From North Asia to South America: Tracing the longest human migration through genomic sequencing

• 成果类型: Article
• 署名作者: Gusareva, Elena S.; Ghosh, Amit Gourav; Kharkov, Vladimir N.; Khor, Seik-Soon; Zarubin, Aleksei; Moshkov, Nikita; Kalsi, Namrata; Ratan, Aakrosh; Heinle, Cassie E.; Cooke, Niall; Bravi, Claudio M.; Smolnikova, Marina V.; Tereshchenko, Sergey Yu.; Kasparov, Eduard W.; Khitrinskaya, Irina; Marusin, Andrey; Razhabov, Magomed O.; Golubenko, Maria V.; Swarovskaya, Maria; Kolesnikov, Nikita A.; Vagaitseva, Ksenia V.; Eremina, Elena R.; Sukhomyasova, Aitalina; Shtygasheva, Olga; Panicker, Deepa; Ang, Poh Nee; Lee, Choou Fook; Koh, Yanqing; Leong, See Ting; Park, Changsook; Lohar, Sachin R.; Yap, Zhei Hwee; Ng, Soo Guek; Dacanay, Justine; Drautz-Moses, Daniela I.; Ramli, Nurul Adilah Binte; Tokunaga, Katsushi; Mcgonigle, Ian; Danjoh, Inaho; Moreno-Estrada, Andres; Tajima, Atsushi; Tanabe, Hideyuki; Nakamura, Yukio; Nakagome, Shigeki; Tatarinova, Tatiana V.; Stepanov, Vadim A.; Schuster, Stephan C.; Kim, Hie Lim
• 署名单位: Nanyang Technological University; Nanyang Technological University; Russian Academy of Sciences; Tomsk National Research Medical Center; Research Institute of Medical Genetics - Tomsk; Japan Institute for Health Security (JIHS); National Center for Global Health & Medicine - Japan; HUN-REN; HUN-REN Biological Research Center; University of Virginia; Trinity College Dublin; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET); Russian Academy of Sciences; Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences; Research Institute for Medical Problems in the North, Siberian Branch, Russian Academy of Sciences; Siberian Branch of the Russian Academy of Sciences; Amirkhanov Institute of Physics, Daghestan Federal Research Centre of the Russian Academy of Sciences; Buryat State University; North-Eastern Federal University in Yakutsk; Katanov Khakass State University; Nanyang Technological University; Nanyang Technological University; Maynooth University; Tohoku University; Kanazawa University; Kanazawa University; Graduate University for Advanced Studies - Japan; RIKEN; University of La Verne; Nanyang Technological University
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-11354
• DOI: 10.1126/science.adk5081
• 发表日期: 2025-05-15
• 关键词: inflammatory-bowel-disease; acute respiratory syndrome; recent positive selection; virus type-i; genetic history; population; identification; expression; admixture; ancestry

摘要

INTRODUCTION: During the late Pleistocene, humans expanded across Eurasia and eventually migrated to the Americas. Those who reached Patagonia, at the southern tip of South America, completed the longest migration out of Africa. RATIONALE: The extent of basal divergences, admixture, and degrees of isolation among Indigenous North Eurasian and Native South American populations remain debated, with most insights derived from genome-wide genotyping data. This study aims to deepen our understanding of the ancient dynamics that shaped contemporary populations in North Eurasia and the Americas. By using large-scale whole-genome sequencing of 1537 individuals from 139 ethnic groups in these regions, we examined population structures, elucidated prehistoric migrations, and explored the influence of past environmental factors on the diversification of human populations. RESULTS: Advances in large-scale genomic sequencing have considerably enhanced our understanding of the genetic ancestry of human populations across North Eurasia and South America. Our analysis reveals that all contemporary Siberians, as well as some Northeast Europeans and Central Asians, share ancestry with the West Siberian groups, represented by the Kets and Nenets. Their ancestors were widespread across Siberia 10,000 years ago (ya), but now these groups face population decline by 73.6% and are becoming a minority. The populations of west Beringia, including the Koryaks, Inuit, and Luoravetlans, are the most genetically distinct from other Siberians. These groups have adapted to Arctic conditions with genetic variations related to lipid metabolism, thermogenesis, sensory perception, and the regulation of reproductive and immune functions. We were not able to identify a specific Siberian group as the direct ancestors of Native Americans owing to deep divergence and limited genetic continuity. However, west Beringian populations remain closely related to Native Americans. Koryaks and Inuit show and 28% Native American ancestry, respectively, owing to gene flow between 700 and 5100 ya. We estimated the split time of Native South Americas into Amazonians, Andeans, Chaco Amerindians, and Patagonians to have occurred 13,900 to 10,000 ya. Migration and settlement across the continent led to population isolations due to geographic boundaries and a reduction in their genetic diversity, particularly affecting immune genes, such as the human leukocyte antigen (HLA) genes. Over the past 10,000 years, all four Native South American lineages have experienced population declines ranging from 38 to 80%. This dramatic decline, combined with the loss of traditional lifestyles, cultural practices, and languages, has pushed some Indigenous communities, such as the Kaw & eacute;sqar, to the brink of extinction. CONCLUSION: The migration to an uninhabited continent of South America through the narrow Isthmus of Panama resulted in a founder effect among Native South Americans, leading to reduced genetic diversity compared with that of Indigenous populations of North Eurasia. Over 13,900 years, geographic barriers within the continent further isolated Indigenous groups, subsequently reducing genetic diversity. These groups faced a profound challenge with the arrival of European colonists in the 1600s, who introduced new adversities that threatened their long-standing endurance.