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1. Lake-centred sedentary lifestyle of early Tibetan Plateau Indigenous populations at high elevation 4,400 years ago

Author

Yang, Xiaoyan, Gao, Yu, Wangdue, Shargan, Ran, Jingkun, Wang, Qing, Chen, Songtao, Yang, Jishuai, Wang, Tianyi, Gu, Zhengquan, Zhang, Ying, Cao, Peng, Dai, Qingyan, Chen, Shungang, Tong, Yan, Jia, Nihanxue, Sun, Qingli, Huang, Yunzhe, Perry, Linda, d’Alpoim Guedes, Jade, Han, Xu, Liu, Feng, Feng, Xiaotian, Yang, Qi, Wang, Yunming, Hu, Shihua, Tian, Yaofei, Guo, Jianglong, Liang, Xinwei, You, Ting, Li, Yazhong, Zhang, Yunan, Deng, Zhenhua, Qin, Ling, Wu, Xiaohong, Zhuang, Yijie, Liu, Yichen, Fu, Qiaomei, and Chen, Fahu

Published
2024
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4. Evolution and legacy of East Asian aurochs

Author

Hou, Jiawen, Guan, Xiwen, Xia, Xiaoting, Lyu, Yang, Liu, Xin, Mazei, Yuri, Xie, Ping, Chang, Fengqin, Zhang, Xiaonan, Chen, Jialei, Li, Xinyi, Zhang, Fengwei, Jin, Liangliang, Luo, Xiaoyu, Sinding, Mikkel-Holger S., Sun, Xin, Achilli, Alessandro, Migliore, Nicola Rambaldi, Zhang, Dongju, Lenstra, Johannes A., Han, Jianlin, Fu, Qiaomei, Liu, Xinyi, Zhang, Xiaoming, Chen, Ningbo, Lei, Chuzhao, and Zhang, Hucai

Published
2024
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7. Ethics of DNA research on human remains: five globally applicable guidelines

Author

Alpaslan-Roodenberg, Songül, Anthony, David, Babiker, Hiba, Bánffy, Eszter, Booth, Thomas, Capone, Patricia, Deshpande-Mukherjee, Arati, Eisenmann, Stefanie, Fehren-Schmitz, Lars, Frachetti, Michael, Fujita, Ricardo, Frieman, Catherine J, Fu, Qiaomei, Gibbon, Victoria, Haak, Wolfgang, Hajdinjak, Mateja, Hofmann, Kerstin P, Holguin, Brian, Inomata, Takeshi, Kanzawa-Kiriyama, Hideaki, Keegan, William, Kelso, Janet, Krause, Johannes, Kumaresan, Ganesan, Kusimba, Chapurukha, Kusimba, Sibel, Lalueza-Fox, Carles, Llamas, Bastien, MacEachern, Scott, Mallick, Swapan, Matsumura, Hirofumi, Morales-Arce, Ana Y, Matuzeviciute, Giedre Motuzaite, Mushrif-Tripathy, Veena, Nakatsuka, Nathan, Nores, Rodrigo, Ogola, Christine, Okumura, Mercedes, Patterson, Nick, Pinhasi, Ron, Prasad, Samayamantri PR, Prendergast, Mary E, Punzo, Jose Luis, Reich, David, Sawafuji, Rikai, Sawchuk, Elizabeth, Schiffels, Stephan, Sedig, Jakob, Shnaider, Svetlana, Sirak, Kendra, Skoglund, Pontus, Slon, Viviane, Snow, Meradeth, Soressi, Marie, Spriggs, Matthew, Stockhammer, Philipp W, Szécsényi-Nagy, Anna, Thangaraj, Kumarasamy, Tiesler, Vera, Tobler, Ray, Wang, Chuan-Chao, Warinner, Christina, Yasawardene, Surangi, and Zahir, Muhammad

Subjects
Human Genome, Genetics, Generic health relevance, American Indian or Alaska Native, Anthropology, Archaeology, Cadaver, Community-Institutional Relations, DNA, Ancient, Guidelines as Topic, Human Genetics, Humans, Indigenous Peoples, Internationality, Molecular Biology, Stakeholder Participation, Translations, General Science & Technology
Abstract

We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.

