(2023).
73. Rubinacci, S., Ribeiro, D. M., Hofmeister, R. & Delaneau, O. Efficient phasing and imputation 
of low-coverage sequencing data using large reference panels. Nat. Genet. 53, 120–126 
(2021).
74. The 1000 Genomes Project Consortium. A global reference for human genetic variation. 
Nature 526, 68–74 (2015).
75. Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse 
populations. Nature 538, 201–206 (2016).
76. Speidel, L. leospeidel/twigstats: Twigstats v1.0.1. Zenodo https://doi.org/10.5281/zenodo. 
13833119 (2024).
77. Skoglund, P. et al. Genetic evidence for two founding populations of the Americas. Nature 
525, 104–108 (2015).
78. Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. 
Nature 505, 43–49 (2014).
79. Prüfer, K. et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 
358, 655–658 (2017).
Acknowledgements L.S. was supported by a Sir Henry Wellcome Fellowship (220457/Z/20/Z). 
P.S. was supported by the European Molecular Biology Organization, the Vallee Foundation, 
the European Research Council (852558), the Wellcome Trust (217223/Z/19/Z) and Francis 
Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research 
Council and the Wellcome Trust. B.R. was supported by the Swedish Research Council  
(2021-03333).
Author contributions P.S. supervised the study. L.S. and P.S. developed the method. L.S, M.S. 
and P.S. curated the dataset. L.S. and P.S. analysed the data and wrote the manuscript. L.S., 
M.S., T.B., B.R., K.A., C.B., A.G., P.H. and P.S. interpreted the results and edited the manuscript.
Funding Open Access funding provided by The Francis Crick Institute.
Competing interests The authors declare no competing interests.
Additional information
Supplementary information The online version contains supplementary material available at 
https://doi.org/10.1038/s41586-024-08275-2.
Correspondence and requests for materials should be addressed to Leo Speidel or  
Pontus Skoglund.
Peer review information Nature thanks Jerome Kelleher, Duncan Sayer and the other, 
anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer 
reports are available.
Reprints and permissions information is available at http://www.nature.com/reprints.