Secrets of the genomes of extinct hominins, or can paleogenomics answer the question: who are we, humans?

Nobel Prize in Physiology or Medicine 2022

Authors

DOI:

https://doi.org/10.15407/visn2022.12.003

Keywords:

Nobel Prize in Physiology or Medicine 2022, Svante Pääbo, human evolution, genome, hominins

Abstract

The Nobel Prize in Physiology or Medicine in 2022 was awarded to Swedish paleogeneticist, specialist in the field of evolutionary genetics, director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany) Professor Svante Pääbo for "for his discoveries concerning the genomes of extinct hominins and human evolution". Explaining the importance of S. Pääbo’s works, the Nobel Committee noted that "he developed methods for analysis and recovering of ancient DNA. In ancient bones, DNA degrades, becomes chemically modified, and is massively contaminated by contact with bacteria and humans handling the specimens. Using available technologies as they develop, S. Pääbo created his own methods for refined analysis of ancient DNA".

References

Physiology or Medicine. 2022 Citation Laureates. https://clarivate.com/citation-laureates/physiology-or-medicine-2022/

Press release: The Nobel Prize in Physiology or Medicine 2022. https://www.nobelprize.org/prizes/medicine/2022/press-release/

Svante Pääbo. Wikipedia. https://en.wikipedia.org/wiki/Svante_Pääbo

Hedestam G.K. Discoveries concerning the genomes of extinct hominins and human evolution. https://www.nobelprize.org/prizes/medicine/2022/advanced-information/

Zukerkandl E., Pauling L. Molecules as documents of evolutionary history. J. Theor. Biol. 1965. 8(2): 357—366. https://doi.org/10.1016/0022-5193(65)90083-4

Pääbo S. Molecular cloning of Ancient Egyptian mummy DNA. Nature. 1985. 314(6012): 644—645. https://doi.org/10.1038/314644a0

Cann R.L., Stoneking M., Wilson A.C. Mitochondrial DNA and human evolution. Nature. 1987. 325(6099): 31—36. https://doi.org/10.1038/325031a0

Paabo S., Wilson A.C. Polymerase chain reaction reveals cloning artefacts. Nature. 1988. 334(6181): 387—388. https://doi.org/10.1038/334387b0

Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Pääbo S., Villablanca F.X., Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA. 1989. 86(16): 6196—6200. https://doi.org/10.1073/pnas.86.16.6196

Poinar H.N., Höss M., Bada J.L., Pääbo S. Amino acid racemization and the preservation of ancient DNA. Science. 1996. 272(5263): 864—866. https://doi.org/10.1126/science.272.5263.864

Mooallemjan J. Neanderthals were people, too. https://www.nytimes.com/2017/01/11/magazine/neanderthals-were-people-too.html

Krings M., Stone A., Schmitz R.W., Krainitzki H., Stoneking M., Pääbo S. Neandertal DNA sequences and the origin of modern humans. Cell. 1997. 90(1): 19—30. https://doi.org/10.1016/s0092-8674(00)80310-4

Lander E.S., Linton L.M., Birren B., 253 co-authors; International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001. 409(6822): 860—921. https://doi.org/10.1038/35057062

Nurk S., Koren S., Rhie A., 96 co-authors, Phillippy A.M. The complete sequence of a human genome. Science. 2022. 376(6588): 44—53. https://doi.org/10.1126/science.abj6987

Venter J.C., Adams M.D., Myers E.W., 270 co-authors, Zhu X. The sequence of the human genome. Science. 2001. 291(5507): 1304—1351. https://doi.org/10.1126/science.1058040

Margulies M., Egholm M., Altman W.E., 52 co-authors, Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005. 437(7057): 376—380. https://doi.org/10.1038/nature03959

Green R.E., Krause J., Briggs A.W., 52 co-authors, Pääbo S. A draft sequence of the Neandertal genome. Science. 2010. 328(5979): 710—722. https://doi.org/10.1126/science.1188021

Krause J., Fu Q., Good J.M., Viola B., Shunkov M.V., Derevianko A.P., Pääbo S. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature. 2010. 464(7290): 894—897. https://doi.org/10.1038/nature08976

Meyer M., Kircher M., Gansauge M.T., 30 co-authors, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012. 338(6104): 222—226. https://doi.org/10.1126/science.122434