Published
2021

9. Neolithic to Bronze Age human maternal genetic history in Yunnan, China

Author

Wei, Xinyu, Zhang, Ming, Min, Rui, Jiang, Zhilong, Xue, Jiayang, Zhu, Zhonghua, Yuan, Haibing, Li, Xiaorui, Zhao, Dongyue, Cao, Peng, Liu, Feng, Dai, Qingyan, Feng, Xiaotian, Yang, Ruowei, Wu, Xiaohong, Hu, Changcheng, Ma, Minmin, Liu, Xu, Wan, Yang, Yang, Fan, Zhou, Ranchao, Kang, Lihong, Dong, Guanghui, Ping, Wanjing, Wang, Tianyi, Miao, Bo, Bai, Fan, Zheng, Yuxin, Liu, Yuxiao, Yang, Melinda A., Wang, Wenjun, Bennett, E. Andrew, and Fu, Qiaomei

Published
2024
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10. Maternal genetic history of ancient Tibetans over the past 4000 years

Author

Zhang, Ganyu, Cui, Can, Wangdue, Shargan, Lu, Hongliang, Chen, Honghai, Xi, Lin, He, Wei, Yuan, Haibing, Tsring, Tinley, Chen, Zujun, Yang, Feng, Tsering, Tashi, Li, Shuai, Tashi, Norbu, Yang, Tsho, Tong, Yan, Wu, Xiaohong, Li, Linhui, He, Yuanhong, Cao, Peng, Dai, Qingyan, Liu, Feng, Feng, Xiaotian, Wang, Tianyi, Yang, Ruowei, Ping, Wanjing, Zhang, Ming, Gao, Xing, Liu, Yichen, Wang, Wenjun, and Fu, Qiaomei

Published
2023
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11. The population history of northeastern Siberia since the Pleistocene

Author

Sikora, Martin, Pitulko, Vladimir V, Sousa, Vitor C, Allentoft, Morten E, Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A, Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V, Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y, Chasnyk, Vyacheslav G, Nikolskiy, Pavel A, Gromov, Andrei V, Khartanovich, Valeriy I, Moiseyev, Vyacheslav, Grebenyuk, Pavel S, Fedorchenko, Alexander Yu, Lebedintsev, Alexander I, Slobodin, Sergey B, Malyarchuk, Boris A, Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U, Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S, Sjögren, Karl-Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J, Excoffier, Laurent, and Willerslev, Eske

Subjects
Asia, DNA, Ancient, Europe, Gene Pool, Genome, Human, Haplotypes, History, 15th Century, History, Ancient, History, Medieval, Human Migration, Humans, Indians, North American, Male, Siberia, General Science & Technology
Abstract

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

Published
2019

12. Ancient DNA reveals the maternal genetic history of East Asian domestic pigs

Author

Zhang, Ming, Liu, Yichen, Li, Zhipeng, Lü, Peng, Gardner, Jacob D., Ye, Maolin, Wang, Jihuai, Yang, Miaomiao, Shao, Jing, Wang, Weilin, Dai, Qingyan, Cao, Peng, Yang, Ruowei, Liu, Feng, Feng, Xiaotian, Zhang, Lizhao, Li, Enwei, Shi, Yunzheng, Chen, Zehui, Zhu, Shilun, Zhai, Weiwei, Deng, Tao, Duan, Ziyuan, Bennett, E. Andrew, Hu, Songmei, and Fu, Qiaomei

Published
2022
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13. Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

Author

Liu, Siyang, Huang, Shujia, Chen, Fang, Zhao, Lijian, Yuan, Yuying, Francis, Stephen Starko, Fang, Lin, Li, Zilong, Lin, Long, Liu, Rong, Zhang, Yong, Xu, Huixin, Li, Shengkang, Zhou, Yuwen, Davies, Robert W, Liu, Qiang, Walters, Robin G, Lin, Kuang, Ju, Jia, Korneliussen, Thorfinn, Yang, Melinda A, Fu, Qiaomei, Wang, Jun, Zhou, Lijun, Krogh, Anders, Zhang, Hongyun, Wang, Wei, Chen, Zhengming, Cai, Zhiming, Yin, Ye, Yang, Huanming, Mao, Mao, Shendure, Jay, Wang, Jian, Albrechtsen, Anders, Jin, Xin, Nielsen, Rasmus, and Xu, Xun

