title: The origin and evolution of maize in the Southwestern United States.
abstract: The origin of maize (Zea mays mays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal(1-4) or highland(5,6) routes of diffusion of maize into the United States. Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized(7). To address these issues, we compared nuclear DNA from 32 archaeological maize samples spanning 6,000 years of evolution to modern landraces. We found that the initial diffusion of maize into the Southwest about 4,000 years ago is likely to have occurred along a highland route, followed by gene flow from a lowland coastal maize beginning at least 2,000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the climatic and cultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content.
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.|The Bioinformatics Centre, University of Copenhagen, 2200 Copenhagen, Denmark.
authors.forename: Rute R
authors.initials: RR
authors.lastname: da Fonseca
authors.affiliation: Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA.
authors.forename: Bruce D
authors.initials: BD
authors.lastname: Smith
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.
authors.forename: Nathan
authors.identifier: http://orcid.org/0000-0003-0359-8450
authors.initials: N
authors.lastname: Wales
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.
authors.forename: Enrico
authors.identifier: http://orcid.org/0000-0001-7885-7811
authors.initials: E
authors.lastname: Cappellini
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Pontus
authors.initials: P
authors.lastname: Skoglund
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Fumagalli
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.
authors.forename: José Alfredo
authors.initials: JA
authors.lastname: Samaniego
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.
authors.forename: Christian
authors.initials: C
authors.lastname: Carøe
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.|Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
authors.forename: María C
authors.initials: MC
authors.lastname: Ávila-Arcos
authors.affiliation: Department of Ecology, Evolution, &Organismal Biology, Iowa State University, 50011, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Hufnagel
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.
authors.forename: Thorfinn Sand
authors.identifier: http://orcid.org/0000-0001-7576-5380
authors.initials: TS
authors.lastname: Korneliussen
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.|Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
authors.forename: Filipe Garrett
authors.initials: FG
authors.lastname: Vieira
authors.affiliation: Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden.|Science for Life Laboratory, Uppsala University, Uppsala 752 36, Sweden.
authors.forename: Mattias
authors.initials: M
authors.lastname: Jakobsson
authors.affiliation: Instituto de Alta Investigación, Universidad de Tarapacá, 15101 Arica, Chile.
authors.forename: Bernardo
authors.initials: B
authors.lastname: Arriaza
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.|Department of Integrative Biology and Statistics, University of California, Berkeley, California 94720-3140, USA.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.affiliation: Department of Ecology, Evolution, &Organismal Biology, Iowa State University, 50011, USA.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Hufford
authors.affiliation: The Bioinformatics Centre, University of Copenhagen, 2200 Copenhagen, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Albrechtsen
authors.affiliation: Department of Plant Sciences, Center for Population Biology and Genome Center, University of California, Davis, California 95616, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Ross-Ibarra
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.|Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia.
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert