Analyses of the 2022 Nobel Prize in Physiology or Medicine: Paleogenomics

References

• Bruner, E., G. Manzi, and J. L. Arsuaga. 2003. Encephalization and allometric trajectories in the genus Homo: Evidence from the Neandertal and modern lineages. Proceedings of the National Academy of Sciences 100 (26):15335–40. doi:10.1073/pnas.2536671100.
   PubMed Web of Science ®Google Scholar
• Castellano, S., G. Parra, F. A. Sanchez-Quinto, F. Racimo, M. Kuhlwilm, M. Kircher, S. Sawyer, Q. Fu, A. Heinze, B. Nickel, et al. 2014. Patterns of coding variation in the complete exomes of three Neandertals. Proceedings of the National Academy of Sciences 111 (18):6666–71. doi:10.1073/pnas.1405138111.
   PubMed Web of Science ®Google Scholar
• Dannemann, M., A. M. Andrés, and J. Kelso. 2016. Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human toll-like receptors. American Journal of Human Genetics 98 (1):22–33. doi:10.1016/j.ajhg.2015.11.015.
   PubMed Web of Science ®Google Scholar
• Dannemann, M., and J. Kelso. 2017. The contribution of Neanderthals to phenotypic variation in modern humans. American Journal of Human Genetics 101 (4):578–89. doi:10.1016/j.ajhg.2017.09.010.
   PubMed Web of Science ®Google Scholar
• Drancourt, M., G. Aboudharam, M. Signoli, O. Dutour, and D. Raoult. 1998. Detection of 400-year-old Yersinia pestis DNA in human dental pulp: An approach to the diagnosis of ancient septicemia. Proceedings of the National Academy of Sciences 95 (21):12637–40. doi:10.1073/pnas.95.21.12637.
   PubMed Web of Science ®Google Scholar
• Ellinghaus, D., F. Degenhardt, L. Bujanda, M. Buti, A. Albillos, P. Invernizzi, J. Fernández, D. Prati, G. Baselli, R. Asselta, et al. 2020. Genomewide association study of severe Covid-19 with respiratory failure. New England Journal of Medicine 383 (16):1522–34. doi:10.1056/NEJMoa2020283.
   PubMed Web of Science ®Google Scholar
• Fondation Louis-Jeantet. n.d. Professor Svante Pääbo winner of the 2005 Louis-Jeantet prize for medecine. Accessed November 24, 2022. https://www.jeantet.ch/en/prix-louis-jeantet/laureats/2005-en/professeur-svante-paabo/.
   Google Scholar
• Fricker, E. J., M. Spigelman, and C. R. Fricker. 1997. The detection of Escherichia coli DNA in the ancient remains of lindow man using the polymerase chain reaction. Letters in Applied Microbiology 24 (5):351–54. doi:10.1046/j.1472-765X.1997.00066.x.
   PubMed Web of Science ®Google Scholar
• Fu, Q., M. Hajdinjak, O. T. Moldovan, S. Constantin, S. Mallick, P. Skoglund, N. Patterson, N. Rohland, I. Lazaridis, B. Nickel, et al. 2015. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524 (7564):216–19. doi:10.1038/nature14558.
   PubMed Web of Science ®Google Scholar
• Fu, Q., H. Li, P. Moorjani, F. Jay, S. Slepchenko, A. A. Bondarev, P. L. F. Johnson, A. A. Petri, K. Prüfer, C. de Filippo, et al. 2014. The complete genome sequence of a 45,000 year old modern human from Western Siberia. Nature 514:445–49. doi:10.1038/nature13810.
   PubMed Web of Science ®Google Scholar
• Gaeta, R. 2021. Ancient DNA and paleogenetics: Risks and potentiality. Pathologica 113 (2):141–46. doi:10.32074/1591-951X-146.
   PubMed Web of Science ®Google Scholar
• Gernaey, A. M., D. E. Minnikin, M. S. Copley, R. A. Dixon, J. C. Middleton, and C. A. Roberts. 2001. Mycolic acids and ancient DNA confirm an osteological diagnosis of tuberculosis. Tuberculosis 81 (4):259–65. doi:10.1054/tube.2001.0295.
   PubMed Web of Science ®Google Scholar
• Green, R. E., J. Krause, A. W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, J. H.-Y. Fritz, et al. 2010. Draft sequence of the Neandertal genome. Science 328 (5979):710–22. doi:10.1126/science.1188021.
