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中国科学院古脊椎所古DNA实验室

Laboratory on Molecular Paleontology of IVPP

 

Add:142 Xizhimenwai Str., Beijing, China

Tel: 86-10-88369320

Introduction Introduction

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►  Laboratory on Molecular Paleontology of IVPP

 

The main purpose of our ancient DNA laboratory is to research topics in evolutionary and population genetics, using molecular genetic approaches to clarify ancient human relationships, archaic hominid introgression into modern humans, migratory routes of early modern humans into Asia and interactions between early modern humans and contemporary local modern humans. Moreover, we use ancient genetic data to investigate the impact of Neolithic agriculture on demographic changes across Europe and Asia and look for potential local adaptations leading up to modern human populations.

Our group is not only highly proficient in using the key technologies required for sequencing ancient DNA, we have also conducted large genome-wide projects and published breakthrough articles, thereby demonstrating keen research perspectives, rigorous scientific practices and strong analytical capabilities in addressing problems in population and evolutionary genetics as well as molecular biology. Our contributions include: the estimation of the proportion and time of gene flow between Neanderthals and Late Pleistocene Central Asian and Siberian humans, using high-quality early modern human genomes; and the discovery that contemporary European populations are comprised of at least three different sources of genetic ancestry, revealing that modern human migration was not straightforward. These are some of the accumulating knowledge and experience within this lab, laying a solid foundation for future research.

Our laboratory has enduring relationships with many international teams at the forefront of ancient DNA research. Most notably, are the continual collaborations with the German Max Planck Institute of Evolutionary Anthropology Professor Svante Pääbo's team. Professor Svante Pääbo is one of the founding members in the field of ancient DNA research, and has had impressive results in leading his team to solve fundamental questions about human origin and evolution, and participating teams are also using advanced experimental and bioinformatics methods leading by international standards. In addition, our laboratory maintains in-depth exchanges and cooperation with the Department of Genetics at Harvard Medical School, in terms of joint research on human origins.

Head of Laboratory Head of Laboratory

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► Qiaomei Fu

 
 

Professor, Head of the Ancient DNA Lab at the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences

 

 

E-mail: fuqiaomei at ivpp.ac.cn

       

Professor Qiaomei Fu completed her PhD under the supervision of Professor Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) Leipzig in 2013. Then, she worked as a postdoctoral research fellow in the population genetics group headed by Professor David Reich of the Genetics Department at Harvard Medical School. In August 2015, she returned to the MPI-EVA as a research scientist, and in January 2016, she began a position as the head of the Laboratory of Molecular Paleontology at the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), Chinese Academy of Sciences. Her present research focuses on using ancient DNA to study gene flow between modern and archaic humans, to determine early modern human migration routes and to explore how agriculture influences the population structure of the Neolithic expansion in Europe and Asia. Her research projects have been published in Nature, Science, PNAS, Current Biology and other international high profile journals. One of these research projects was awarded "one of the top 2014 annual ten scientific events" in Nature. In 2016,she was selected as one of ten "Science stars of China"  in Nature. In 2017, she was selected for the International Young Scientist Award, organized by the Howard Hughes Medical Institute (HHMI).

 

Team Team

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Postdoctoral Fellows

 

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  Melinda Yang

             E-mail:    melyang at ivpp.ac.cn

Melinda Yang received her PhD at UC Berkeley, where she developed methods of studying demographic history in populations using ancient and modern genomic data. Using these methods, she has uncovered greater details in both human and horse evolutionary history. Her primary interest is in human evolutionary genomics and the overlap with archaeology. At the Molecular Paleontology Lab, she will study the ancient genomics of prehistoric and early modern humans, using their data to help clarify East Asian prehistory in the last fifty to three thousand years.

 

Master Student

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  Manyu Ding

 

Staff

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  Zhaoxia Zhang

             Laboratory equipment maintenance and DNA sequencing.

             E-mail:    zhangzhaoxia at ivpp.ac.cn

  Peng Cao

             DNA extraction, DNA library preparation and DNA sequencing.

             E-mail:    caopeng at ivpp.ac.cn

  Weihong Hou

             DNA extraction, DNA library preparation and DNA sequencing.

