The origin and evolution of maize in the Southwestern United States (original) (raw)

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Acknowledgements

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.

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Authors and Affiliations

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. Department of Anthropology, Program in Human Ecology and Archaeobiology, 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. Department of Environment and Agriculture, Trace and Environmental DNA Laboratory, Curtin University, Perth, Western Australia, 6102, Australia
    M. Thomas P. Gilbert

Authors

1. Rute R. da Fonseca
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2. Bruce D. Smith
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3. Nathan Wales
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4. Enrico Cappellini
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5. Pontus Skoglund
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6. Matteo Fumagalli
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7. José Alfredo Samaniego
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8. Christian Carøe
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9. María C. Ávila-Arcos
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10. David E. Hufnagel
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11. Thorfinn Sand Korneliussen
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12. Filipe Garrett Vieira
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13. Mattias Jakobsson
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14. Bernardo Arriaza
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15. Eske Willerslev
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16. Rasmus Nielsen
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17. Matthew B. Hufford
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18. Anders Albrechtsen
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19. Jeffrey Ross-Ibarra
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20. M. Thomas P. Gilbert
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Contributions

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.

Corresponding authors

Correspondence toRute R. da Fonseca or M. Thomas P. Gilbert.

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The authors declare no competing financial interests.

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da Fonseca, R., Smith, B., Wales, N. et al. The origin and evolution of maize in the Southwestern United States.Nature Plants 1, 14003 (2015). https://doi.org/10.1038/nplants.2014.3

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• Received: 06 June 2014
• Accepted: 08 October 2014
• Published: 08 January 2015
• DOI: https://doi.org/10.1038/nplants.2014.3