Subjects
Clinical Research, Human Genome, Genetics, Infectious Diseases, Prevention, Emerging Infectious Diseases, 2.1 Biological and endogenous factors, Aetiology, Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, Infection, Reproductive health and childbirth, Good Health and Well Being, Adult, Alleles, Asian People, China, DNA, Ethnicity, Female, Gene Frequency, Genetic Testing, Genetic Variation, Genetics, Population, Genome-Wide Association Study, Genomics, Human Migration, Humans, Pregnancy, Prenatal Diagnosis, Sequence Analysis, DNA, genome-wide association study, low-pass sequencing, non-invasive prenatal testing, plasma virome, population genetics, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses.

Published
2018

14. 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, Quirong, Niyazi, Alipujiang, Dong, Guanghui, Cao, Peng, Liu, Feng, and Dai, Qingyan

Subjects
Mummies -- Genetic aspects -- Origin -- Environmental aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious.sup.1. Here we present genomic data from 5 individuals dating to around 3000-2800 bc from the Dzungarian Basin and 13 individuals dating to around 2100-1700 bc from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo.sup.1,2 or to have originated among the Bactria-Margiana Archaeological Complex.sup.3 or Inner Asian Mountain Corridor cultures.sup.4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert. A genomic analysis of human remains from the Bronze Age provides insights into the origin of the Tarim Basin mummies from the Xinjiang region., Author(s): Fan Zhang [sup.1] , Chao Ning [sup.2] , Ashley Scott [sup.2] , Qiaomei Fu [sup.3] , Rasmus Bjørn [sup.2] , Wenying Li [sup.4] , Dong Wei [sup.5] , Wenjun [...]

Published
2021
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17. Human population history at the crossroads of East and Southeast Asia since 11,000 years ago

Author

Wang, Tianyi, Wang, Wei, Xie, Guangmao, Li, Zhen, Fan, Xuechun, Yang, Qingping, Wu, Xichao, Cao, Peng, Liu, Yichen, Yang, Ruowei, Liu, Feng, Dai, Qingyan, Feng, Xiaotian, Wu, Xiaohong, Qin, Ling, Li, Fajun, Ping, Wanjing, Zhang, Lizhao, Zhang, Ming, Liu, Yalin, Chen, Xiaoshan, Zhang, Dongju, Zhou, Zhenyu, Wu, Yun, Shafiey, Hassan, Gao, Xing, Curnoe, Darren, Mao, Xiaowei, Bennett, E. Andrew, Ji, Xueping, Yang, Melinda A., and Fu, Qiaomei

Published
2021
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20. Massive migration from the steppe is a source for Indo-European languages in Europe

Author

Haak, Wolfgang, Lazaridis, Iosif, Patterson, Nick, Rohland, Nadin, Mallick, Swapan, Llamas, Bastien, Brandt, Guido, Nordenfelt, Susanne, Harney, Eadaoin, Stewardson, Kristin, Fu, Qiaomei, Mittnik, Alissa, Bánffy, Eszter, Economou, Christos, Francken, Michael, Friederich, Susanne, Pena, Rafael Garrido, Hallgren, Fredrik, Khartanovich, Valery, Khokhlov, Aleksandr, Kunst, Michael, Kuznetsov, Pavel, Meller, Harald, Mochalov, Oleg, Moiseyev, Vayacheslav, Nicklisch, Nicole, Pichler, Sandra L., Risch, Roberto, Guerra, Manuel A. Rojo, Roth, Christina, Szécsényi-Nagy, Anna, Wahl, Joachim, Meyer, Matthias, Krause, Johannes, Brown, Dorcas, Anthony, David, Cooper, Alan, Alt, Kurt Werner, and Reich, David

Subjects
Quantitative Biology - Populations and Evolution
Abstract

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6 . By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

Published
2015
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21. Exceptional Nitrate Reduction to Ammonia Catalyst Enabled by BO2− Anion Induction Effects Combining Heterogeneous Branching Architecture‐Driven Mass Transport Enhancement.