Fu Q., Hajdinjak M., Moldovan O.T., 12 coauthors, Pääbo S. An early modern human from Romania with a recent Neanderthal ancestor. Nature. 2015. 524(7564): 216—219. https://doi.org/10.1038/nature14558

Fu Q., Li H., Moorjani P., 24 coauthors, Pääbo S. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature. 2014. 514(7523): 445—449. https://doi.org/10.1038/nature13810

Callaway E. Modern human genomes reveal our inner Neanderthal. https://www.nature.com/articles/nature.2014.14615

Gibbons A. Modern human females and male Neandertals had trouble making babies. Here’s why. https://www.science.org/content/article/modern-human-females-and-male-neandertals-had-trouble-making-babies-here-s-why

Uthmeier T. On the trail of the last Neanderthals. https://www.fau.eu/2013/06/05/news/research/on-the-trail-of-the-last-neanderthals/

Prüfer K., Racimo F., Patterson N., 41 co-authors, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014. 505(7481): 43—49. https://doi.org/10.1038/nature12886

Krause J., Lalueza-Fox C., Orlando L., Enard W., Green R.E., Burbano H.A., Hublin J.J., Hänni C., Fortea J., de la Rasilla M., Bertranpetit J., Rosas A., Pääbo S. The derived FOXP2 variant of modern humans was shared with Neandertals. Curr. Biol. 2007. 17(21): 1908—1912. https://doi.org/10.1016/j.cub.2007.10.008

Huerta-Sánchez E., Jin X., Asan, 23 coauthors, Nielsen R. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature. 2014. 512(7513): 194—197. https://doi.org/10.1038/nature13408

Dannemann M., Kelso J. The contribution of Neanderthals to phenotypic variation in modern humans. Am. J. Hum. Genet. 2017. 101(4): 578—589. https://doi.org/10.1016/j.ajhg.2017.09.010

Ding Q., Hu Y., Xu S., Wang J., Jin L. Neanderthal introgression at chromosome 3p21.31 was under positive natural selection in East Asians. Mol. Biol. Evol. 2014. 31(3): 683—695. https://doi.org/10.1093/molbev/mst260

Dannemann M., Andrés A.M., Kelso J. Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human Toll-like receptors. Am. J. Hum. Genet. 2016. 98(1): 22—33. https://doi.org/10.1016/j.ajhg.2015.11.015

Mendez F.L., Watkins J.C., Hammer M.F. A haplotype at STAT2 introgressed from neanderthals and serves as a candidate of positive selection in Papua New Guinea. Am. J. Hum. Genet. 2012. 91(2): 265—274. https://doi.org/10.1016/j.ajhg.2012.06.015

Mendez F.L., Watkins J.C., Hammer M.F. Neandertal origin of genetic variation at the cluster of OAS immunity genes. Mol. Biol. Evol. 2013. 30(4): 798—801. https://doi.org/10.1093/molbev/mst004

Zeberg H., Pääbo S. A genomic region associated with protection against severe COVID-19 is inherited from Neandertals. Proc. Natl. Acad. Sci. USA. 2021. 118(9): e2026309118. https://doi.org/10.1073/pnas.2026309118

Zeberg H., Pääbo S. The major genetic risk factor for severe COVID-19 is inherited from Neanderthals. Nature. 2020. 587(7835): 610—612. https://doi.org/10.1038/s41586-020-2818-3

Zimmer C. Man’s genome from 45,000 years ago is reconstructed. https://www.nytimes.com/2014/10/23/science/research-humans-interbred-with-neanderthals.html

Meyer M., Arsuaga J.L., de Filippo C., Nagel S., Aximu-Petri A., Nickel B., Martínez I., Gracia A., Bermúdez de Castro J.M., Carbonell E., Viola B., Kelso J., Prüfer K., Pääbo S. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature. 2016. 531(7595): 504—507. https://doi.org/10.1038/nature17405

Genomes Project Consortium, Abecasis G.R., Altshuler D., Auton A., Brooks L.D., Durbin R.M., Gibbs R.A., Hurles M.E., McVean G.A. A map of human genome variation from population-scale sequencing. Nature. 2010. 467(7319): 1061—1073. https://doi.org/10.1038/nature09534

Mallick S., Li H., Lipson M., 75 co-authors, Reich D. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016. 538(7624): 201—206. https://doi.org/10.1038/nature18964

