title: Detection of human adaptation during the past 2000 years.
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 ~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.
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA. yairf@stanford.edu pritch@stanford.edu.|Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
authors.forename: Yair
authors.initials: Y
authors.lastname: Field
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA.
authors.forename: Evan A
authors.initials: EA
authors.lastname: Boyle
authors.affiliation: Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA.
authors.forename: Natalie
authors.initials: N
authors.lastname: Telis
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA.|Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
authors.forename: Ziyue
authors.initials: Z
authors.lastname: Gao
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA.|Wellcome Trust Center for Human Genetics, and Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK.
authors.forename: Kyle J
authors.initials: KJ
authors.lastname: Gaulton
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA.
authors.forename: David
authors.initials: D
authors.lastname: Golan
authors.affiliation: Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199-EGID, F-59000 Lille, France.|Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
authors.forename: Loic
authors.initials: L
authors.lastname: Yengo
authors.affiliation: Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199-EGID, F-59000 Lille, France.
authors.forename: Ghislain
authors.initials: G
authors.lastname: Rocheleau
authors.affiliation: Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199-EGID, F-59000 Lille, France.|Imperial College, Department of Genomics of Common Disease, London Hammersmith Hospital, London, UK.
authors.forename: Philippe
authors.initials: P
authors.lastname: Froguel
authors.affiliation: Wellcome Trust Center for Human Genetics, and Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK.
authors.forename: Mark I
authors.initials: MI
authors.lastname: McCarthy
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA. yairf@stanford.edu pritch@stanford.edu.|Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.|Department of Biology, Stanford University, Stanford, CA, USA.
authors.forename: Jonathan K
authors.initials: JK
authors.lastname: Pritchard
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D005127:Eye Color / Q000235:genetics; D005787:Gene Frequency; D056426:Genetic Loci; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006200:Hair Color / Q000235:genetics; D006239:Haplotypes; D006801:Humans / Q000235:genetics; D043322:Lactase / Q000235:genetics*; D008285:Major Histocompatibility Complex / Q000235:genetics*; D010375:Pedigree; D012641:Selection, Genetic; D006113:United Kingdom
chemical_list: D043322:Lactase