Author

Ding, Liping, Yan, Han, Zhang, Lin, Bai, Ruijie, Du, Qian, Xu, Chun, Gu, Haojie, Guo, Suer, Cheng, Guoxia, Fu, Qiaomei, Liu, Siqi, Yin, Kang, Li, Qi, and Wang, Yanqing

Subjects
ELECTRON density, DENITRIFICATION, BIOMIMETICS, CATALYTIC activity, BINDING energy, MASS transfer, PHASE-transfer catalysis, ELECTROLYTIC reduction
Abstract

In this paper, an exceptional nitrate reduction to ammonia catalyst is reported, enabled by BO2− anion induction effects combining heterogeneous branching architecture‐driven mass transport enhancement strategies. The implantation of the BO2− anion can inductively enhance the electron cloud density and electron transmission paths of intrinsic catalysts, makes electron more active to improve the conductivity, regulates the adsorption and desorption rates of intermediates by space barrier effect, reduces the binding energy of the electron and 3d orbital of Ni in NiFe(BO2)O(OH), thereby lowing the transform free energy of the determining *NO3 to *HNO3 step. 3D hollow sea urchin lattice heterogeneous branching structure can self‐drive generate differentiated micro convection intervals, which will be beneficial for improving mass transfer dynamics especially localized disturbance mass transfer effect of catalyst for nitrate reduction reaction (NO3RR) catalysis process. Amazingly, the as‐prepared 3D NiFe metaborate oxyhydroxide hollow bionic sea urchins lattice catalyst has a high NH3 rate 6.27mmol·h−1·cm−2 with 98.7% Faradaic efficiency at low ‐0.25V(vs RHE) NO3RR potential. Moreover, the catalytic activity of this highly stable catalyst decreases only slightly over 100 h at ultra‐high 1500mA·cm−2 current. This work breaks through the bottleneck that plagues the performance improvement of non Cu‐based high‐current NO3RR catalysts. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Ancient mitogenomes reveal the maternal genetic history of East Asian dogs

Author

Zhang, Ming, primary, Song, Yanbo, additional, Wang, Caihui, additional, Sun, Guoping, additional, Zhuang, Lina, additional, Guo, Mingjian, additional, Ren, Lele, additional, Wangdue, Shargan, additional, Dong, Guanghui, additional, Dai, Qingyan, additional, Cao, Peng, additional, Yang, Ruowei, additional, Liu, Feng, additional, Feng, Xiaotian, additional, Bennett, E Andrew, additional, Zhang, Xiaoling, additional, Chen, Xi, additional, Wang, Fen, additional, Luan, Fengshi, additional, Dong, Wenbin, additional, Lu, Guoquan, additional, Hao, Daohua, additional, Hou, Hongwei, additional, Wang, Hui, additional, Qiao, Hong, additional, Wang, Zhongxin, additional, Hu, Xiaojun, additional, He, Wei, additional, Xi, Lin, additional, Wang, Weilin, additional, Shao, Jing, additional, Sun, Zhouyong, additional, Yue, Lianjian, additional, Ding, Yan, additional, Tashi, Norbu, additional, Yang, Tsho, additional, Tong, Yan, additional, Yang, Yangheshan, additional, Zhu, Shilun, additional, Miao, Bo, additional, Wang, Wenjun, additional, Zhang, Lizhao, additional, Hu, Songmei, additional, Ni, Xijun, additional, and Fu, Qiaomei, additional

Published
2024
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25. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Author

Hajdinjak, Mateja, Mafessoni, Fabrizio, Skov, Laurits, Vernot, Benjamin, Hübner, Alexander, Fu, Qiaomei, Essel, Elena, Nagel, Sarah, Nickel, Birgit, Richter, Julia, Moldovan, Oana Teodora, Constantin, Silviu, Endarova, Elena, Zahariev, Nikolay, Spasov, Rosen, Welker, Frido, Smith, Geoff M., Sinet-Mathiot, Virginie, Paskulin, Lindsey, Fewlass, Helen, Talamo, Sahra, Rezek, Zeljko, Sirakova, Svoboda, Sirakov, Nikolay, McPherron, Shannon P., Tsanova, Tsenka, Hublin, Jean-Jacques, Peter, Benjamin M., Meyer, Matthias, Skoglund, Pontus, Kelso, Janet, and Pääbo, Svante

Published
2021
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26. 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

27. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years

Author

Moorjani, Priya, Sankararaman, Sriram, Fu, Qiaomei, Przeworski, Molly, Patterson, Nick, and Reich, David

Subjects
Human Genome, Genetics, Biotechnology, Generic health relevance, Animals, Biological Evolution, Genetic Techniques, Genome, Human, Humans, Neanderthals, Polymorphism, Single Nucleotide, Radiometric Dating, molecular clock, generation interval, ancient DNA, branch shortening
Abstract

The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen's age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and (14)C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the (14)C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26-30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier.

