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Eight thousand years of natural selection in Europe

Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Bastien Llamas, Joseph Pickrell, Harald Meller, Manuel A. Rojo Guerra, Johannes Krause, David Anthony, Dorcas Brown, Carles Lalueza Fox, Alan Cooper, Kurt W. Alt, Wolfgang Haak, Nick Patterson, David Reich
doi: https://doi.org/10.1101/016477
Iain Mathieson
1Harvard Medical School, Department of Genetics, Boston MA, USA
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  • For correspondence: iain_mathieson@hms.harvard.edu reich@genetics.med.harvard.edu
Iosif Lazaridis
1Harvard Medical School, Department of Genetics, Boston MA, USA
2Broad Institute of MIT and Harvard, Cambridge MA, USA
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Nadin Rohland
1Harvard Medical School, Department of Genetics, Boston MA, USA
2Broad Institute of MIT and Harvard, Cambridge MA, USA
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Swapan Mallick
1Harvard Medical School, Department of Genetics, Boston MA, USA
2Broad Institute of MIT and Harvard, Cambridge MA, USA
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Bastien Llamas
3Australian Centre for Ancient DNA, School of Biological Sciences & Environment Institute, The University of Adelaide, Adelaide South Australia, Australia
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Joseph Pickrell
4New York Genome Center, New York NY, USA
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Harald Meller
5State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
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Manuel A. Rojo Guerra
6Departament of Prehistory and Archaeology. University of Valladolid, Spain
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Johannes Krause
7Institute for Archaeological Sciences, University of Tübingen, Tübingen, 72074, Germany
8Department of Paleoanthropology, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
9Max Planck Institute for the Science of Human History, D-07745 Jena, Germany
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David Anthony
10Hartwick College, Department of Anthropology, Oneonta NY, USA
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Dorcas Brown
10Hartwick College, Department of Anthropology, Oneonta NY, USA
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Carles Lalueza Fox
11Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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Alan Cooper
3Australian Centre for Ancient DNA, School of Biological Sciences & Environment Institute, The University of Adelaide, Adelaide South Australia, Australia
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Kurt W. Alt
5State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
12Danube Private University, Krems, Austria
13Institute for Prehistory and Archaeological Science, University of Basel, Basel, Switzerland
14Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
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Wolfgang Haak
3Australian Centre for Ancient DNA, School of Biological Sciences & Environment Institute, The University of Adelaide, Adelaide South Australia, Australia
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Nick Patterson
1Harvard Medical School, Department of Genetics, Boston MA, USA
2Broad Institute of MIT and Harvard, Cambridge MA, USA
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David Reich
1Harvard Medical School, Department of Genetics, Boston MA, USA
2Broad Institute of MIT and Harvard, Cambridge MA, USA
15Howard Hughes Medical Institute, Harvard Medical School, Boston MA, USA
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  • For correspondence: iain_mathieson@hms.harvard.edu reich@genetics.med.harvard.edu
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Abstract

The arrival of farming in Europe beginning around 8,500 years ago required adaptation to new environments, pathogens, diets, and social organizations. While evidence of natural selection can be revealed by studying patterns of genetic variation in present-day people1-6, these pattern are only indirect echoes of past events, and provide little information about where and when selection occurred. Ancient DNA makes it possible to examine populations as they were before, during and after adaptation events, and thus to reveal the tempo and mode of selection7,8. Here we report the first genome-wide scan for selection using ancient DNA, based on 83 human samples from Holocene Europe analyzed at over 300,000 positions. We find five genome-wide signals of selection, at loci associated with diet and pigmentation. Surprisingly in light of suggestions of selection on immune traits associated with the advent of agriculture and denser living conditions, we find no strong sweeps associated with immunological phenotypes. We also report a scan for selection for complex traits, and find two signals of selection on height: for short stature in Iberia after the arrival of agriculture, and for tall stature on the Pontic-Caspian steppe earlier than 5,000 years ago. A surprise is that in Scandinavian hunter-gatherers living around 8,000 years ago, there is a high frequency of the derived allele at the EDAR gene that is the strongest known signal of selection in East Asians and that is thought to have arisen in East Asia. These results document the power of ancient DNA to reveal features of past adaptation that could not be understood from analyses of present-day people.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 14, 2015.
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Eight thousand years of natural selection in Europe
Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Bastien Llamas, Joseph Pickrell, Harald Meller, Manuel A. Rojo Guerra, Johannes Krause, David Anthony, Dorcas Brown, Carles Lalueza Fox, Alan Cooper, Kurt W. Alt, Wolfgang Haak, Nick Patterson, David Reich
bioRxiv 016477; doi: https://doi.org/10.1101/016477
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Eight thousand years of natural selection in Europe
Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Bastien Llamas, Joseph Pickrell, Harald Meller, Manuel A. Rojo Guerra, Johannes Krause, David Anthony, Dorcas Brown, Carles Lalueza Fox, Alan Cooper, Kurt W. Alt, Wolfgang Haak, Nick Patterson, David Reich
bioRxiv 016477; doi: https://doi.org/10.1101/016477

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