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5. Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors

Author

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, and Jeong, Choongwon

Subjects
Human Genome, Genetics, Adaptation, Physiological, Altitude, Genome, History, Ancient, Humans, Nepal, Tibet
Abstract

Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.

Published
2022

7. Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean

Author

Skourtanioti, Eirini, Ringbauer, Harald, Gnecchi Ruscone, Guido Alberto, Bianco, Raffaela Angelina, Burri, Marta, Freund, Cäcilia, Furtwängler, Anja, Gomes Martins, Nuno Filipe, Knolle, Florian, Neumann, Gunnar U., Tiliakou, Anthi, Agelarakis, Anagnostis, Andreadaki-Vlazaki, Maria, Betancourt, Philip, Hallager, Birgitta P., Jones, Olivia A., Kakavogianni, Olga, Kanta, Athanasia, Karkanas, Panagiotis, Kataki, Efthymia, Kissas, Konstantinos, Koehl, Robert, Kvapil, Lynne, Maran, Joseph, McGeorge, Photini J. P., Papadimitriou, Alkestis, Papathanasiou, Anastasia, Papazoglou-Manioudaki, Lena, Paschalidis, Kostas, Polychronakou-Sgouritsa, Naya, Preve, Sofia, Prevedorou, Eleni-Anna, Price, Gypsy, Protopapadaki, Eftychia, Schmidt-Schultz, Tyede, Schultz, Michael, Shelton, Kim, Wiener, Malcolm H., Krause, Johannes, Jeong, Choongwon, and Stockhammer, Philipp W.

Published
2023
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9. Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia

Author

Wang, Ke, Yu, He, Radzevičiūtė, Rita, Kiryushin, Yuriy F., Tishkin, Alexey A., Frolov, Yaroslav V., Stepanova, Nadezhda F., Kiryushin, Kirill Yu., Kungurov, Artur L., Shnaider, Svetlana V., Tur, Svetlana S., Tiunov, Mikhail P., Zubova, Alisa V., Pevzner, Maria, Karimov, Timur, Buzhilova, Alexandra, Slon, Viviane, Jeong, Choongwon, Krause, Johannes, and Posth, Cosimo

Published
2023
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10. Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

Author

Gelabert, Pere, Blazyte, Asta, Chang, Yongjoon, Fernandes, Daniel M., Jeon, Sungwon, Hong, Jin Geun, Yoon, Jiyeon, Ko, Youngmin, Oberreiter, Victoria, Cheronet, Olivia, Özdoğan, Kadir T., Sawyer, Susanna, Yang, Songhyok, Greytak, Ellen McRae, Choi, Hansol, Kim, Jungeun, Kim, Jong-Il, Jeong, Choongwon, Bae, Kidong, Bhak, Jong, and Pinhasi, Ron

Published
2022
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11. Ancient genomes reveal origin and rapid trans-Eurasian migration of 7th century Avar elites

Author

Gnecchi-Ruscone, Guido Alberto, Szécsényi-Nagy, Anna, Koncz, István, Csiky, Gergely, Rácz, Zsófia, Rohrlach, A.B., Brandt, Guido, Rohland, Nadin, Csáky, Veronika, Cheronet, Olivia, Szeifert, Bea, Rácz, Tibor Ákos, Benedek, András, Bernert, Zsolt, Berta, Norbert, Czifra, Szabolcs, Dani, János, Farkas, Zoltán, Hága, Tamara, Hajdu, Tamás, Jászberényi, Mónika, Kisjuhász, Viktória, Kolozsi, Barbara, Major, Péter, Marcsik, Antónia, Kovacsóczy, Bernadett Ny., Balogh, Csilla, Lezsák, Gabriella M., Ódor, János Gábor, Szelekovszky, Márta, Szeniczey, Tamás, Tárnoki, Judit, Tóth, Zoltán, Tutkovics, Eszter K., Mende, Balázs G., Geary, Patrick, Pohl, Walter, Vida, Tivadar, Pinhasi, Ron, Reich, David, Hofmanová, Zuzana, Jeong, Choongwon, and Krause, Johannes

Published
2022
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17. The genomic origins of the Bronze Age Tarim Basin mummies