   PubMed Web of Science ®Google Scholar
• Hajdinjak, M., Q. Fu, A. Hübner, M. Petr, F. Mafessoni, S. Grote, P. Skoglund, V. Narasimham, H. Rougier, I. Crevecoeur, et al. 2018. Reconstructing the genetic history of late Neanderthals. Nature 555 (7698):652–56. doi:10.1038/nature26151.
   PubMed Web of Science ®Google Scholar
• Higham, T., K. Douka, R. Wood, C. B. Ramsey, F. Brock, L. Basell, M. Camps, A. Arrizabalaga, J. Baena, C. Barroso-Ruíz, et al. 2014. The timing and spatiotemporal patterning of Neanderthal disappearance. Nature 512 (7514):306–09. doi:10.1038/nature13621.
   PubMed Web of Science ®Google Scholar
• Hublin, J. J. 2009. Origin of Neandertals. Proceedings of the National Academy of Sciences 106 (38):16022–27. doi:10.1073/pnas.0904119106.
   PubMed Web of Science ®Google Scholar
• Huerta-Sánchez, E., X. Jin, Z. Asan, B. Bianba, M. Peter, N. Vinckenbosch, Y. Liang, X. Yi, M. He, M. Somel, et al. 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512 (7513):194–97. doi:10.1038/nature13408.
   PubMed Web of Science ®Google Scholar
• Ko, K. H. 2016. Hominin interbreeding and the evolution of human variation. Journal of Biological Research 23 (17):1–9. doi:10.1186/s40709-016-0054-7.
   Web of Science ®Google Scholar
• Kocher, T. D., W. K. Thomas, A. Meyer, S. V. Edwards, S. Paabo, F. X. Villablanca, and A. C. Wilson. 1989. Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the United States of America 86 (16):6196–6200. doi:10.1073/pnas.86.16.6196.
   PubMed Web of Science ®Google Scholar
• Kolbert, E. 2011. Sleeping with the enemy. The New Yorker 87 (24):64–75. Accessed November 24, 2022. https://www.newyorker.com/magazine/2011/08/15/sleeping-with-the-enemy.
   Google Scholar
• Krause, J., Q. Fu, J. M. Good, B. Viola, M. V. Shunkov, A. P. Derevianko, and S. Pääbo. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464 (7290):894–97. doi:10.1038/nature08976.
   PubMed Web of Science ®Google Scholar
• Krings, M., A. Stone, R. W. Schmitz, H. Krainitzki, M. Stoneking, and S. Pääbo. 1997. Neandertal DNA sequences and the origin of modern humans. Cell 90 (1):19–30. doi:10.1016/S0092-8674(00)80310-4.
   PubMed Web of Science ®Google Scholar
• Mafessoni, F., S. Grote, C. de Filippo, V. Slon, K. A. Kolobova, B. Viola, S. V. Markin, M. Chintalapati, S. Peyregne, L. Skov, et al. 2020. A high-coverage Neandertal genome from Chagyrskaya Cave. Proceedings of the National Academy of Sciences 117 (26):15132–36. doi:10.1073/pnas.2004944117.
   PubMed Web of Science ®Google Scholar
• Max Planck Institute for Evolutionary Anthropology. 2022. Svante Pääbo. Accessed November 24, 2022. https://www.eva.mpg.de/genetics/staff/paabo/#c28042.
   Google Scholar
• Mays, S., and G. M. Taylor. 2003. A first prehistoric case of tuberculosis from Britain. International Journal of Osteoarchaeology 13 (4):189–96. doi:10.1002/oa.671.
   Web of Science ®Google Scholar
• Meyer, M., J. L. Arsuaga, C. de Filippo, S. Nagel, A. Aximu-Petri, B. Nickel, I. Martínez, A. Gracia, J. M. Bermúdez de Castro, E. Carbonell, et al. 2016. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 531 (7595):504–07. doi:10.1038/nature17405.
   PubMed Web of Science ®Google Scholar
• Meyer, M., M. Kircher, M.-T. Gansauge, H. Li, F. Racimo, S. Mallick, J. G. Schraiber, F. Jay, K. Prüfer, C. de Filippo, et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338 (6104):222–26. doi:10.1126/science.1224344.
   PubMed Web of Science ®Google Scholar
• Mikkelsen, T. S., L. W. Hillier, E. E. Eichler, M. C. Zody, D. B. Jaffe, S.-P. Yang, W. Enard, I. Hellmann, K. Lindblad-Toh, T. K. Altheide, et al. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (7055):69–87. doi:10.1038/nature04072.