Published
2016

29. Ancient human genomes suggest three ancestral populations for present-day Europeans

Author

Lazaridis, Iosif, Patterson, Nick, Mittnik, Alissa, Renaud, Gabriel, Mallick, Swapan, Kirsanow, Karola, Sudmant, Peter H., Schraiber, Joshua G., Castellano, Sergi, Lipson, Mark, Berger, Bonnie, Economou, Christos, Bollongino, Ruth, Fu, Qiaomei, Bos, Kirsten I., Nordenfelt, Susanne, Li, Heng, de Filippo, Cesare, Prüfer, Kay, Sawyer, Susanna, Posth, Cosimo, Haak, Wolfgang, Hallgren, Fredrik, Fornander, Elin, Rohland, Nadin, Delsate, Dominique, Francken, Michael, Guinet, Jean-Michel, Wahl, Joachim, Ayodo, George, Babiker, Hamza A., Bailliet, Graciela, Balanovska, Elena, Balanovsky, Oleg, Barrantes, Ramiro, Bedoya, Gabriel, Ben-Ami, Haim, Bene, Judit, Berrada, Fouad, Bravi, Claudio M., Brisighelli, Francesca, Busby, George, Cali, Francesco, Churnosov, Mikhail, Cole, David E. C., Corach, Daniel, Damba, Larissa, van Driem, George, Dryomov, Stanislav, Dugoujon, Jean-Michel, Fedorova, Sardana A., Romero, Irene Gallego, Gubina, Marina, Hammer, Michael, Henn, Brenna, Hervig, Tor, Hodoglugil, Ugur, Jha, Aashish R., Karachanak-Yankova, Sena, Khusainova, Rita, Khusnutdinova, Elza, Kittles, Rick, Kivisild, Toomas, Klitz, William, Kučinskas, Vaidutis, Kushniarevich, Alena, Laredj, Leila, Litvinov, Sergey, Loukidis, Theologos, Mahley, Robert W., Melegh, Béla, Metspalu, Ene, Molina, Julio, Mountain, Joanna, Näkkäläjärvi, Klemetti, Nesheva, Desislava, Nyambo, Thomas, Osipova, Ludmila, Parik, Jüri, Platonov, Fedor, Posukh, Olga, Romano, Valentino, Rothhammer, Francisco, Rudan, Igor, Ruizbakiev, Ruslan, Sahakyan, Hovhannes, Sajantila, Antti, Salas, Antonio, Starikovskaya, Elena B., Tarekegn, Ayele, Toncheva, Draga, Turdikulova, Shahlo, Uktveryte, Ingrida, Utevska, Olga, Vasquez, René, Villena, Mercedes, Voevoda, Mikhail, Winkler, Cheryl, Yepiskoposyan, Levon, Zalloua, Pierre, Zemunik, Tatijana, Cooper, Alan, Capelli, Cristian, Thomas, Mark G., Ruiz-Linares, Andres, Tishkoff, Sarah A., Singh, Lalji, Thangaraj, Kumarasamy, Villems, Richard, Comas, David, Sukernik, Rem, Metspalu, Mait, Meyer, Matthias, Eichler, Evan E., Burger, Joachim, Slatkin, Montgomery, Pääbo, Svante, Kelso, Janet, Reich, David, and Krause, Johannes

Subjects
Quantitative Biology - Populations and Evolution
Abstract

We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.

