TY - UNPB

T1 - Population Genomics of Stone Age Eurasia

AU - Allentoft, Morten E.

AU - Sikora, Martin

AU - Refoyo-Martínez, Alba

AU - Irving-Pease, Evan K.

AU - Fischer, Anders

AU - Barrie, William

AU - Ingason, Andrés

AU - Stenderup, Jesper

AU - Sjögren, Karl-Göran

AU - Pearson, Alice

AU - Mota, Barbara

AU - Paulsson, Bettina Schulz

AU - Halgren, Alma

AU - Macleod, Ruairidh

AU - Schjellerup Jørkov, Marie Louise

AU - Demeter, Fabrice

AU - Novosolov, Maria

AU - Sørensen, Lasse

AU - Nielsen, Poul-Otto

AU - Henriksen, Rasmus H. A.

AU - Vimala, Tharsika

AU - McColl, Hugh

AU - Margaryan, Ashot

AU - Ilardo, Melissa

AU - Vaughn, Andrew

AU - Mortensen, Morten Fischer

AU - Nielsen, Anne Birgitte

AU - Hede, Mikkel Ulfeldt

AU - Rasmussen, Peter

AU - Vinner, Lasse

AU - Renaud, Gabriel

AU - Stern, Aaron

AU - Trolle Jensen, Theis Zetner

AU - Johannsen, Niels Nørkjær

AU - Scorrano, Gabriele

AU - Schroeder, Hannes

AU - Lysdahl, Per

AU - Ramsøe, Abigail Daisy

AU - Skorobogatov, Andrei

AU - Schork, Andrew Joseph

AU - Rosengren, Anders

AU - Ruter, Anthony

AU - Outram, Alan

AU - Timoshenko, Aleksey A.

AU - Buzhilova, Alexandra

AU - Coppa, Alfredo

AU - Zubova, Alisa

AU - Silva, Ana Maria

AU - Hansen, Anders J.

AU - Gromov, Andrey

AU - Logvin, Andrey

AU - Gotfredsen, Anne Birgitte

AU - Nielsen, Bjarne Henning

AU - González-Rabanal, Borja

AU - Lalueza-Fox, Carles

AU - McKenzie, Catriona J.

AU - Gaunitz, Charleen

AU - Blasco, Concepción

AU - Liesau, Corina

AU - Martinez-Labarga, Cristina

AU - Pozdnyakov, Dmitri V.

AU - Cuenca-Solana, David

AU - Lordkipanidze, David O.

AU - En’shin, Dmitri

AU - Salazar-García, Domingo C

AU - Price, T. Douglas

AU - Borić, Dušan

AU - Kostyleva, Elena

AU - Veselovskaya, Elizaveta V.

AU - Usmanova, Emma R.

AU - Cappellini, Enrico

AU - Petersen, Erik Brinch

AU - Kannegaard, Esben

AU - Radina, Francesca

AU - Yediay, Fulya Eylem

AU - Duday, Henri

AU - Gutiérrez-Zugasti, Igor

AU - Potekhina, Inna

AU - Shevnina, Irina

AU - Altinkaya, Isin

AU - Guilaine, Jean

AU - Hansen, Jesper

AU - Tortosa, Joan Emili Aura

AU - Zilhão, João

AU - Vega, Jorge

AU - Pedersen, Kristoffer Buck

AU - Tunia, Krzysztof

AU - Zhao, Lei

AU - Mylnikova, Liudmila N.

AU - Larsson, Lars

AU - Metz, Laure

AU - Yeppiskoposyan, Levon

AU - Pedersen, Lisbeth

AU - Sarti, Lucia

AU - Orlando, Ludovic

AU - Slimak, Ludovic

AU - Klassen, Lutz

AU - Blank, Malou

AU - González-Morales, Manuel

AU - Silvestrini, Mara

AU - Vretemark, Maria

AU - Nesterova, Marina S.

AU - Rykun, Marina

AU - Rolfo, Mario Federico

AU - Szmyt, Marzena

AU - Przybyła, Marcin

AU - Calattini, Mauro

AU - Sablin, Mikhail

AU - Dobisíková, Miluše

AU - Meldgaard, Morten

AU - Johansen, Morten

AU - Berezina, Natalia

AU - Card, Nick

AU - Saveliev, Nikolai A.

AU - Poshekhonova, Olga

AU - Rickards, Olga

AU - Lozovskaya, Olga V.

AU - Uldum, Otto Christian

AU - Aurino, Paola

AU - Kosintsev, Pavel

AU - Courtaud, Patrice

AU - Ríos, Patricia

AU - Mortensen, Peder

AU - Lotz, Per

AU - Persson, Per Åke

AU - Bangsgaard, Pernille

AU - Damgaard, Peter de Barros

AU - Petersen, Peter Vang

AU - Martinez, Pilar Prieto

AU - Włodarczak, Piotr

AU - Smolyaninov, Roman V.

AU - Maring, Rikke

AU - Menduiña, Roberto

AU - Badalyan, Ruben

AU - Iversen, Rune

AU - Turin, Ruslan

AU - Vasilyiev, Sergey

AU - Wåhlin, Sidsel

AU - Borutskaya, Svetlana

AU - Skochina, Svetlana

AU - Sørensen, Søren Anker

AU - Andersen, Søren H.

AU - Jørgensen, Thomas

AU - Serikov, Yuri B.

AU - Molodin, Vyacheslav I.

AU - Smrcka, Vaclav

AU - Merz, Victor

AU - Appadurai, Vivek

AU - Moiseyev, Vyacheslav

AU - Magnusson, Yvonne

AU - Kjær, Kurt H.

AU - Lynnerup, Niels

AU - Lawson, Daniel J.

AU - Sudmant, Peter H.

AU - Rasmussen, Simon

AU - Korneliussen, Thorfinn

AU - Durbin, Richard

AU - Nielsen, Rasmus

AU - Delaneau, Olivier

AU - Werge, Thomas

AU - Racimo, Fernando

AU - Kristiansen, Kristian

AU - Willerslev, Eske

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

U2 - 10.1101/2022.05.04.490594

DO - 10.1101/2022.05.04.490594

M3 - Preprint

T3 - bioRxiv

SP - 1

EP - 71

BT - Population Genomics of Stone Age Eurasia

ER -