen; Jacobs, Guy S. (1 November 2023). "Deep ancestry of Bornean hunter-gatherers supports long-term local ancestry dynamics". Cell Reports. 42 (11): 113346. doi:10.1016/j.celrep.2023.113346. ISSN 2211-1247. PMID 37917587.
  18. ^ Changmai, Piya; Pinhasi, Ron; Pietrusewsky, Michael; Stark, Miriam T.; Ikehara-Quebral, Rona Michi; Reich, David; Flegontov, Pavel (29 December 2022). "Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st–3rd centuries CE". Scientific Reports. 12 (1): 22507. Bibcode:2022NatSR..1222507C. doi:10.1038/s41598-022-26799-3. ISSN 2045-2322. PMC 9800559. PMID 36581666.
  19. ^ Liu, Chi-Chun; Witonsky, David; Gosling, Anna; Lee, Ju Hyeon; Ringbauer, Harald; Hagan, Richard; Patel, Nisha; Stahl, Raphaela; Novembre, John; Aldenderfer, Mark; Warinner, Christina; Di Rienzo, Anna; Jeong, Choongwon (8 March 2022). "Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors". Nature Communications. 13 (1): 1203. Bibcode:2022NatCo..13.1203L. doi:10.1038/s41467-022-28827-2. ISSN 2041-1723. PMC 8904508. PMID 35260549. 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 Eurasian genetic diversity. This deep Eurasian lineage is likely to represent the Paleolithic genetic substratum of the Plateau populations.
  20. ^ Wang, Hongru; Yang, Melinda A.; Wangdue, Shargan; Lu, Hongliang; Chen, Honghai; Li, Linhui; Dong, Guanghui; Tsring, Tinley; Yuan, Haibing; He, Wei; Ding, Manyu; Wu, Xiaohong; Li, Shuai; Tashi, Norbu; Yang, Tsho (15 March 2023). "Human genetic history on the Tibetan Plateau in the past 5100 years". Science Advances. 9 (11): eadd5582. Bibcode:2023SciA....9D5582W. doi:10.1126/sciadv.add5582. ISSN 2375-2548. PMC 10022901. PMID 36930720.
  21. ^ Vallini, Pagani, Leonardo, Luca (December 2022). "The future of the Eurasian past: highlighting plotholes and pillars of human population movements in the Late Pleistocene". Journal of Anthropological Sciences. 100 (100): 231–241. doi:10.4436/JASS.10013. PMID 36565457.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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