Ust'-Ishim man

''Ust'-Ishim man is the term given to the 45,000-year-old remains of one of the early modern humans to inhabit western Siberia.[1] The fossil is notable in that it had intact DNA which permitted the complete sequencing of its genome, the oldest modern human genome to be so decoded.[1]

The remains consist of a single bone—left femur—of a male hunter-gatherer, which was discovered in 2008[2] protruding from the bank of the Irtysh River by Nikolai Peristov, a Russian sculptor who specialises in carving mammoth ivory.[1] Peristov showed the fossil to a forensic investigator who suggested that it might be of human origin.[1] The fossil was named after the Ust'-Ishim District of Siberia where it had been discovered.[1]

Genome sequencing

The fossil was examined by paleoanthropologists in the Max Planck Institute for Evolutionary Anthropology, located in Leipzig, Germany. Carbon dating showed that the fossil dates back to 45,000 years ago, making it the oldest human fossil to be so dated.[1] Scientists found the DNA intact and were able to sequence the complete genome of Ust'-Ishim man to contemporary standards of quality.[1] Though genomes have been sequenced of hominins pre-dating Ust'-Ishim man, this is the oldest modern human genome to be sequenced to date.[3]

Y-DNA and mtDNA

Ust'-Ishim man belongs to Y-DNA haplogroup K2a*, which is defined by the SNP M2308. The two subclades of K2a known from living men, the rare K2a1-Y28299[4] and the very common NO-M214, belong to a branch distinct from Ust'-Ishim man's.[5] In the original paper, he was classified only as Haplogroup K2 (the clade ancestral to K2a). It may be inferred that K2a emerged in or near South Asia approximately 47,000 years BP – i.e. K2 is estimated to have originated in South East Asia, about 47,000–55,000 BP,[6] while its secondary descendant NO* is believed to have emerged approximately 38,000 to 47,000 BP.[5][7][8]

He belonged to mitochondrial DNA haplogroup R*, differing from the root sequence of R by a single mutation.

Both of these haplogroups and descendant subclades are now found among populations throughout Eurasia, Oceania and The Americas, although no direct descendants of Ust Ishim man's specific lineages are known from modern populations.

Examination of the sequenced genome indicates that Ust'-Ishim man lived at a point in time (270,000 to 45,000 years ago) between the first wave of anatomically modern humans that migrated out of Africa and the divergence of that population into distinct populations, in terms of autosomal DNA in different parts of Eurasia.[2] Consequently, Ust'-Ishim man is not more closely related to the first two major migrations of Homo Sapiens eastward from Africa into Asia: a group that migrated along the coast of South Asia, or a group that moved north-east through Central Asia.[9] When compared to other ancient remains, Ust'-Ishim man is more closely related, in terms of autosomal DNA to Tianyuan man, found near Beijing and dating from 42,000 to 39,000 years ago; Mal'ta boy (or MA-1), a child who lived 24,000 years ago along the Bolshaya Belaya River near today's Irkutsk in Siberia, or; La Braña man – a hunter-gatherer who lived in La Braña (modern Spain) about 8,000 years ago.[3][10][11]

Relationship with Neanderthals

Analysis of modern human genomes reveals that humans interbred with Neanderthals between 37,000 and 86,000 years ago,[12] resulting in the DNA of humans outside Africa containing between 1.5 and 2.1 percent DNA of Neanderthal origin.[13] Neanderthal DNA in modern humans occurs in broken fragments; however, the Neanderthal DNA in Ust'-Ishim man occurs in clusters, indicating that Ust'-Ishim man lived in the immediate aftermath of the genetic interchange.[3] The genomic sequencing of Ust'-Ishim man has led to refinement of the estimated date of mating between the two hominin species to between 52,000 and 58,000 years ago.[3]

No relationship between Denisovans and the Ust'-Ishim man has been checked, although Denisovans have some descendants in Oceania and Asia.

Relationship with modern human populations

Ust’-Ishim is more closely related to modern East Asian and Oceanian populations than to modern West Eurasian populations, such as the current residents of the Ust’-Ishim area.[3] Modern West Eurasians are more closely related to other ancient remains.[14]

In a 2016 study, modern Tibetans were identified as the modern population that has the most alleles in common with Ust'-Ishim man.[15] According to a 2017 study, "Siberian and East Asian populations shared 38% of their ancestry"[16] with Ust’-Ishim man.

