Population Genomics of Stone Age Eurasia

Research output: Working paperPreprintResearch

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    Submitted manuscript, 12.9 MB, PDF document

  • Anders Fischer
  • William Barrie
  • Andrés Ingason
  • Jesper Stenderup
  • Karl-Göran Sjögren
  • Alice Pearson
  • Barbara Mota
  • Bettina Schulz Paulsson
  • Alma Halgren
  • Ruairidh Macleod
  • Lasse Sørensen
  • Poul-Otto Nielsen
  • Melissa Ilardo
  • Andrew Vaughn
  • Morten Fischer Mortensen
  • Anne Birgitte Nielsen
  • Mikkel Ulfeldt Hede
  • Peter Rasmussen
  • Aaron Stern
  • Niels Nørkjær Johannsen
  • Per Lysdahl
  • Abigail Daisy Ramsøe
  • Andrei Skorobogatov
  • Andrew Joseph Schork
  • Anders Rosengren
  • Alan Outram
  • Aleksey A. Timoshenko
  • Alexandra Buzhilova
  • Alfredo Coppa
  • Alisa Zubova
  • Ana Maria Silva
  • Andrey Gromov
  • Andrey Logvin
  • Anne Birgitte Gotfredsen
  • Bjarne Henning Nielsen
  • Borja González-Rabanal
  • Carles Lalueza-Fox
  • Catriona J. McKenzie
  • Concepción Blasco
  • Corina Liesau
  • Cristina Martinez-Labarga
  • Dmitri V. Pozdnyakov
  • David Cuenca-Solana
  • David O. Lordkipanidze
  • Dmitri En’shin
  • Domingo C Salazar-García
  • T. Douglas Price
  • Dušan Borić
  • Elena Kostyleva
  • Elizaveta V. Veselovskaya
  • Emma R. Usmanova
  • Enrico Cappellini
  • Esben Kannegaard
  • Francesca Radina
  • Yediay, Fulya Eylem
  • Henri Duday
  • Igor Gutiérrez-Zugasti
  • Inna Potekhina
  • Irina Shevnina
  • Altinkaya, Isin
  • Jean Guilaine
  • Jesper Hansen
  • Joan Emili Aura Tortosa
  • João Zilhão
  • Jorge Vega
  • Kristoffer Buck Pedersen
  • Krzysztof Tunia
  • Zhao, Lei
  • Liudmila N. Mylnikova
  • Lars Larsson
  • Laure Metz
  • Levon Yeppiskoposyan
  • Lisbeth Pedersen
  • Lucia Sarti
  • Ludovic Orlando
  • Ludovic Slimak
  • Lutz Klassen
  • Malou Blank
  • Manuel González-Morales
  • Mara Silvestrini
  • Maria Vretemark
  • Marina S. Nesterova
  • Marina Rykun
  • Mario Federico Rolfo
  • Marzena Szmyt
  • Marcin Przybyła
  • Mauro Calattini
  • Mikhail Sablin
  • Miluše Dobisíková
  • Meldgaard, Morten
  • Morten Johansen
  • Natalia Berezina
  • Nick Card
  • Nikolai A. Saveliev
  • Olga Poshekhonova
  • Olga Rickards
  • Olga V. Lozovskaya
  • Otto Christian Uldum
  • Paola Aurino
  • Pavel Kosintsev
  • Patrice Courtaud
  • Patricia Ríos
  • Peder Mortensen
  • Per Lotz
  • Per Åke Persson
  • Pernille Bangsgaard
  • Peter de Barros Damgaard
  • Peter Vang Petersen
  • Pilar Prieto Martinez
  • Piotr Włodarczak
  • Roman V. Smolyaninov
  • Rikke Maring
  • Roberto Menduiña
  • Ruben Badalyan
  • Iversen, Rune
  • Ruslan Turin
  • Sergey Vasilyiev
  • Sidsel Wåhlin
  • Svetlana Borutskaya
  • Svetlana Skochina
  • Søren Anker Sørensen
  • Søren H. Andersen
  • Thomas Jørgensen
  • Yuri B. Serikov
  • Vyacheslav I. Molodin
  • Vaclav Smrcka
  • Victor Merz
  • Vivek Appadurai
  • Vyacheslav Moiseyev
  • Yvonne Magnusson
  • Kjær, Kurt H.
  • Lynnerup, Niels
  • Daniel J. Lawson
  • Peter H. Sudmant
  • Rasmussen, Simon
  • Korneliussen, Thorfinn Sand
  • Richard Durbin
  • Rasmus Nielsen
  • Olivier Delaneau
  • Werge, Thomas
  • Racimo, Fernando
  • Kristian Kristiansen
  • Willerslev, Eske
The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this “Great Divide”, including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.Competing Interest StatementThe authors have declared no competing interest.
Original languageEnglish
Pages1-71
DOIs
Publication statusPublished - 2022
SeriesbioRxiv

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