UYSD: a novel data repository accessible via public website for worldwide population frequencies of Y-SNP haplogroups

Ralf A. Zandstra D. van Wersch B. Köksal Z. Larmuseau M.H.D. Rosa A. Jobling M.A. D’Amato M.E. Courts C. Gysi M. Haas C. Flores R. Neis M. Wetton J.H. Kiesler K. Ameur A. Azonbakin S. Bôžiková A. Choma A. De Ungria M.C. Corradini B. Cruz C. Dunkelmann B. Ferri G. Fleckhaus J. Fragou D. Gaens N. Gonçalves R. Havaš Auguštin D. Helm K. Hölzl-Müller P. Kaliszan M. Kasu M. Kovatsi L. Lesaoana M. Mizuno N. Neuhuber F. Nováčková J. Ňuňuková A. Pamjav H. Parson W. Ramankulov Y. Rangel Villalobos H. Rębała K. Rootsi S. Salvador J. Šarac J. Steffen C.R. Stenzl V. Török T. Villems R. Watahiki H. Zhabagin M. Schneider P.M. Kayser M.
July 2025 Springer Nature

European Journal of Human Genetics
2025 #33 Issue 7 904 - 912 pp.

For decades, there has been scientific interest in the variation and geographic distribution of paternal lineages associated with the human Y chromosome. However, the relevant data have been dispersed across numerous publications, making it difficult to consolidate. Additionally, understanding the relationships between different variants, and the tools used to analyze them, have evolved over time, further complicating efforts to harmonize this information. The Universal Y-SNP Database (UYSD) marks a substantial advancement by providing a comprehensive and accessible platform for Y-SNP and haplogroup data from populations around the world. UYSD harmonizes diverse datasets into a unified repository, facilitating the exploration of global Y-chromosomal variation. The platform handles data generated with both high- and low-throughput technology and is compatible with the automated analysis software tool, Yleaf v3. Key functionalities include the ability to: i) visualize haplogroup distributions on an interactive world map, ii) estimate haplogroup frequencies in geographic regions with sparse data through interpolation, and iii) display detailed phylogenetic trees of Y-chromosomal haplogroups. Currently, UYSD encompasses data from over 6,600 males across 27 populations. This dataset largely aligns with known global Y-haplogroup patterns, but also reveals unexplored finer-scale geographic variations. While the present dataset is largely European-centered, UYSD is designed for ongoing expansion by the scientific community, aiming to include more global data and higher-resolution population sequencing data. The platform thus offers valuable insights into human genetic diversity and migration patterns, serving several fields of research such as: human population genetics, genetic anthropology, ancient DNA analysis and forensic genetics.

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Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
Laboratory of Human Genetic Genealogy, Department Human Genetics, KU Leuven, Leuven, Belgium
University of Madeira, Funchal, Portugal
University of Leicester, Leicester, United Kingdom
University of the Western Cape, Western Cape, South Africa
University Hospital of Cologne, Institute of Legal Medicine, Cologne, Germany
University of Zurich, Zurich, Switzerland
University of Tartu, Tartu, Estonia
National Institute of Standards and Technology, Gaithersburg, MD, United States
Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
SciLifeLab, Uppsala University, Uppsala, Sweden
Institute of Forensic Science, Bratislava, Slovakia
University of the Philippines Diliman, Quezon City, Philippines
Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
University of Salzburg, Salzburg, Austria
Ludwig Maximilian University, Institute of Legal Medicine, Munich, Germany
Aristotle University of Thessaloniki, Thessaloniki, Greece
Institute for Anthropological Research, Zagreb, Croatia
Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
Medical University of Gdansk, Gdańsk, Poland
Lesotho Mounted Police, Maseru, Lesotho
National Research Institute of Police Science, Kashiwa, Japan
Institute of Criminalistics, Prague, Czech Republic
Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, Budapest, Hungary
Forensic Science Program, The Pennsylvania State University, University Park, PA, United States
Nazarbayev University, Astana, Kazakhstan
University of Guadalajara, Guadalajara, Mexico
University of Szeged, Szeged, Hungary
National Center for Biotechnology, Astana, Kazakhstan
Department of Pathology and Clinical Bioinformatics, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands

Department of Genetic Identification
Laboratory of Human Genetic Genealogy
University of Madeira
University of Leicester
University of the Western Cape
University Hospital of Cologne
University of Zurich
University of Tartu
National Institute of Standards and Technology
Department of Immunology
SciLifeLab
Institute of Forensic Science
University of the Philippines Diliman
Institute of Legal Medicine
University of Salzburg
Ludwig Maximilian University
Aristotle University of Thessaloniki
Institute for Anthropological Research
Institute of Legal Medicine
Medical University of Gdansk
Lesotho Mounted Police
National Research Institute of Police Science
Institute of Criminalistics
Hungarian Institute for Forensic Sciences
Forensic Science Program
Nazarbayev University
University of Guadalajara
University of Szeged
National Center for Biotechnology
Department of Pathology and Clinical Bioinformatics

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