title: Selective sweep on human amylase genes postdates the split with Neanderthals.
abstract: Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.
authors.affiliation: Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.
authors.forename: Charlotte E
authors.initials: CE
authors.lastname: Inchley
authors.affiliation: Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.
authors.forename: Cynthia D A
authors.initials: CD
authors.lastname: Larbey
authors.affiliation: School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.|Scientific Research Centre, University of Salahaddin, Erbil, Kurdistan, Iraq.
authors.forename: Nzar A A
authors.initials: NA
authors.lastname: Shwan
authors.affiliation: Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.|Estonian Biocentre, Tartu, 51010, Estonia.
authors.forename: Luca
authors.initials: L
authors.lastname: Pagani
authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia.
authors.forename: Lauri
authors.initials: L
authors.lastname: Saag
authors.affiliation: Division of Biological Sciences, University of Montana, Missoula, MT, USA.
authors.forename: Tiago
authors.initials: T
authors.lastname: Antão
authors.affiliation: Complexity Institute, Nanyang Technological University, Singapore.
authors.forename: Guy
authors.initials: G
authors.lastname: Jacobs
authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia.|Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
authors.forename: Georgi
authors.initials: G
authors.lastname: Hudjashov
authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia.
authors.forename: Ene
authors.initials: E
authors.lastname: Metspalu
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, Estonia.|Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
authors.forename: Mario
authors.initials: M
authors.lastname: Mitt
authors.affiliation: Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.|Thoraxclinic at the University Hospital Heidelberg, 69126 Heidelberg, Germany.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Eichstaedt
authors.affiliation: Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
authors.forename: Boris
authors.initials: B
authors.lastname: Malyarchuk
authors.affiliation: Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
authors.forename: Miroslava
authors.initials: M
authors.lastname: Derenko
authors.affiliation: Division of Radiation Oncology, National Cancer Centre, Singapore.
authors.forename: Joseph
authors.initials: J
authors.lastname: Wee
authors.affiliation: RIPAS Hospital, Bandar Seri Begawan, Brunei Darussalam.
authors.forename: Syafiq
authors.initials: S
authors.lastname: Abdullah
authors.affiliation: Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France.
authors.forename: François-Xavier
authors.initials: FX
authors.lastname: Ricaut
authors.affiliation: Department of Applied Social Sciences, University of Winchester, Sparkford Road, Winchester SO22 4NR, UK.
authors.forename: Maru
authors.initials: M
authors.lastname: Mormina
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, Estonia.
authors.forename: Reedik
authors.initials: R
authors.lastname: Mägi
authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia.|Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Estonia.|Estonian Academy of Sciences, 10130 Tallinn, Estonia.
authors.forename: Richard
authors.initials: R
authors.lastname: Villems
authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia.
authors.forename: Mait
authors.initials: M
authors.lastname: Metspalu
authors.affiliation: Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.
authors.forename: Martin K
authors.initials: MK
authors.lastname: Jones
authors.affiliation: School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
authors.forename: John A L
authors.initials: JA
authors.lastname: Armour
authors.affiliation: Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.|Estonian Biocentre, Tartu, 51010, Estonia.
authors.forename: Toomas
authors.initials: T
authors.lastname: Kivisild
mesh_terms: D000681:Amylases / Q000235:genetics*; D000818:Animals; D019143:Evolution, Molecular; D005260:Female; D018628:Gene Dosage; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D008297:Male; D059125:Neanderthals
chemical_list: D000681:Amylases