Author

Zhang, Fan, Ning, Chao, Scott, Ashley, Fu, Qiaomei, Bjørn, Rasmus, Li, Wenying, Wei, Dong, Wang, Wenjun, Fan, Linyuan, Abuduresule, Idilisi, Hu, Xingjun, Ruan, Qiurong, Niyazi, Alipujiang, Dong, Guanghui, Cao, Peng, Liu, Feng, Dai, Qingyan, Feng, Xiaotian, Yang, Ruowei, Tang, Zihua, Ma, Pengcheng, Li, Chunxiang, Gao, Shizhu, Xu, Yang, Wu, Sihao, Wen, Shaoqing, Zhu, Hong, Zhou, Hui, Robbeets, Martine, Kumar, Vikas, Krause, Johannes, Warinner, Christina, Jeong, Choongwon, and Cui, Yinqiu

Published
2021
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18. Evidence for early dispersal of domestic sheep into Central Asia

Author

Taylor, William T. T., Pruvost, Mélanie, Posth, Cosimo, Rendu, William, Krajcarz, Maciej T., Abdykanova, Aida, Brancaleoni, Greta, Spengler, Robert, Hermes, Taylor, Schiavinato, Stéphanie, Hodgins, Gregory, Stahl, Raphaela, Min, Jina, Alisher kyzy, Saltanat, Fedorowicz, Stanisław, Orlando, Ludovic, Douka, Katerina, Krivoshapkin, Andrey, Jeong, Choongwon, Warinner, Christina, and Shnaider, Svetlana

Published
2021
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19. Genome of a middle Holocene hunter-gatherer from Wallacea

Author

Carlhoff, Selina, Duli, Akin, Nägele, Kathrin, Nur, Muhammad, Skov, Laurits, Sumantri, Iwan, Oktaviana, Adhi Agus, Hakim, Budianto, Burhan, Basran, Syahdar, Fardi Ali, McGahan, David P., Bulbeck, David, Perston, Yinika L., Newman, Kim, Saiful, Andi Muhammad, Ririmasse, Marlon, Chia, Stephen, Hasanuddin, Pulubuhu, Dwia Aries Tina, Suryatman, Supriadi, Jeong, Choongwon, Peter, Benjamin M., Prüfer, Kay, Powell, Adam, Krause, Johannes, Posth, Cosimo, and Brumm, Adam

Published
2021
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20. A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe

Author

Jeong, Choongwon, Wang, Ke, Wilkin, Shevan, Taylor, William Timothy Treal, Miller, Bryan K., Bemmann, Jan H., Stahl, Raphaela, Chiovelli, Chelsea, Knolle, Florian, Ulziibayar, Sodnom, Khatanbaatar, Dorjpurev, Erdenebaatar, Diimaajav, Erdenebat, Ulambayar, Ochir, Ayudai, Ankhsanaa, Ganbold, Vanchigdash, Chuluunkhuu, Ochir, Battuga, Munkhbayar, Chuluunbat, Tumen, Dashzeveg, Kovalev, Alexey, Kradin, Nikolay, Bazarov, Bilikto A., Miyagashev, Denis A., Konovalov, Prokopiy B., Zhambaltarova, Elena, Miller, Alicia Ventresca, Haak, Wolfgang, Schiffels, Stephan, Krause, Johannes, Boivin, Nicole, Erdene, Myagmar, Hendy, Jessica, and Warinner, Christina

Published
2020
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22. Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus

Author

Skourtanioti, Eirini, Erdal, Yilmaz S., Frangipane, Marcella, Balossi Restelli, Francesca, Yener, K. Aslıhan, Pinnock, Frances, Matthiae, Paolo, Özbal, Rana, Schoop, Ulf-Dietrich, Guliyev, Farhad, Akhundov, Tufan, Lyonnet, Bertille, Hammer, Emily L., Nugent, Selin E., Burri, Marta, Neumann, Gunnar U., Penske, Sandra, Ingman, Tara, Akar, Murat, Shafiq, Rula, Palumbi, Giulio, Eisenmann, Stefanie, D’Andrea, Marta, Rohrlach, Adam B., Warinner, Christina, Jeong, Choongwon, Stockhammer, Philipp W., Haak, Wolfgang, and Krause, Johannes

