Welcome to Ke's Lab
We study paleogenomics and evolution!
Lab Overview
We are a research group (led by Dr. Ke Wang) at the forefront of understanding the evolutionary history of humans through the lenses of paleogenomics, bioinformatics, and population genetics.
The inhabitation of modern Homo Sapiens on our planet has a long history over 100,000 years, who have left numerous traces of skeletons, created objects (such as lithics and metal artifacts), and caused subsequent local ecological changes. Archaeological excavations of human skeletons allow scientists to reveal the distribution of human fossils and their associated objects buried alongside them that constitute a critical feature of their archaeological cultural label. In the last decades, the successful retrieval of ancient DNA from human remains dated to the last 10,000 years has revolutionized our understanding of the settlement and peopling history of modern humans. Paleogenomics, compared to modern genomics, has resolved many key population history questions in a much more direct way. It meanwhile allows direct comparison between genetic evidence, and archaeological cultural hypotheses, sometimes, even linguistic theories.
While when the time scope of research question is beyond the capability of ancient DNA (too old to be recovered), the bioinfomatic methods based on the currently available data for estimating population evolutionary events become indispensible. The development of new bioinfomatic tools for population history analyses replies heavily on the mathmatical framework established in theoretical population genetics and evolutonary biology. One of the classic framework is coalescent theory, which is the theoretical basis of the presented developed tool here (MSMC-IM). Another widely recognised framework is site-frequency spectrum, which, compared to coalescent theory, would benefit from larger sample size (for more accurate frequency estimates, intuitively). We hope to leverage pros and cons from both frameworks to achieve more accurate estimates on the human evolutionary history.
Research Interests
Paleogenomics
Bioinformatic methods development
Intergrating genetics, archaeology and languagues
Tools
Developed bioinformatic tool for inferring migration rate and effective population size across populations available at: MSMC-IM.
More tools are coming...
People
Principal Investigator
Wang, Ke 王轲 (Ph.D)
PhD student: Yin, Zi 殷姿
I obtained my Bachelor degree in Medical Laboratory Technology from Tianjin Medical University in 2020 and my Master degree in Immunology from Shanghai Jiao Tong University School of Medicine in 2023. I am currently pursuing a PhD in Human Genetics and Anthropology at the School of Life Sciences, Fudan University. My main work involves constructing whole-genome libraries and conducting data analysis, with a focus on the genetic structure and admixture of populations, exploring the history of population interactions and migrations.
PhD student: Sun, Hengxi 孙恒玺
I received my Master's degree in Biology and Medicine from Northwest A&F University and am currently pursuing a PhD in Biology at Fudan University. My research is centered on the evolutionary analysis of ancient microorganisms, employing advanced sequencing technologies to uncover insights into microbial adaptations into past human activities over time.
PhD student: Gao, Yan 高焱
Yan Gao is a doctoral student at Fudan University. He received his Bachelor's degree from Zhejiang Occean University in 2021 and his Master's degree from Shantou University in 2024. In recent years, Yan has primarily focused on understanding the molecular mechanisms of adaptive evolution in marine organisms, such as fish and crabs, as well as their population genetic structures. Currently, his research interest is dedicated to integrating ancient DNA data with modern genomic data to explore the spatiotemporal changes of ancient human populations and their adaptive evolutionary mechanisms.
Master student: Qi, Yimeng 齐艺萌
I am currently pursuing my Master's degree in Biology and Medicine at Fudan University, studying population genetics and human history in Central and East Asia. Prior to this, I worked as an immunological detection researcher at IVC Company after receiving my Bachelor's degree in Biotechnology from Nanchang University (2021). My research interests lie in understanding human population history through an interdisciplinary approach, combining evidence from population genetics, archaeological findings, and paleoclimatic records. Currently, I focus on reconstructing migration patterns and demographic history across the Asian continent, using ancient DNA data to investigate historical population dynamics and social structures.
Master student: Zhang, Chengcheng 张骋骋
Chengcheng is a master student of the School of Life Sciences at Fudan University. She is from Tai'an, Shandong Province. She graduated from the School of Life Sciences at Jilin University, and joined the laboratory in September 2024. She participated in iGEM during her undergraduate studies and conducted research on acute myeloid leukemia with basic knowledge in molecular and cell experiments. She likes citywalks, swimming, and cat petting.
Bachelor student: Chen, Lingyu 陈泠妤
A curious student majoring in biology, who wants to learn and study anthropology through both evolutionary biology and cultural sociology.
