The Selection Landscape and Genetic Legacy of Ancient Eurasians

Research output: Working paperPreprintResearch

Standard

The Selection Landscape and Genetic Legacy of Ancient Eurasians. / Irving-Pease, Evan; Refoyo Martínez, Alba; Ingason, Andrés; Pearson, Alice; Fischer, Anders; Barrie, William; Sjögren, Karl-Göran; Halgren, Alma S.; Macleod, Ruairidh; Demeter, Fabrice; Henriksen, Rasmus Henrik Amund; Vimala, Tharsika; McColl, Hugh; Vaughn, Andrew; Stern, Aaron J.; Speidel, Leo; Scorrano, Gabriele; Ramsøe, Abigail; Schork, Andrew J.; Rosengren, Anders; Zhao, Lei; Kristiansen, Kristian; Sudmant, Peter H.; Lawson, Daniel J.; Durbin, Richard; Korneliussen, Thorfinn; Werge, Thomas; Allentoft, Morten E.; Sikora, Martin; Nielsen, Rasmus; Racimo, Fernando; Willerslev, Eske.

bioRxiv, 2022.

Research output: Working paperPreprintResearch

Harvard

Irving-Pease, E, Refoyo Martínez, A, Ingason, A, Pearson, A, Fischer, A, Barrie, W, Sjögren, K-G, Halgren, AS, Macleod, R, Demeter, F, Henriksen, RHA, Vimala, T, McColl, H, Vaughn, A, Stern, AJ, Speidel, L, Scorrano, G, Ramsøe, A, Schork, AJ, Rosengren, A, Zhao, L, Kristiansen, K, Sudmant, PH, Lawson, DJ, Durbin, R, Korneliussen, T, Werge, T, Allentoft, ME, Sikora, M, Nielsen, R, Racimo, F & Willerslev, E 2022 'The Selection Landscape and Genetic Legacy of Ancient Eurasians' bioRxiv. https://doi.org/10.1101/2022.09.22.509027

APA

Irving-Pease, E., Refoyo Martínez, A., Ingason, A., Pearson, A., Fischer, A., Barrie, W., Sjögren, K-G., Halgren, A. S., Macleod, R., Demeter, F., Henriksen, R. H. A., Vimala, T., McColl, H., Vaughn, A., Stern, A. J., Speidel, L., Scorrano, G., Ramsøe, A., Schork, A. J., ... Willerslev, E. (2022). The Selection Landscape and Genetic Legacy of Ancient Eurasians. bioRxiv. https://doi.org/10.1101/2022.09.22.509027

Vancouver

Irving-Pease E, Refoyo Martínez A, Ingason A, Pearson A, Fischer A, Barrie W et al. The Selection Landscape and Genetic Legacy of Ancient Eurasians. bioRxiv. 2022. https://doi.org/10.1101/2022.09.22.509027

Author

Irving-Pease, Evan ; Refoyo Martínez, Alba ; Ingason, Andrés ; Pearson, Alice ; Fischer, Anders ; Barrie, William ; Sjögren, Karl-Göran ; Halgren, Alma S. ; Macleod, Ruairidh ; Demeter, Fabrice ; Henriksen, Rasmus Henrik Amund ; Vimala, Tharsika ; McColl, Hugh ; Vaughn, Andrew ; Stern, Aaron J. ; Speidel, Leo ; Scorrano, Gabriele ; Ramsøe, Abigail ; Schork, Andrew J. ; Rosengren, Anders ; Zhao, Lei ; Kristiansen, Kristian ; Sudmant, Peter H. ; Lawson, Daniel J. ; Durbin, Richard ; Korneliussen, Thorfinn ; Werge, Thomas ; Allentoft, Morten E. ; Sikora, Martin ; Nielsen, Rasmus ; Racimo, Fernando ; Willerslev, Eske. / The Selection Landscape and Genetic Legacy of Ancient Eurasians. bioRxiv, 2022.

Bibtex

@techreport{a21bb1387e7548efbb656a12ba6cebb7,
title = "The Selection Landscape and Genetic Legacy of Ancient Eurasians",
abstract = "The Eurasian Holocene (beginning c. 12 thousand 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 an imputed dataset of >1600 complete ancient genome sequences, and new computational methods for locating selection in time and space, we reconstructed the selection landscape of the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, possibly associated with the dietary shift occurring in this period. We show that the selection on loci such as the FADS cluster, associated with fatty acid metabolism, and the lactase persistence locus, began earlier than previously thought. A substantial amount of selection is also found in the HLA region and other loci associated with immunity, possibly due to the increased exposure to pathogens during the Neolithic, which may explain the current high prevalence of auto-immune disease, such as psoriasis, due to genetic trade-offs. By using ancient populations to infer local ancestry tracks in hundreds of thousands of samples from the UK Biobank, we find strong genetic differentiation among ancient Europeans in loci associated with anthropometric traits and susceptibility to several diseases that contribute to present-day disease burden. These were previously thought to be caused by local selection, but in fact can be attributed to differential genetic contributions from various source populations that are ancestral to present-day Europeans. Thus, alleles associated with increased height seem to have increased in frequency following the Yamnaya migration into northwestern Europe around 5,000 years ago. Alleles associated with increased risk of some mood-related phenotypes are overrepresented in the farmer ancestry component entering Europe from Anatolia around 11,000 years ago, while western hunter-gatherers show a strikingly high contribution of alleles conferring risk of traits related to diabetes. Our results paint a picture of the combined contributions of migration and selection in shaping the phenotypic landscape of present-day Europeans that suggests a combination of ancient selection and migration, rather than recent local selection, is the primary driver of present-day phenotypic differences in Europe.",
author = "Evan Irving-Pease and {Refoyo Mart{\'i}nez}, Alba and Andr{\'e}s Ingason and Alice Pearson and Anders Fischer and William Barrie and Karl-G{\"o}ran Sj{\"o}gren and Halgren, {Alma S.} and Ruairidh Macleod and Fabrice Demeter and Henriksen, {Rasmus Henrik Amund} and Tharsika Vimala and Hugh McColl and Andrew Vaughn and Stern, {Aaron J.} and Leo Speidel and Gabriele Scorrano and Abigail Rams{\o}e and Schork, {Andrew J.} and Anders Rosengren and Lei Zhao and Kristian Kristiansen and Sudmant, {Peter H.} and Lawson, {Daniel J.} and Richard Durbin and Thorfinn Korneliussen and Thomas Werge and Allentoft, {Morten E.} and Martin Sikora and Rasmus Nielsen and Fernando Racimo and Eske Willerslev",
year = "2022",
doi = "10.1101/2022.09.22.509027",
language = "English",
publisher = "bioRxiv",
type = "WorkingPaper",
institution = "bioRxiv",