Published
2020
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25. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Mallick, Swapan, Li, Heng, Lipson, Mark, Mathieson, Iain, Gymrek, Melissa, Racimo, Fernando, Zhao, Mengyao, Chennagiri, Niru, Nordenfelt, Susanne, Tandon, Arti, Skoglund, Pontus, Lazaridis, Iosif, Sankararaman, Sriram, Fu, Qiaomei, Rohland, Nadin, Renaud, Gabriel, Erlich, Yaniv, Willems, Thomas, Gallo, Carla, Spence, Jeffrey P, Song, Yun S, Poletti, Giovanni, Balloux, Francois, van Driem, George, de Knijff, Peter, Romero, Irene Gallego, Jha, Aashish R, Behar, Doron M, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Moreno-Estrada, Andres, Posukh, Olga L, Balanovska, Elena, Balanovsky, Oleg, Karachanak-Yankova, Sena, Sahakyan, Hovhannes, Toncheva, Draga, Yepiskoposyan, Levon, Tyler-Smith, Chris, Xue, Yali, Abdullah, M Syafiq, Ruiz-Linares, Andres, Beall, Cynthia M, Di Rienzo, Anna, Jeong, Choongwon, Starikovskaya, Elena B, Metspalu, Ene, Parik, Jüri, Villems, Richard, Henn, Brenna M, Hodoglugil, Ugur, Mahley, Robert, Sajantila, Antti, Stamatoyannopoulos, George, Wee, Joseph TS, Khusainova, Rita, Khusnutdinova, Elza, Litvinov, Sergey, Ayodo, George, Comas, David, Hammer, Michael F, Kivisild, Toomas, Klitz, William, Winkler, Cheryl A, Labuda, Damian, Bamshad, Michael, Jorde, Lynn B, Tishkoff, Sarah A, Watkins, W Scott, Metspalu, Mait, Dryomov, Stanislav, Sukernik, Rem, Singh, Lalji, Thangaraj, Kumarasamy, Pääbo, Svante, Kelso, Janet, Patterson, Nick, and Reich, David

Subjects
Human Genome, Genetics, Animals, Australia, Black People, Datasets as Topic, Genetic Variation, Genetics, Population, Genome, Human, Genomics, History, Ancient, Human Migration, Humans, Mutation Rate, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Phylogeny, Racial Groups, Sequence Analysis, DNA, Species Specificity, Time Factors, General Science & Technology
Abstract

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Published
2016

26. Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc

Author

Jeong, Choongwon, Ozga, Andrew T, Witonsky, David B, Malmström, Helena, Edlund, Hanna, Hofman, Courtney A, Hagan, Richard W, Jakobsson, Mattias, Lewis, Cecil M, Aldenderfer, Mark S, Di Rienzo, Anna, and Warinner, Christina

Subjects
Genetics, Altitude, Gene Flow, Genome, Human, Humans, Nepal, Paleodontology, Phylogeography, Sequence Analysis, DNA, Tibet, Ancient DNA, population genetics, high altitude, EGLN1, EPAS1
Abstract

The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04×-7.25×, mean 2.16×) and mitochondrial genomes (20.8×-1,311.0×, mean 482.1×) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations.

Published
2016

27. The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

Author

Kim, Kwondo, Kwon, Taehyung, Dessie, Tadelle, Yoo, DongAhn, Mwai, Okeyo Ally, Jang, Jisung, Sung, Samsun, Lee, SaetByeol, Salim, Bashir, Jung, Jaehoon, Jeong, Heesu, Tarekegn, Getinet Mekuriaw, Tijjani, Abdulfatai, Lim, Dajeong, Cho, Seoae, Oh, Sung Jong, Lee, Hak-Kyo, Kim, Jaemin, Jeong, Choongwon, Kemp, Stephen, Hanotte, Olivier, and Kim, Heebal

Published
2020
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28. A genomic investigation on the origins of the Korean brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphasidae).