Published
2013
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30. Ancient DNA analysis

Author

Orlando, Ludovic, Allaby, Robin, Skoglund, Pontus, Der Sarkissian, Clio, Stockhammer, Philipp W., Ávila-Arcos, María C., Fu, Qiaomei, Krause, Johannes, Willerslev, Eske, Stone, Anne C., and Warinner, Christina

Published
2021
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32. Genome sequence of a 45,000-year-old modern human from western Siberia

Author

Fu, Qiaomei, Li, Heng, Moorjani, Priya, Jay, Flora, Slepchenko, Sergey M, Bondarev, Aleksei A, Johnson, Philip LF, Aximu-Petri, Ayinuer, Prüfer, Kay, de Filippo, Cesare, Meyer, Matthias, Zwyns, Nicolas, Salazar-García, Domingo C, Kuzmin, Yaroslav V, Keates, Susan G, Kosintsev, Pavel A, Razhev, Dmitry I, Richards, Michael P, Peristov, Nikolai V, Lachmann, Michael, Douka, Katerina, Higham, Thomas FG, Slatkin, Montgomery, Hublin, Jean-Jacques, Reich, David, Kelso, Janet, Viola, T Bence, and Pääbo, Svante

Subjects
Genetics, Biotechnology, Human Genome, Alleles, Animals, Chromosomes, Human, Pair 12, Diet, Evolution, Molecular, Fossils, Genome, Human, Humans, Hybridization, Genetic, Male, Molecular Sequence Data, Mutation Rate, Neanderthals, Phylogeny, Population Density, Population Dynamics, Principal Component Analysis, Sequence Analysis, DNA, Siberia, General Science & Technology
Abstract

We present the high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia. This individual derives from a population that lived before-or simultaneously with-the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000-13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10(-9) to 0.6 × 10(-9) per site per year, a Y chromosomal mutation rate of 0.7 × 10(-9) to 0.9 × 10(-9) per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10(-8) to 3.2 × 10(-8) per site per year based on the age of the bone.

Published
2014

34. The complete genome sequence of a Neanderthal from the Altai Mountains

Author

Prüfer, Kay, Racimo, Fernando, Patterson, Nick, Jay, Flora, Sankararaman, Sriram, Sawyer, Susanna, Heinze, Anja, Renaud, Gabriel, Sudmant, Peter H, de Filippo, Cesare, Li, Heng, Mallick, Swapan, Dannemann, Michael, Fu, Qiaomei, Kircher, Martin, Kuhlwilm, Martin, Lachmann, Michael, Meyer, Matthias, Ongyerth, Matthias, Siebauer, Michael, Theunert, Christoph, Tandon, Arti, Moorjani, Priya, Pickrell, Joseph, Mullikin, James C, Vohr, Samuel H, Green, Richard E, Hellmann, Ines, Johnson, Philip LF, Blanche, Hélène, Cann, Howard, Kitzman, Jacob O, Shendure, Jay, Eichler, Evan E, Lein, Ed S, Bakken, Trygve E, Golovanova, Liubov V, Doronichev, Vladimir B, Shunkov, Michael V, Derevianko, Anatoli P, Viola, Bence, Slatkin, Montgomery, Reich, David, Kelso, Janet, and Pääbo, Svante

Subjects
Human Genome, Genetics, Africa, Animals, Caves, DNA Copy Number Variations, Female, Fossils, Gene Flow, Gene Frequency, Genome, Heterozygote, Humans, Inbreeding, Models, Genetic, Neanderthals, Phylogeny, Population Density, Siberia, Toe Phalanges, General Science & Technology
Abstract

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

Published
2014

36. A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau

Author

Chen, Fahu, Welker, Frido, Shen, Chuan-Chou, Bailey, Shara E., Bergmann, Inga, Davis, Simon, Xia, Huan, Wang, Hui, Fischer, Roman, Freidline, Sarah E., Yu, Tsai-Luen, Skinner, Matthew M., Stelzer, Stefanie, Dong, Guangrong, Fu, Qiaomei, Dong, Guanghui, Wang, Jian, Zhang, Dongju, and Hublin, Jean-Jacques

Published
2019
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37. A high-coverage Neandertal genome from Vindija Cave in Croatia

