He Yu, Ph.D.
Ancient Genomics Research group
Assistant Professor, College of Life Sciences, Peking University
tel：
E-mail：yuhe@pku.edu.cn
The development of ancient DNA techniques together with genome-wide sequencing enables us to reconstruct the evolutionary history of organisms living in the past, by directly retrieving information from archaeological or paleontological remains. The research focus of our lab is the population genomics of ancient human and animals. We aim to
1. Understand the genetic history of human populations in East Asia and their interactions with populations across Eurasia.
2. Investigate the evolutionary history of domesticated or commensal animals which are closely associated to human, and their implications to the development of human society.
1. Population dynamics of Upper Paleolithic to Early Bronze Age Siberian
The Lake Baikal region has been inhabited by modern humans since the Upper Paleolithic, while the precise history of its peoples over this long time-span is still largely unknown. In this study, we generate genome-wide data from Upper Paleolithic to Early Bronze Age inpiduals from the Lake Baikal and its surrounding regions, and further reconstructYersinia pestisgenomes from two of these inpiduals. Combining human, pathogen and isotope evidences, we demonstrate the most deeply pergent connection between Upper Paleolithic Siberians and the First Americans, suggesting that the First Native American ancestry was much more widely distributed across Siberia. Combining human genomic, pathogen genomic and isotopic evidence, we also reveal human and pathogen mobility across Eurasia during the Early Bronze Age in a multi-disciplinary approach.
2. Palaeogenomics of European black rat associated with human economic history
The black rat (Rattus rattus) is one of the most widely distributed mammal species thanks to its commensal relationship with humans, which makes it an ideal proxy to understand human population movement and society development in the history. In this study we generate a chromosome-levelde novogenome assembly of the black rat, and ancient genomes of black rats from Europe and North Africa. We detect population turnover in temperate Europe coincident with the black rat population decline revealed by archaeological evidence between the 6th and 10th centuries CE, which could be the result of the breakdown of the Roman Empire alongside its well-connected settlements, or additionally impacted by the First plague Pandemic, and/or the climatic cooling of Late Antique Little Ice Age.
3. Genomic background of Chinese domestic cat and wildcat
The domestic cat (Felis catus) is one of the most popular pets in human society, whose domestication origin and history have attracted wide public attention and scientific interest, while little is known about the ancestry of domestic cats from East Asia and its relationship with endemic Chinese mountain cat (F. bieti). We conduct range-wide sample collection and whole genome sequencing of domestic cats and wildcats in China. Based on phylogenomic reconstruction, population structure and demographic history analysis, this study confirms that domestic cats in China shared the same origin with worldwide domestic cats from African wildcat (F. s. lybica) in the Near East, and reveals contemporary genetic introgression between the Chinese mountain cat and its sympatric domestic cats, consistent with the late arrival of domestic cats in the Qinghai-Tibet Plateau.
Ghalichi A, Reinhold S, Rohrlach AB, Kalmykov AA, Childebayeva A, Yu H, Aron F, Semerau L, Bastert-Lamprichs K, Belinskiy AB, et al. (2024) The rise and transformation of Bronze Age pastoralists in the Caucasus. Nature, 635: 917-925.
Higgins OA, Modi A, Cannariato C, Diroma MA, Lugli F, Ricci S, Zaro V, Vai S, Vazzana A, Romandini M, Yu, H, et al. (2024). Life history and ancestry of the late upper palaeolithic infant from grotta delle mura, Italy. Nat. Commun., 15: 8248.
Posth C, Yu H, Ghalichi A et al. (2023) Palaeogenomics of upper palaeolithic to neolithic european hunter-gatherers. Nature, 615: 117-126.
Villalba-Mouco V, van de Loosdrecht MS, Rohrlach AB, Fewlass H, Talamo S, Yu H, Aron F, Lalueza-Fox C, Cabello L, Cantalejo Duarte et al. (2023) A 23,000-year-old southern Iberian inpidual links human groups that lived in Western Europe before and after the Last Glacial Maximum. Nat. Ecol. Evol., 7: 597-609.
Wang K, Yu H, Radzevičiūtė R, Kiryushin YF, Tishkin AA, Frolov YV, Stepanova NF, Kiryushin KY, Kungurov AL, Shnaider SV, et al. (2023) Middle holocene siberian genomes reveal highly connected gene pools throughout North Asia. Curr. Biol., 33: 423-433.
Yu H, Jamieson A, Hulme-Beaman A, Conroy CJ, Knight B, Speller C, Al-Jarah H, Eager H, Trinks A, Adikari G, Baron H, Bohlendorf-Arslan B, Bohingamuwa W, Crowther A, Cucchi T, Esser K, Fleisher J, Gidney L, Gladilina E, Gol'din P, Goodman SM, Hamilton-Dyer S, Helm R, Hillman C, Kallala N, Kivikero H, Kovacs ZE, Kunst GK, Kysely R, Linderholm A, Maraoui-Telmini B, Markovic N, Morales-Muniz A, Nabais M, O'Connor T, Oueslati T, Morales EMQ, Pasda K, Perera J, Perera N, Radbauer S, Ramon J, Rannamae E, Grego JS, Treasure E, Valenzuela-Lamas S, van der Jagt I, Van Neer W, Vigne JD, Walker T, Wynne-Jones S, Zeiler J, Dobney K, Boivin N, Searle JB, Krause-Kyora B, Krause J, Larson G, Orton D. (2022) Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history. Nat. Commun., 13: 2399.
Yu H, van de Loosdrecht MS, ManninoMA, Talamo S, Rohrlach AB, Childebayeva A, Villalba-Mouco V, Aron F, Brandt G, Burri M, Freund C, Radzeviciute R, Stahl R, Wissgott A, Fewlass H, Tagliacozzo A, Piperno M, Tusa S, Collina C, Schimmenti V, Di Salvo R, Prüfer K, Posth C, Hublin J-J, Gronenborn D, Binder D, Jeong C, Haak W, Krause J. (2022) Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily. iScience, 25: 104244.
Yu H, Xing YT, Meng H, He B, Li WJ, Qi XZ, Zhao JY, Zhuang Y, Xu X, O’Brien SJ, Luo SJ. (2021) Genomic evidence for the Chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats. Science Advances, 7: eabg0221.
Prüfer K, Posth C,Yu H, Stoessel A, Deviese T, Mattonai M, Ribechini E, Higham T, Petr Velem.nský, Brůžek J, Krause J. (2021) A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. Nature Ecology and Evolution, 5: 820-825.
Yu H, Spyrou MA, Karapetian M, Shaider S, Radzevičiūtė R, Nägele K, Neumann GU, Penske S, Zech J, Lucas M, LeRoux P, Roberts P, Pavlenok G, Buzhilova A, Posth C, Jeong C, Krause J. (2020) Paleolithic to Bronze Age Siberians reveal connections with First Americans and across Eurasia. Cell, 181: 1232-1245.
Xu Zhou, Yu Han, Xiaole Lei, Xueyuan Liang, Xinmeng Liu, Zhihan Zhao, Wenqin Yu, Jiangyue Zhang, Xingyu Shi, Changtai Hu, Yiwen Wang, Chenyu Zhu, Haiyan Yue