             E-mail:    houweihong at ivpp.ac.cn

  Xiao Wang

             Next-generation data analysis and server maintenance.

             E-mail:    xiaowang at ivpp.ac.cn

Major Publications Major Publications

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►  Major Publications

 

(1) Skoglund P, Posth C, Sirak K, Spriggs M, Valentin F, Bedford S, Clark GR, Reepmeyer C, Petchey F, Fernandes D, Fu Q, Harney E, Lipson M et al. Genomic insights into the peopling of the Southwest Pacific. Nature. 2016, 538(7626):510-513.
 
(2) Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.Nature. 2016, 538(7624):201-206.
 
(3) Lazaridis I, Nadel D, Rollefson G, Merrett DC, Rohland N, Mallick S, Fernandes D, Novak M, Gamarra B, Sirak K, Connell S, Stewardson K, Harney E, Fu Q, Gonzalez-Fortes G, Jones ER et al. Genomic insights into the origin of farming in the ancient Near East. Nature. 2016,536(7617):419-24.
 
(4) Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S, Fernandes D, Furtwangler A, Haak W, Meyer M, Mittnik A et al: The genetic history of Ice Age Europe. Nature 2016.
 
(5) Moorjani P, Sankararaman S, Fu Q, Przeworski M, Patterson N, Reich D: A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proc Natl Acad Sci U S A 2016, 113(20):5652-5657.
 
(6) Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M et al: Ancient gene flow from early modern humans into Eastern Neanderthals. Nature 2016, 530(7591):429-433.
 
(7) Key FM, Fu Q, Romagne F, Lachmann M, Andres AM: Human adaptation and population differentiation in the light of ancient genomes. Nat Commun 2016, 7:10775.
 
(8) Fu Q, Hajdinjak M, Moldovan OT, Constantin S, Mallick S, Skoglund P, Patterson N, Rohland N, Lazaridis I, Nickel B et al: An early modern human from Romania with a recent Neanderthal ancestor. Nature 2015, 524(7564):216-219.
 
(9) Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, Bondarev AA, Johnson PL, Aximu-Petri A, Prufer K, de Filippo C et al: Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 2014, 514(7523):445-449.
 
(10) Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K et al: Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 2015, 522(7555):207-211.
 
(11) Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M et al: Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 2014, 513(7518):409-413.
 
(12) Castellano S, Parra G, Sanchez-Quinto FA, Racimo F, Kuhlwilm M, Kircher M, Sawyer S, Fu Q, Heinze A, Nickel B et al: Patterns of coding variation in the complete exomes of three Neandertals. Proc Natl Acad Sci U S A 2014, 111(18):6666-6671.
 
(13) Ko AM, Chen CY, Fu Q, Delfin F, Li M, Chiu HL, Stoneking M, Ko YC: Early Austronesians: into and out of Taiwan. Am J Hum Genet 2014, 94(3):426-436.
 
(14) Prufer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C et al: The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 2014, 505(7481):43-49.
 
(15) Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, Arsuaga JL, Martinez I, Gracia A, de Castro JM, Carbonell E et al: A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 2014, 505(7483):403-406.
 
(16) Benazzi S, Peresani M, Talamo S, Fu Q, Mannino MA, Richards MP, Hublin JJ: A reassessment of the presumed Neandertal remains from San Bernardino Cave, Italy. J Hum Evol 2014, 66:89-94.
 
(17) Fu Q, Mittnik A, Johnson PL, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J et al: A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol 2013, 23(7):553-559.
 
(18) Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Paabo S: DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci U S A 2013, 110(6):2223-2227.
 
(19) Fu Q, Rudan P, Paabo S, Krause J: Complete mitochondrial genomes reveal neolithic expansion into Europe. PLoS One 2012, 7(3):e32473.
 
(20) Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K, de Filippo C et al: A high-coverage genome sequence from an archaic Denisovan individual. Science 2012, 338(6104):222-226.
 
(21) Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL et al: Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 2010, 468(7327):1053-1060.
 
(22) Fu Q, Jin S, Hu Y: Agricultural development and human diets in Gouwan site,Xichuan,Henan. Chinese Sci Bull 2010(07):614-620.
 
(23) Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Paabo S: The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 2010, 464(7290):894-897.