Author

Prüfer, Kay, de Filippo, Cesare, Grote, Steffi, Mafessoni, Fabrizio, Korlević, Petra, Hajdinjak, Mateja, Vernot, Benjamin, Skov, Laurits, Hsieh, Pinghsun, Peyrégne, Stéphane, Reher, David, Hopfe, Charlotte, Nagel, Sarah, Maricic, Tomislav, Fu, Qiaomei, Theunert, Christoph, Rogers, Rebekah, Skoglund, Pontus, Chintalapati, Manjusha, Dannemann, Michael, Nelson, Bradley J., Key, Felix M., Rudan, Pavao, Kućan, Željko, Gušić, Ivan, Golovanova, Liubov V., Doronichev, Vladimir B., Patterson, Nick, Reich, David, Eichler, Evan E., Slatkin, Montgomery, Schierup, Mikkel H., Andrés, Aida M., Kelso, Janet, Meyer, Matthias, and Pääbo, Svante

Published
2017

39. Reconstructing the genetic history of late Neanderthals

Author

Hajdinjak, Mateja, Fu, Qiaomei, Hübner, Alexander, Petr, Martin, Mafessoni, Fabrizio, Grote, Steffi, Skoglund, Pontus, Narasimham, Vagheesh, Rougier, Hélène, Crevecoeur, Isabelle, Semal, Patrick, Soressi, Marie, Talamo, Sahra, Hublin, Jean-Jacques, Gušić, Ivan, Kućan, Željko, Rudan, Pavao, Golovanova, Liubov V., Doronichev, Vladimir B., Posth, Cosimo, Krause, Johannes, Korlević, Petra, Nagel, Sarah, Nickel, Birgit, Slatkin, Montgomery, Patterson, Nick, Reich, David, Prüfer, Kay, Meyer, Matthias, Pääbo, Svante, and Kelso, Janet

Published
2018
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40. Human genetic history on the Tibetan Plateau in the past 5100 years

Author

Wang, Hongru, primary, Yang, Melinda A., additional, Wangdue, Shargan, additional, Lu, Hongliang, additional, Chen, Honghai, additional, Li, Linhui, additional, Dong, Guanghui, additional, Tsring, Tinley, additional, Yuan, Haibing, additional, He, Wei, additional, Ding, Manyu, additional, Wu, Xiaohong, additional, Li, Shuai, additional, Tashi, Norbu, additional, Yang, Tsho, additional, Yang, Feng, additional, Tong, Yan, additional, Chen, Zujun, additional, He, Yuanhong, additional, Cao, Peng, additional, Dai, Qingyan, additional, Liu, Feng, additional, Feng, Xiaotian, additional, Wang, Tianyi, additional, Yang, Ruowei, additional, Ping, Wanjing, additional, Zhang, Zhaoxia, additional, Gao, Yang, additional, Zhang, Ming, additional, Wang, Xiaoji, additional, Zhang, Chao, additional, Yuan, Kai, additional, Ko, Albert Min-Shan, additional, Aldenderfer, Mark, additional, Gao, Xing, additional, Xu, Shuhua, additional, and Fu, Qiaomei, additional

Published
2023
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46. Patterns of coding variation in the complete exomes of three Neandertals

Author

Castellano, Sergi, Parra, Genís, Sánchez-Quinto, Federico A., Racimo, Fernando, Kuhlwilm, Martin, Kircher, Martin, Sawyer, Susanna, Fu, Qiaomei, Heinze, Anja, Nickel, Birgit, Dabney, Jesse, Siebauer, Michael, White, Louise, Burbano, Hernán A., Renaud, Gabriel, Stenzel, Udo, Lalueza-Fox, Carles, de la Rasilla, Marco, Rosas, Antonio, Rudan, Pavao, Brajković, Dejana, Kucan, Željko, Gušic, Ivan, Shunkov, Michael V., Derevianko, Anatoli P., Viola, Bence, Meyer, Matthias, Kelso, Janet, Andrés, Aida M., and Pääbo, Svante