}

RIS

TY - UNPB

T1 - The Selection Landscape and Genetic Legacy of Ancient Eurasians

AU - Irving-Pease, Evan

AU - Refoyo Martínez, Alba

AU - Ingason, Andrés

AU - Pearson, Alice

AU - Fischer, Anders

AU - Barrie, William

AU - Sjögren, Karl-Göran

AU - Halgren, Alma S.

AU - Macleod, Ruairidh

AU - Demeter, Fabrice

AU - Henriksen, Rasmus Henrik Amund

AU - Vimala, Tharsika

AU - McColl, Hugh

AU - Vaughn, Andrew

AU - Stern, Aaron J.

AU - Speidel, Leo

AU - Scorrano, Gabriele

AU - Ramsøe, Abigail

AU - Schork, Andrew J.

AU - Rosengren, Anders

AU - Zhao, Lei

AU - Kristiansen, Kristian

AU - Sudmant, Peter H.

AU - Lawson, Daniel J.

AU - Durbin, Richard

AU - Korneliussen, Thorfinn

AU - Werge, Thomas

AU - Allentoft, Morten E.

AU - Sikora, Martin

AU - Nielsen, Rasmus

AU - Racimo, Fernando

AU - Willerslev, Eske

PY - 2022

Y1 - 2022

N2 - The Eurasian Holocene (beginning c. 12 thousand 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 an imputed dataset of >1600 complete ancient genome sequences, and new computational methods for locating selection in time and space, we reconstructed the selection landscape of the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, possibly associated with the dietary shift occurring in this period. We show that the selection on loci such as the FADS cluster, associated with fatty acid metabolism, and the lactase persistence locus, began earlier than previously thought. A substantial amount of selection is also found in the HLA region and other loci associated with immunity, possibly due to the increased exposure to pathogens during the Neolithic, which may explain the current high prevalence of auto-immune disease, such as psoriasis, due to genetic trade-offs. By using ancient populations to infer local ancestry tracks in hundreds of thousands of samples from the UK Biobank, we find strong genetic differentiation among ancient Europeans in loci associated with anthropometric traits and susceptibility to several diseases that contribute to present-day disease burden. These were previously thought to be caused by local selection, but in fact can be attributed to differential genetic contributions from various source populations that are ancestral to present-day Europeans. Thus, alleles associated with increased height seem to have increased in frequency following the Yamnaya migration into northwestern Europe around 5,000 years ago. Alleles associated with increased risk of some mood-related phenotypes are overrepresented in the farmer ancestry component entering Europe from Anatolia around 11,000 years ago, while western hunter-gatherers show a strikingly high contribution of alleles conferring risk of traits related to diabetes. Our results paint a picture of the combined contributions of migration and selection in shaping the phenotypic landscape of present-day Europeans that suggests a combination of ancient selection and migration, rather than recent local selection, is the primary driver of present-day phenotypic differences in Europe.

AB - The Eurasian Holocene (beginning c. 12 thousand 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 an imputed dataset of >1600 complete ancient genome sequences, and new computational methods for locating selection in time and space, we reconstructed the selection landscape of the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, possibly associated with the dietary shift occurring in this period. We show that the selection on loci such as the FADS cluster, associated with fatty acid metabolism, and the lactase persistence locus, began earlier than previously thought. A substantial amount of selection is also found in the HLA region and other loci associated with immunity, possibly due to the increased exposure to pathogens during the Neolithic, which may explain the current high prevalence of auto-immune disease, such as psoriasis, due to genetic trade-offs. By using ancient populations to infer local ancestry tracks in hundreds of thousands of samples from the UK Biobank, we find strong genetic differentiation among ancient Europeans in loci associated with anthropometric traits and susceptibility to several diseases that contribute to present-day disease burden. These were previously thought to be caused by local selection, but in fact can be attributed to differential genetic contributions from various source populations that are ancestral to present-day Europeans. Thus, alleles associated with increased height seem to have increased in frequency following the Yamnaya migration into northwestern Europe around 5,000 years ago. Alleles associated with increased risk of some mood-related phenotypes are overrepresented in the farmer ancestry component entering Europe from Anatolia around 11,000 years ago, while western hunter-gatherers show a strikingly high contribution of alleles conferring risk of traits related to diabetes. Our results paint a picture of the combined contributions of migration and selection in shaping the phenotypic landscape of present-day Europeans that suggests a combination of ancient selection and migration, rather than recent local selection, is the primary driver of present-day phenotypic differences in Europe.

U2 - 10.1101/2022.09.22.509027

DO - 10.1101/2022.09.22.509027

M3 - Preprint

BT - The Selection Landscape and Genetic Legacy of Ancient Eurasians

PB - bioRxiv

ER -

ID: 327770149