Author

Jeong, Suyeon, Gill, Haechan, Yu, Taeuk, Na, Jinho, Ki, Hohun, Koo, Hyun‐Na, Kim, Gil‐Hah, Kim, Dongyoung, Jo, Sung‐Hwan, Jeong, Choongwon, and Cho, Soowon

Subjects
NILAPARVATA lugens, SOUTHEAST Asians, GENETIC drift, GENE flow, POPULATION dynamics, HEMIPTERA
Abstract

Nilaparvata lugens, the brown planthopper (BPH), is a serious pest species. BPHs cause significant damage to rice plants in Korea as well as other countries in East and Southeast Asia. As BPHs cannot survive winter in Korea, they annually migrate into Korea from foreign countries. The BPHs found in Korea are believed to originate from China, but most BPHs in China are also known to originate from Southeast Asia. To understand the origin of Korean BPHs, we conducted a genotyping‐by‐sequencing (GBS) study. We sampled BPHs from five locations in Korea and five countries in Southeast Asia and analyzed the GBS and sequencing results using various methods based on the f statistics and admixture graph analyses. We confirmed that the domestic BPHs shared a greater genetic drift than the BPHs from Southeast Asian populations over several years, implying that a continuous genetic substratum of Korea exists. This genetic substratum is genetically closer to BPHs from the southern part (Thailand and Cambodia) of Southeast Asia than to BPHs from the northern part (Bhutan, Myanmar and Laos) of Southeast Asia. In addition, direct gene flows from Southeast Asia seem possible, so Korea is considered a hotspot where diverse BPH populations mix. Therefore, the origin of Korean BPHs extends beyond China and as far as southern Southeast Asia. This result will help to understand and control the population dynamics of the Korean BPH population. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

Author

Jeong, Choongwon, Wilkin, Shevan, Amgalantugs, Tsend, Bouwman, Abigail S., Taylor, William Timothy Treal, Hagan, Richard W., Bromage, Sabri, Tsolmon, Soninkhishig, Trachsel, Christian, Grossmann, Jonas, Littleton, Judith, Makarewicz, Cheryl A., Krigbaum, John, Burri, Marta, Scott, Ashley, Davaasambuu, Ganmaa, Wright, Joshua, Irmer, Franziska, Myagmar, Erdene, Boivin, Nicole, Robbeets, Martine, Rühli, Frank J., Krause, Johannes, Frohlich, Bruno, Hendy, Jessica, and Warinner, Christina

Published
2018

33. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations

Author

van de Loosdrecht, Marieke, Bouzouggar, Abdeljalil, Humphrey, Louise, Posth, Cosimo, Barton, Nick, Aximu-Petri, Ayinuer, Nickel, Birgit, Nagel, Sarah, Talbi, El Hassan, El Hajraoui, Mohammed Abdeljalil, Amzazi, Saaïd, Hublin, Jean-Jacques, Pääbo, Svante, Schiffels, Stephan, Meyer, Matthias, Haak, Wolfgang, Jeong, Choongwon, and Krause, Johannes

Published
2018

36. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America

Author

Flegontov, Pavel, Altınışık, N. Ezgi, Changmai, Piya, Rohland, Nadin, Mallick, Swapan, Adamski, Nicole, Bolnick, Deborah A., Broomandkhoshbacht, Nasreen, Candilio, Francesca, Culleton, Brendan J., Flegontova, Olga, Friesen, T. Max, Jeong, Choongwon, Harper, Thomas K., Keating, Denise, Kennett, Douglas J., Kim, Alexander M., Lamnidis, Thiseas C., Lawson, Ann Marie, Olalde, Iñigo, Oppenheimer, Jonas, Potter, Ben A., Raff, Jennifer, Sattler, Robert A., Skoglund, Pontus, Stewardson, Kristin, Vajda, Edward J., Vasilyev, Sergey, Veselovskaya, Elizaveta, Hayes, M. Geoffrey, O’Rourke, Dennis H., Krause, Johannes, Pinhasi, Ron, Reich, David, and Schiffels, Stephan

Published
2019
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37. The genetic history of admixture across inner Eurasia