Published
2014

48. Genomic insights into the origin of farming in the ancient Near East

Author

Lazaridis, Iosif, Nadel, Dani, Rollefson, Gary, Merrett, Deborah C., Rohland, Nadin, Mallick, Swapan, Fernandes, Daniel, Novak, Mario, Gamarra, Beatriz, Sirak, Kendra, Connell, Sarah, Stewardson, Kristin, Harney, Eadaoin, Fu, Qiaomei, Gonzalez-Fortes, Gloria, Jones, Eppie R., Roodenberg, Songl Alpaslan, Lengyel, Gyrgy, Bocquentin, Fanny, Gasparian, Boris, Monge, Janet M., Gregg, Michael, Eshed, Vered, Mizrahi, Ahuva-Sivan, Meiklejohn, Christopher, Gerritsen, Fokke, Bejenaru, Luminita, Blher, Matthias, Campbell, Archie, Cavalleri, Gianpiero, Comas, David, Froguel, Philippe, Gilbert, Edmund, Kerr, Shona M., Kovacs, Peter, Krause, Johannes, McGettigan, Darren, Merrigan, Michael, Merriwether, D. Andrew, OReilly, Seamus, Richards, Martin B., Semino, Ornella, Shamoon-Pour, Michel, Stefanescu, Gheorghe, Stumvoll, Michael, Tnjes, Anke, Torroni, Antonio, Wilson, James F., Yengo, Loic, Hovhannisyan, Nelli A., Patterson, Nick, Pinhasi, Ron, and Reich, David

Subjects
Middle East -- Social aspects, Genome-wide association studies, Agriculture -- Genetic aspects -- History, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between 12,000 and 1,400 bc, from Natufian huntergatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a Basal Eurasian lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local huntergatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the huntergatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia., Author(s): Iosif Lazaridis (corresponding author) [1, 2]; Dani Nadel [3]; Gary Rollefson [4]; Deborah C. Merrett [5]; Nadin Rohland [1]; Swapan Mallick [1, 2, 6]; Daniel Fernandes [7, 8]; Mario [...]

Published
2016
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49. Ancient gene flow from early modern humans into Eastern Neanderthals

Author

Kuhlwilm, Martin, Gronau, Ilan, Hubisz, Melissa J., de Filippo, Cesare, Prado-Martinez, Javier, Kircher, Martin, Fu, Qiaomei, Burbano, Hernan A., Lalueza-Fox, Carles, de la Rasilla, Marco, Rosas, Antonio, Rudan, Pavao, Brajkovic, Dejana, Kucan, Zeljko, Gusic, Ivan, Marques-Bonet, Tomas, Andres, Aida M., Viola, Bence, Paabo, Svante, Meyer, Matthias, Siepel, Adam, and Castellano, Sergi

Subjects
Neanderthals -- Genetic aspects -- Research, Genomes -- Natural history -- Research, Gene flow -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought., Based on the fossil record, Neanderthals diverged from modern humans at least 430,000 years ago (1), and the analysis of a Neanderthal genome from a cave in the Altai Mountains [...]

Published
2016
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50. The genetic history of Ice Age Europe

Author

Fu, Qiaomei, Posth, Cosimo, Hajdinjak, Mateja, Petr, Martin, Mallick, Swapan, Fernandes, Daniel, Furtwängler, Anja, Haak, Wolfgang, Meyer, Matthias, Mittnik, Alissa, Nickel, Birgit, Peltzer, Alexander, Rohland, Nadin, Slon, Viviane, Talamo, Sahra, Lazaridis, Iosif, Lipson, Mark, Mathieson, Iain, Schiffels, Stephan, Skoglund, Pontus, Derevianko, Anatoly P., Drozdov, Nikolai, Slavinsky, Vyacheslav, Tsybankov, Alexander, Cremonesi, Renata Grifoni, Mallegni, Francesco, Gély, Bernard, Vacca, Eligio, Morales, Manuel R. González, Straus, Lawrence G., Neugebauer-Maresch, Christine, Teschler-Nicola, Maria, Constantin, Silviu, Moldovan, Oana Teodora, Benazzi, Stefano, Peresani, Marco, Coppola, Donato, Lari, Martina, Ricci, Stefano, Ronchitelli, Annamaria, Valentin, Frédérique, Thevenet, Corinne, Wehrberger, Kurt, Grigorescu, Dan, Rougier, Hélène, Crevecoeur, Isabelle, Flas, Damien, Semal, Patrick, Mannino, Marcello A., Cupillard, Christophe, Bocherens, Hervé, Conard, Nicholas J., Harvati, Katerina, Moiseyev, Vyacheslav, Drucker, Dorothée G., Svoboda, Jiří, Richards, Michael P., Caramelli, David, Pinhasi, Ron, Kelso, Janet, Patterson, Nick, Krause, Johannes, Pääbo, Svante, and Reich, David

Published
2016
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