Detection of human adaptation during the past 2000 years
Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele freq...
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| Published in | Science (American Association for the Advancement of Science) Vol. 354; no. 6313; pp. 760 - 764 |
|---|---|
| Main Authors | , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
American Association for the Advancement of Science
11.11.2016
The American Association for the Advancement of Science |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0036-8075 1095-9203 1095-9203 |
| DOI | 10.1126/science.aag0776 |
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| Abstract | Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2OOO to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans. |
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| AbstractList | Evolutionary analyses aim to identify recent genetic changes that are likely to have been subject to selection. Field et al. present a method to identify such changes, the singleton density score, which they applied to over 3000 human genomes. Over the past ∼100 generations (2000 to 3000 years), Europeans are likely to have experienced selection for genetic variants, including those that affect skin and hair pigmentation, as well as height. Science, this issue p. 760 Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans. Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2OOO to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans. Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans. Identifying genes under recent selectionEvolutionary analyses aim to identify recent genetic changes that are likely to have been subject to selection. Field et al. present a method to identify such changes, the singleton density score, which they applied to over 3000 human genomes. Over the past similar to 100 generations (2000 to 3000 years), Europeans are likely to have experienced selection for genetic variants, including those that affect skin and hair pigmentation, as well as height.Science, this issue p. 760 Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans. Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans. Evolutionary analyses aim to identify recent genetic changes that are likely to have been subject to selection. Field et al. present a method to identify such changes, the singleton density score, which they applied to over 3000 human genomes. Over the past ∼100 generations (2000 to 3000 years), Europeans are likely to have experienced selection for genetic variants, including those that affect skin and hair pigmentation, as well as height. Science , this issue p. 760 The singleton density score identifies evidence of recent selection in Europeans. Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans. |
| Author | Boyle, Evan A Gao, Ziyue Rocheleau, Ghislain Telis, Natalie Field, Yair Yengo, Loic Pritchard, Jonathan K. Golan, David Gaulton, Kyle J. Froguel, Philippe McCarthy, Mark I. |
| AuthorAffiliation | 3 Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA 5 Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199–EGID, F-59000 Lille, France 4 Wellcome Trust Center for Human Genetics, and Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK 6 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia 8 Department of Biology, Stanford University, Stanford, CA, USA 7 Imperial College, Department of Genomics of Common Disease, London Hammersmith Hospital, London, UK 1 Department of Genetics, Stanford University, Stanford, CA 94305, USA 2 Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA |
| AuthorAffiliation_xml | – name: 7 Imperial College, Department of Genomics of Common Disease, London Hammersmith Hospital, London, UK – name: 5 Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199–EGID, F-59000 Lille, France – name: 4 Wellcome Trust Center for Human Genetics, and Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK – name: 8 Department of Biology, Stanford University, Stanford, CA, USA – name: 2 Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA – name: 6 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia – name: 1 Department of Genetics, Stanford University, Stanford, CA 94305, USA – name: 3 Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA |
| Author_xml | – sequence: 1 givenname: Yair surname: Field fullname: Field, Yair – sequence: 2 givenname: Evan A surname: Boyle fullname: Boyle, Evan A – sequence: 3 givenname: Natalie surname: Telis fullname: Telis, Natalie – sequence: 4 givenname: Ziyue surname: Gao fullname: Gao, Ziyue – sequence: 5 givenname: Kyle J. surname: Gaulton fullname: Gaulton, Kyle J. – sequence: 6 givenname: David surname: Golan fullname: Golan, David – sequence: 7 givenname: Loic surname: Yengo fullname: Yengo, Loic – sequence: 8 givenname: Ghislain surname: Rocheleau fullname: Rocheleau, Ghislain – sequence: 9 givenname: Philippe surname: Froguel fullname: Froguel, Philippe – sequence: 10 givenname: Mark I. surname: McCarthy fullname: McCarthy, Mark I. – sequence: 11 givenname: Jonathan K. surname: Pritchard fullname: Pritchard, Jonathan K. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27738015$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | Copyright © 2016 American Association for the Advancement of Science Copyright © 2016, American Association for the Advancement of Science. Copyright © 2016, American Association for the Advancement of Science |
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| Snippet | Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer... Evolutionary analyses aim to identify recent genetic changes that are likely to have been subject to selection. Field et al. present a method to identify such... Evolutionary analyses aim to identify recent genetic changes that are likely to have been subject to selection. Field et al. present a method to identify such... Identifying genes under recent selectionEvolutionary analyses aim to identify recent genetic changes that are likely to have been subject to selection. Field... |
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| SubjectTerms | Adaptation Adaptation, Physiological - genetics Density Evolutionary biology Eye Color - genetics Frequency shift Gene Frequency Genes Genetic Loci Genetic variance Genetics Genome, Human Genome-Wide Association Study Genomes Hair Hair Color - genetics Haplotypes Humans - genetics Lactase Lactase - genetics Major Histocompatibility Complex - genetics Pedigree Phenotypic variations Pigmentation Population genetics Selection, Genetic United Kingdom |
| Title | Detection of human adaptation during the past 2000 years |
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