The selection landscape and genetic legacy of ancient Eurasians

Evan K. Irving-Pease (), Alba Refoyo-Martínez, William Barrie, Andrés Ingason, Alice Pearson, Anders Fischer, Karl-Göran Sjögren, Alma S. Halgren, Ruairidh Macleod, Fabrice Demeter, Rasmus A. Henriksen, Tharsika Vimala, Hugh McColl, Andrew H. Vaughn, Leo Speidel, Aaron J. Stern, Gabriele Scorrano, Abigail Ramsøe, Andrew J. Schork, Anders Rosengren, Lei Zhao, Kristian Kristiansen, Astrid K. N. Iversen, Lars Fugger, Peter H. Sudmant, Daniel J. Lawson, Richard Durbin, Thorfinn Korneliussen, Thomas Werge, Morten E. Allentoft, Martin Sikora, Rasmus Nielsen (), Fernando Racimo () and Eske Willerslev ()
Additional contact information
Evan K. Irving-Pease: University of Copenhagen
Alba Refoyo-Martínez: University of Copenhagen
William Barrie: University of Cambridge
Andrés Ingason: University of Copenhagen
Alice Pearson: University of Cambridge
Anders Fischer: University of Copenhagen
Karl-Göran Sjögren: University of Gothenburg
Alma S. Halgren: University of California Berkeley
Ruairidh Macleod: University of Cambridge
Fabrice Demeter: University of Copenhagen
Rasmus A. Henriksen: University of Copenhagen
Tharsika Vimala: University of Copenhagen
Hugh McColl: University of Copenhagen
Andrew H. Vaughn: University of California
Leo Speidel: University College London
Aaron J. Stern: University of California
Gabriele Scorrano: University of Copenhagen
Abigail Ramsøe: University of Copenhagen
Andrew J. Schork: Copenhagen University Hospital
Anders Rosengren: University of Copenhagen
Lei Zhao: University of Copenhagen
Kristian Kristiansen: University of Copenhagen
Astrid K. N. Iversen: University of Oxford
Lars Fugger: University of Oxford
Peter H. Sudmant: University of California Berkeley
Daniel J. Lawson: University of Bristol
Richard Durbin: University of Cambridge
Thorfinn Korneliussen: University of Copenhagen
Thomas Werge: University of Copenhagen
Morten E. Allentoft: University of Copenhagen
Martin Sikora: University of Copenhagen
Rasmus Nielsen: University of Copenhagen
Fernando Racimo: University of Copenhagen
Eske Willerslev: University of Copenhagen

Nature, 2024, vol. 625, issue 7994, 312-320

Abstract: Abstract The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer’s disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.

Date: 2024
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DOI: 10.1038/s41586-023-06705-1

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