Author

Jeong, Choongwon, Balanovsky, Oleg, Lukianova, Elena, Kahbatkyzy, Nurzhibek, Flegontov, Pavel, Zaporozhchenko, Valery, Immel, Alexander, Wang, Chuan-Chao, Ixan, Olzhas, Khussainova, Elmira, Bekmanov, Bakhytzhan, Zaibert, Victor, Lavryashina, Maria, Pocheshkhova, Elvira, Yusupov, Yuldash, Agdzhoyan, Anastasiya, Koshel, Sergey, Bukin, Andrei, Nymadawa, Pagbajabyn, Turdikulova, Shahlo, Dalimova, Dilbar, Churnosov, Mikhail, Skhalyakho, Roza, Daragan, Denis, Bogunov, Yuri, Bogunova, Anna, Shtrunov, Alexandr, Dubova, Nadezhda, Zhabagin, Maxat, Yepiskoposyan, Levon, Churakov, Vladimir, Pislegin, Nikolay, Damba, Larissa, Saroyants, Ludmila, Dibirova, Khadizhat, Atramentova, Lubov, Utevska, Olga, Idrisov, Eldar, Kamenshchikova, Evgeniya, Evseeva, Irina, Metspalu, Mait, Outram, Alan K., Robbeets, Martine, Djansugurova, Leyla, Balanovska, Elena, Schiffels, Stephan, Haak, Wolfgang, Reich, David, and Krause, Johannes

Published
2019
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39. Ancient genomes from northern China suggest links between subsistence changes and human migration

Author

Ning, Chao, Li, Tianjiao, Wang, Ke, Zhang, Fan, Li, Tao, Wu, Xiyan, Gao, Shizhu, Zhang, Quanchao, Zhang, Hai, Hudson, Mark J., Dong, Guanghui, Wu, Sihao, Fang, Yanming, Liu, Chen, Feng, Chunyan, Li, Wei, Han, Tao, Li, Ruo, Wei, Jian, Zhu, Yonggang, Zhou, Yawei, Wang, Chuan-Chao, Fan, Shengying, Xiong, Zenglong, Sun, Zhouyong, Ye, Maolin, Sun, Lei, Wu, Xiaohong, Liang, Fawei, Cao, Yanpeng, Wei, Xingtao, Zhu, Hong, Zhou, Hui, Krause, Johannes, Robbeets, Martine, Jeong, Choongwon, and Cui, Yinqiu

Published
2020
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42. Language continuity despite population replacement in Remote Oceania

Author

Posth, Cosimo, Nägele, Kathrin, Colleran, Heidi, Valentin, Frédérique, Bedford, Stuart, Kami, Kaitip W., Shing, Richard, Buckley, Hallie, Kinaston, Rebecca, Walworth, Mary, Clark, Geoffrey R., Reepmeyer, Christian, Flexner, James, Maric, Tamara, Moser, Johannes, Gresky, Julia, Kiko, Lawrence, Robson, Kathryn J., Auckland, Kathryn, Oppenheimer, Stephen J., Hill, Adrian V. S., Mentzer, Alexander J., Zech, Jana, Petchey, Fiona, Roberts, Patrick, Jeong, Choongwon, Gray, Russell D., Krause, Johannes, and Powell, Adam

Published
2018
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43. Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions

Author

Wang, Chuan-Chao, Reinhold, Sabine, Kalmykov, Alexey, Wissgott, Antje, Brandt, Guido, Jeong, Choongwon, Cheronet, Olivia, Ferry, Matthew, Harney, Eadaoin, Keating, Denise, Mallick, Swapan, Rohland, Nadin, Stewardson, Kristin, Kantorovich, Anatoly R., Maslov, Vladimir E., Petrenko, Vladimira G., Erlikh, Vladimir R., Atabiev, Biaslan Ch., Magomedov, Rabadan G., Kohl, Philipp L., Alt, Kurt W., Pichler, Sandra L., Gerling, Claudia, Meller, Harald, Vardanyan, Benik, Yeganyan, Larisa, Rezepkin, Alexey D., Mariaschk, Dirk, Berezina, Natalia, Gresky, Julia, Fuchs, Katharina, Knipper, Corina, Schiffels, Stephan, Balanovska, Elena, Balanovsky, Oleg, Mathieson, Iain, Higham, Thomas, Berezin, Yakov B., Buzhilova, Alexandra, Trifonov, Viktor, Pinhasi, Ron, Belinskij, Andrej B., Reich, David, Hansen, Svend, Krause, Johannes, and Haak, Wolfgang

Published
2019
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