   PubMed Web of Science ®Google Scholar
• NobelPrize.org. 2022. Advanced information. Nobel Media AB 2022. Accessed October 6, 2022. https://www.nobelprize.org/prizes/medicine/2022/advanced-information/.
   Google Scholar
• Pääbo, S. 1985. Preservation of DNA in ancient Egyptian mummies. Journal of Archaeological Science 12 (6):411–17. doi:10.1016/0305-4403(85)90002-0.
   Web of Science ®Google Scholar
• Pääbo, S. 1989. Ancient DNA: Extraction, characterization, molecular cloning, and enzymatic amplification. Proceedings of the National Academy of Sciences 86 (6):1939–43. doi:10.1073/pnas.86.6.1939.
   PubMed Web of Science ®Google Scholar
• Pääbo, S., R. G. Higuchi, and A. C. Wilson. 1989. Ancient DNA and the polymerase chain reaction. The Journal of Biological Chemistry 264 (17):9709–12. doi:10.1016/S0021-9258(18)81710-0.
   PubMed Web of Science ®Google Scholar
• Pääbo, S., and A. C. Wilson. 1988. Polymerase chain reaction reveals cloning artefacts. Nature 334 (6181):387–88. doi:10.1038/334387b0.
   PubMed Web of Science ®Google Scholar
• Ponce de León, M. S., and C. P. E. Zollikofer. 2001. Neanderthal cranial ontogeny and its implications for late hominid diversity. Nature 412 (6846):534=538. doi:10.1038/35087573.
   PubMed Web of Science ®Google Scholar
• Prüfer, K., C. de Filippo, S. Grote, F. Mafessoni, P. Korlević, M. Hajdinjak, B. Vernot, L. Skov, P. Hsieh, S. Peyrégne, et al. 2017. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358 (6363):655–58. doi:10.1126/science.aao1887.
   PubMed Web of Science ®Google Scholar
• Prüfer, K., F. Racimo, N. Patterson, F. Jay, S. Sankararaman, S. Sawyer, A. Heinze, G. Renaud, P. H. Sudmant, C. de Filippo, et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505 (7481):43–49. doi:10.1038/nature12886.
   PubMed Web of Science ®Google Scholar
• Raoult, D., G. Aboudharam, E. Crubézy, G. Larrouy, B. Ludes, and M. Drancourt. 2000. Molecular identification by “suicide PCR” of Yersinia pestis as the agent of medieval black death. Proceedings of the National Academy of Sciences 97 (23):12800–03. doi:10.1073/pnas.220225197.
   PubMed Web of Science ®Google Scholar
• Reich, D., B. Viola, S. Pääbo, R. E. Green, M. Kircher, J. Krause, N. Patterson, E. Y. Durand, A. W. Briggs, U. Stenzel, et al. 2010. Genetic history of an archaic hominin group from Denisova cave in Siberia. Nature 468 (7327):1053–60. doi:10.1038/nature09710.
   PubMed Web of Science ®Google Scholar
• Richards, M. P., and E. Trinkaus. 2009. Isotopic evidence for the diets of European Neanderthals and early modern humans. Proceedings of the National Academy of Sciences 106 (38):16034–39. doi:10.1073/pnas.0903821106.
   PubMed Web of Science ®Google Scholar
• Roberts, C., and S. Ingham. 2008. Using ancient DNA analysis in palaeopathology: A critical analysis of published papers, with recommendations for future work. International Journal of Osteoarchaeology 18 (6):600–13. doi:10.1002/oa.966.
   Web of Science ®Google Scholar
• Sankararaman, S., S. Mallick, M. Dannemann, K. Prüfer, J. Kelso, S. Pääbo, N. Patterson, and D. Reich. 2014. The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507 (7492):354–57. doi:10.1038/nature12961.
   PubMed Web of Science ®Google Scholar
• Sawyer, S., G. Renaud, B. Viola, J.-J. Hublin, M.-T. Gansauge, M. V. Shunkov, A. P. Derevianko, K. Prüfer, J. Kelso, and S. Pääbo. 2015. Nuclear and mitochondrial DNA sequences from two Denisovan individuals. Proceedings of the National Academy of Sciences 112 (51):15696–700. doi:10.1073/pnas.1519905112.