Publications(selected)
Wang, K., Prüfer, K.,Krause-Kyora, B.,et al. (2023) High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry. Cell Genomics 3(9) (Cover Page)
Wang, K.* Yu, H., Radzeviciute, R. et al. (2023) Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia. Current Biology 33(3): 423-433 (* correspondence).
Naegele, K., Rivollat, M., Yu, H., Wang, K.(2022) Ancient genomic research – From broad strokes to nuanced reconstructions of the past. Journal of Anthropological Sciences 100.
Wang, K., Bleasdale, M., Le Moyne, C. et al. (2022) 4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists. Scientific Reports 12(20939)
Jeong, C. +, Wang, K.+, Wilkin, S., Taylor, W. T. T., et al (2020) A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe. Cell, 2020;183: 890–904.e29. (+equal contribution)
Wang, K.+, Goldstein, S.+, Bleasdale, M., et al (2020). Ancient genomes reveal complex patterns of population movement, interaction and replacement in sub-Saharan Africa. Science Advances, 2020;6: eaaz0183. (+equal contribution)
Schiffels, S., Wang, K. (2020) MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent. In: Dutheil J. (eds) Statistical Population Genomics. Methods in Molecular Biology, vol 2090. Humana, New York, NY
Wang, K., Mathieson, I., O’Connell, J., Schiffels, S. (2020) Tracking human population structure through time from whole genome sequences. PLoS Genetics 16(3): e1008552.
Public Outreach (updating)
2024
Talk "Ancient DNA reveals the genetic ancestry, family pedigree and phenotypes of ancient Eurasian populations" (Chinese), October, Annual conference of the Bioinformatics Society of China, Haikou, China
Talk "The co-evolution of genes and cultures in human evolutionary history from the perspective of ancient DNA" (Chinese), April, Medical School of Fudan University, Shanghai, China
Talk "The settlement history of Altai inhabitants from the perspective of paleogenomics" (Chinese), March, The first annual conference of Genomics and Bioinformatics of China, Wuhan, China
2023
Talk "Ancient DNA sheds new lights into the Tyrolean Iceman mummy" (Chinese), December, Annual conference of the Chinese Society for the History of Science and Technology, Beijing, China
Talk "High-coverage genome of the Tyrolean mummy reveals the Anatolian ancestry and potential phenotypic traits of Iceman” (Chinese), November, Annual conference of the Genetics Society of China, Wuhan, China
Talk “The ancient population dynamics across North Asia and Eurasian Steppe” (Chinese), October, Annual conference of the Environmental Archeology Society of China, Kaifeng, China
Talk "High-coverage genome of the Tyrolean Iceman reveals high Anatolian farmer ancestry", October, SMBE Shanghai, Shanghai, China
Talk "The prehistorical migration and adxmiture history of Eurasian steppe populations and northern Siberians" (Chinese), September, International conference on the ancient cultures along Silk Road and Dunhuang, Dunhuang, China
Talk "New insights into the peopling history of Eurasian Steppe and Siberia" (Chinese), August, Annual conference of the Anthropological Archaeological Society of China, Tongliao, China
Lecture “Ancient DNA reveals highly connected gene pools across North Asia” (Chinese), November, Kunming Institute of Zoology Chines Academy of Sciences, Kunming, China
Lecture “Genomic insights into the peopling of Eurasia and Africa Steppe” (Chinese), November, China University of Geosciences, Wuhan, China
Lecture “Ancient population dynamics across North Asia and Eurasian Steppe” (Chinese), August, Jilin University, Changchun, China
Lecture "Ancient genomes reveal the migration and admixture history of early Africans" (Chinese), June, East China Normal University, Shanghai, China
Lecture "Investigating human origins from the perspective of molecular anthropology" (Chinese), April, Shaanxi Normal University, Xi'an, China
2022-2017 (Selected)
Seminar Lecture "Using ancient DNA to learn about recent human evolution", 2022 October, Department of Anthropology and Human Genetics, Fudan University, Shanghai, China
EMBO Talk "Reconstructing population separation history from whole genome sequences", 2019 March, EMBO | EMBL Symposium: Reconstructing the Human Past - Using Ancient and Modern Genomics, Heidelberg, Germany
Talk "Investigating East African population structure through ancient genomes", International conference - “Africa, the cradle of human diversity”, 2019 May, Uppsala University, Uppsala, Sweden