References

1. Callaway, Ewen & Nature magazine (23 October 2014). "45,000-Year-Old Man's Genome Sequenced". Scientific American. Retrieved 24 October 2014.
2. "Earliest modern human sequenced". Max-Planck-Gesellschaft. 22 October 2014. Retrieved 30 October 2014.
3. Wade, Lizzie (22 October 2014). "Oldest human genome reveals when our ancestors had sex with Neandertals". Science. American Association for the Advancement of Science. Retrieved 24 October 2014.
4. https://yfull.com/tree/K-Y28299/
5. Poznik, G. D; Xue, Y; Mendez, F. L; Willems, T. F; Massaia, A; Wilson Sayres, M. A; Ayub, Q; McCarthy, S. A; Narechania, A; Kashin, S; Chen, Y; Banerjee, R; Rodriguez-Flores, J. L; Cerezo, M; Shao, H; Gymrek, M; Malhotra, A; Louzada, S; Desalle, R; Ritchie, G. R; Cerveira, E; Fitzgerald, T. W; Garrison, E; Marcketta, A; Mittelman, D; Romanovitch, M; Zhang, C; Zheng-Bradley, X; Abecasis, G. R; et al. (2016). "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences". Nature Genetics. 48 (6): 593–599. doi:10.1038/ng.3559. PMC 4884158. PMID 27111036.
6. Karafet, Tatiana M; Mendez, Fernando L; Sudoyo, Herawati; Lansing, J Stephen; Hammer, Michael F (2014). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia". European Journal of Human Genetics. 23 (3): 369–73. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
7. YFull Haplogroup YTree v5.06 at 25 September 2017
8. Karmin, Monika; Saag, Lauri; Vicente, Mário; et al. (2015). "", "A recent bottleneck of Y chromosome diversity coincides with a global change in culture". Genome Research. 25 (4): 459–466. doi:10.1101/gr.186684.114. PMC 4381518. PMID 25770088.
9. Qiaomei Fu, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L. F. Johnson, Ayinuer Aximu-Petri, Kay Prüfer, Cesare de Filippo, Matthias Meyer, Nicolas Zwyns, Domingo C. Salazar-García, Yaroslav V. Kuzmin, Susan G. Keates, Pavel A. Kosintsev, Dmitry I. Razhev, Michael P. Richards, Nikolai V. Peristov, Michael Lachmann, Katerina Douka, Thomas F. G. Higham, Montgomery Slatkin, Jean-Jacques Hublin, David Reich, Janet Kelso, T. Bence Viola & Svante Pääbo (23 October 2014). "Genome sequence of a 45,000-year-old modern human from western Siberia". Nature. 514 (7523): 445–449. doi:10.1038/nature13810. hdl:10550/42071. PMC 4753769. PMID 25341783.CS1 maint: multiple names: authors list (link)
10. Balter, Michael (25 October 2013). "Ancient DNA Links Native Americans With Europe". Science. 342 (6157): 409–410. doi:10.1126/science.342.6157.409. PMID 24159019. Retrieved 25 October 2014.
11. Balter, Michael (26 January 2014). "How Farming Reshaped Our Genomes". Science. American Association for the Advancement of Science. Retrieved 25 October 2014.
12. Choi, Charles Q. (4 October 2012). "Humans Broke Off Neanderthal Sex After Discovering Eurasia". LiveScience. Retrieved 25 October 2014.
13. Choi, Charles Q. (18 December 2013). "Neanderthal Woman's Genome Reveals Unknown Human Lineage". LiveScience. Retrieved 25 October 2014.
14. Gibbons, Ann (4 September 2014). "Three-part ancestry for Europeans". Science. American Association for the Advancement of Science. Archived from the original on 11 October 2014. Retrieved 30 October 2014.
15. Lu, Dongsheng; et al. (September 1, 2016). "Ancestral Origins and Genetic History of Tibetan Highlanders". The American Journal of Human Genetics. 99: 7.
16. Wong, Emily H. M.; Khrunin, Andrey; Nichols, Larissa; Pushkarev, Dmitry; Khokhrin, Denis; Verbenko, Dmitry; Evgrafov, Oleg; Knowles, James; Novembre, John (2017-01-01). "Reconstructing genetic history of Siberian and Northeastern European populations". Genome Research. 27 (1): 1–14. doi:10.1101/gr.202945.115. ISSN 1088-9051. PMC 5204334. PMID 27965293.

Bibliography

• Qiaomei Fu, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L. F. Johnson, Ayinuer Aximu-Petri, Kay Prüfer, Cesare de Filippo, Matthias Meyer, Nicolas Zwyns, Domingo C. Salazar-García, Yaroslav V. Kuzmin, Susan G. Keates, Pavel A. Kosintsev, Dmitry I. Razhev, Michael P. Richards, Nikolai V. Peristov, Michael Lachmann, Katerina Douka, Thomas F. G. Higham, Montgomery Slatkin, Jean-Jacques Hublin, David Reich, Janet Kelso, T. Bence Viola & Svante Pääbo (23 October 2014). "Genome sequence of a 45,000-year-old modern human from western Siberia". Nature. 514 (7523): 445–449. doi:10.1038/nature13810. hdl:10550/42071. PMC 4753769. PMID 25341783.CS1 maint: multiple names: authors list (link)