   PubMed Web of Science ®Google Scholar
• Schrenk, F. 2009. The Neanderthals. In Peoples of the ancient world, ed. F. Schrenk, S. Müller, and C. Hemm. Trans. P. G. Jestice, 1–178. London: Routledge.
   Google Scholar
• Slon, V., F. Mafessoni, B. Vernot, C. de Filippo, S. Grote, B. Viola, M. Hajdinjak, S. Peyrégne, S. Nagel, S. Brown, et al. 2018. The genome of the offspring of a Neanderthal mother and a Denisovan father. Nature 561 (7721):113–16. doi:10.1038/s41586-018-0455-x.
   PubMed Web of Science ®Google Scholar
• Slon, V., B. Viola, G. Renaud, M.-T. Gansauge, S. Benazzi, S. Sawyer, J.-J. Hublin, M. V. Shunkov, A. P. Derevianko, J. Kelso, et al. 2017. A fourth Denisovan individual. Science Advances. 3(7):e1700186. doi:10.1126/sciadv.1700186.
   PubMed Web of Science ®Google Scholar
• Smith, T. M., M. Toussaint, D. J. Reid, A. J. Olejniczak, and J.-J. Hublin. 2007. Rapid dental development in a middle paleolithic Belgian Neanderthal. Proceedings of the National Academy of Sciences 104 (51):20220–25. doi:10.1073/pnas.0707051104.
   PubMed Web of Science ®Google Scholar
• Steegmann, A. T., F. J. Cerny, and T. W. Holliday. 2002. Neandertal cold adaptation: Physiological and energetic factors. American Journal of Human Biology 14 (5):566–83. doi:10.1002/ajhb.10070.
   PubMed Web of Science ®Google Scholar
• Tattersall, I. 1999. The last Neanderthal: The rise, success, and mysterious extinction of our closest human relatives. Rev. ed. Boulder, CO: Westview Press.
   Google Scholar
• Vernot, B., E. I. Zavala, A. Gómez-Olivencia, Z. Jacobs, V. Slon, F. Mafessoni, F. Romagné, A. Pearson, M. Petr, N. Sala, et al. 2021. Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science 372 (6542):1–9. doi:10.1126/science.abf1667.
   Web of Science ®Google Scholar
• Villanea, F. A., and J. G. Schraiber. 2019. Multiple episodes of interbreeding between Neanderthal and modern humans. Nature Ecology & Evolution 3 (1):39–44. doi:10.1038/s41559-018-0735-8.
   PubMed Web of Science ®Google Scholar
• Weber, M., I. Hellmann, M. B. Stadler, L. Ramos, S. Pääbo, M. Rebhan, and D. Schübeler. 2007. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genetics 39 (4):457–466. doi:10.1038/ng1990.
   PubMed Web of Science ®Google Scholar
• Wiechmann, I., and G. Grupe. 2005. Detection of Yersinia pestis DNA in two early medieval skeletal finds from Aschheim (upper bavaria, 6th century A.D.). American Journal of Physical Anthropology 126 (1):48–55. doi:10.1002/ajpa.10276.
   PubMed Web of Science ®Google Scholar
• Wilshaw, A. 2018. Out of Africa hypothesis. In The international encyclopedia of biological anthropology. 1–7. University of Cambridge: Wiley Online Library, John Wiley & Sons, Ltd. doi:10.1002/9781118584538.ieba0357.
   Google Scholar
• Yang, M. A., and Q. Fu. 2018. Insights into modern human prehistory using ancient genomes. Trends in Genetics 34 (3):184–96. doi:10.1016/j.tig.2017.11.008.
   PubMed Web of Science ®Google Scholar
• Zagorski, N. 2006. Profile of Svante Pääbo. Proceedings of the National Academy of Sciences of the United States of America 103 (37):13575–77. doi:10.1073/pnas.0606596103.
   PubMed Web of Science ®Google Scholar
• Zeberg, H., and S. Pääbo. 2020. The major genetic risk factor for severe COVID-19 is inherited from Neanderthals. Nature 587 (7835):610–12. doi:10.1038/s41586-020-2818-3.
   PubMed Web of Science ®Google Scholar
• Zeberg, H., and S. Pääbo. 2021. A genomic region associated with protection against severe COVID-19 is inherited from Neandertals. Proceedings of the National Academy of Sciences 118 (9):1–5. doi:10.1073/pnas.2026309118.
   Web of Science ®Google Scholar