The origin of maize (Zea mays mays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal1,​2,​3,​4 or highland5,6 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 uncharacterized7. 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.

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The authors acknowledge the following grants: Marie Curie Actions IEF 272927 and COFUND DFF-1325-00136, Danish National Research Foundation DNRF94, Danish Council for Independent Research 10-081390 and 1325-00136, Lundbeck Foundation grant R52-A5062, Vand Fondecyt Grant 1130261, a grant from the UC Davis Genome Center for the highland maize sequence and NSF IOS-1238014. R.F. is supported by a Young Investigator grant (VKR023446) from Villum Fonden. P.S. was funded by the Wenner-Gren foundation. The authors thank Ângela Ribeiro, Shohei Takuno and Philip Johnson for comments and discussion and staff at the Danish National High-Throughput DNA Sequencing for technical support.

Author information


  1. Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark

    • Rute R. da Fonseca
    • , Nathan Wales
    • , Enrico Cappellini
    • , José Alfredo Samaniego
    • , Christian Carøe
    • , María C. Ávila-Arcos
    • , Thorfinn Sand Korneliussen
    • , Filipe Garrett Vieira
    • , Eske Willerslev
    • , Rasmus Nielsen
    •  & M. Thomas P. Gilbert
  2. The Bioinformatics Centre, University of Copenhagen, 2200 Copenhagen, Denmark

    • Rute R. da Fonseca
    •  & Anders Albrechtsen
  3. Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA

    • Bruce D. Smith
  4. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Pontus Skoglund
  5. Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA

    • Matteo Fumagalli
    •  & Filipe Garrett Vieira
  6. Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

    • María C. Ávila-Arcos
  7. Department of Ecology, Evolution, & Organismal Biology, Iowa State University, 50011, USA

    • David E. Hufnagel
    •  & Matthew B. Hufford
  8. Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden

    • Mattias Jakobsson
  9. Science for Life Laboratory, Uppsala University, Uppsala 752 36, Sweden

    • Mattias Jakobsson
  10. Instituto de Alta Investigación, Universidad de Tarapacá, 15101 Arica, Chile

    • Bernardo Arriaza
  11. Department of Integrative Biology and Statistics, University of California, Berkeley, California 94720-3140, USA

    • Rasmus Nielsen
  12. Department of Plant Sciences, Center for Population Biology and Genome Center, University of California, Davis, California 95616, USA

    • Jeffrey Ross-Ibarra
  13. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia

    • M. Thomas P. Gilbert


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M.T.P.G., B.D.S. and R.R.F. conceived and headed the project. M.T.P.G., N.W. and E.C. designed the experimental research project setup. R.R.F. designed the bioinformatics and population genetics setup with input from M.T.P.G., A.A. and J.R.I. Both B.D.S. and B.A. provided ancient samples and associated context information. M.B.H. and J.R.I. provided sequence data for the highland Palomero de Jalisco landrace. B.D.S. provided the archaeological background and performed the radiocarbon dating. N.W., E.C. and C.C. performed the ancient DNA extractions, library construction and capture with input from M.T.P.G. Both M.C.A. and J.A.S. provided bioinformatics support for the optimization of the capture-related laboratory work. J.A.S. annotated the silent and non-synonymous sites. TSK designed the tool to filter transitions in bam files. R.R.F. chose the capture targets, performed the quality filtering and mapping of the ancient datasets, and prepared the maize HapMap2 data and the modern genome data for all downstream analyses. R.R.F. performed the error determination, neutrality tests, NGSadmix, TreeMix, phylogenetic and demographic inference analyses with input from A.A. and J.R.I. D-statistics analysis was performed by P.S. with input from M.J. Both R.R.F. and M.F. performed the PBS-based selection analyses with input from R.N. Both D.E.H. and M.B.H. performed the STRUCTURE analysis. F.G.V. performed the inbreeding analysis. R.R.F., B.D.S., M.B.H., J.R.I. and M.T.P.G. wrote the manuscript with critical input from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Rute R. da Fonseca or M. Thomas P. Gilbert.

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