Moraes F., Góes A. A decade of human genome project conclusion: Scientific diffusion about our genome knowledge. Biochem. Mol. Biol. Educ. 2016. 44(3): 215—223. https://doi.org/10.1002/bmb.20952

Davis N. Ancient Siberia was home to previously unknown humans, say scientists. https://www.theguardian.com/science/2019/jun/05/ancient-siberia-was-home-to-previously-unknown-humans-say-scientists

Wade L. Mummy genomes reveal just how catastrophic European contact was for New World. https://www.science.org/content/article/mummy-genomes-reveal-just-how-catastrophic-european-contact-was-new-world

Price M. Oldest cousin of Native Americans found in Russia. https://www.science.org/content/article/oldest-cousin-native-americans-found-russia

Balter M. Mysterious Indo-European homeland may have been in the steppes of Ukraine and Russia. https://www.science.org/content/article/mysterious-indo-european-homeland-may-have-been-steppes-ukraine-and-russia

Yamnaya culture. Wikipedia. https://en.wikipedia.org/wiki/Yamnaya_culture

Pennisi E. Humans are still evolving – and we can watch it happen. https://www.science.org/content/article/humans-are-still-evolving-and-we-can-watch-it-happen

Gibbons A. How Europeans evolved white skin. https://www.science.org/content/article/how-europeans-evolved-white-skin

Gramling C. The ‘hobbit’ was a separate species of human, new dating reveals. https://www.science.org/content/article/hobbit-was-separate-species-human-new-dating-reveals

Gibbons A. New human species discovered. https://www.science.org/doi/10.1126/science.349.6253.1149

Gibbons A. First DNA extracted from an ancient African skeleton shows widespread mixing with Eurasians. https://www.science.org/content/article/first-dna-extracted-ancient-african-skeleton-shows-widespread-mixing-eurasians

Price M. Africans, too, carry Neanderthal genetic legacy. Science. 2020. 367(6477): 497. https://doi.org/10.1126/science.367.6477.497

Marchant J. Egyptian mummies yield genetic secrets. https://www.nature.com/news/egyptian-mummies-yield-genetic-secrets-1.12793

Gibbons A. DNA from cave dirt tells tale of how some Neanderthals disappeared. https://www.science.org/content/article/dna-cave-dirt-tells-tale-how-some-neanderthals-disappeared

Warren M. Biggest Denisovan fossil yet spills ancient human's secrets. Nature. 2019. 569(7754): 16—17. https://doi.org/10.1038/d41586-019-01395-0

Bahrampour T. They considered themselves white, but DNA tests told a more complex story. https://www.washingtonpost.com/local/social-issues/they-considered-themselves-white-but-dna-tests-told-a-more-complex-story/2018/02/06/16215d1a-e181-11e7-8679-a9728984779c_story.html

Vasiljevic N., Lim M., Humble E., Seah A., Kratzer A., Morf N.V., Prost S., Ogden R. Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification. Forensic Sci. Int. Genet. 2021. 53: 102493. https://doi.org/10.1016/j.fsigen.2021.102493

Ponce de León M.S., Bienvenu T., Marom A., Engel S., Tafforeau P., Alatorre Warren J.L., Lordkipanidze D., Kurniawan I., Murti D.B., Suriyanto R.A., Koesbardiati T., Zollikofer C.P.E. The primitive brain of early Homo. Science. 2021. 372(6538): 165—171. https://doi.org/10.1126/science.aaz0032

Richerson P.J., Gavrilets S., de Waal F.B.M. Modern theories of human evolution foreshadowed by Darwin's Descent of Man. Science. 2021. 372(6544): eaba3776. https://doi.org/10.1126/science.aba3776

Dolgin E. Evolutionary sprint made us human. https://www.science.org/content/article/evolutionary-sprint-made-us-human

Pennisi E. Virus fighter may have played a key role in human evolution. https://www.science.org/content/article/virus-fighter-may-have-played-key-role-human-evolution

Reardon S. Step aside CRISPR, RNA editing is taking off. Nature. 2020. 578(7793): 24—27. https://doi.org/10.1038/d41586-020-00272-5

Grover N. Swedish geneticist wins Nobel medicine prize for decoding ancient DNA. https://www.reuters.com/world/svante-paabo-wins-2022-nobel-prize-medicine-2022-10-03/

Published

2022-12-29