title: Independent Molecular Basis of Convergent Highland Adaptation in Maize.
abstract: Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Shohei
authors.initials: S
authors.lastname: Takuno
authors.affiliation: Department of Evolution and Ecology, University of California, Davis, California 95616 Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-0371.
authors.forename: Peter
authors.initials: P
authors.lastname: Ralph
authors.affiliation: School of Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853-2703.
authors.forename: Kelly
authors.initials: K
authors.lastname: Swarts
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853-2703.
authors.forename: Rob J
authors.initials: RJ
authors.lastname: Elshire
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853-2703.
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Glaubitz
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853-2703 United States Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853.
authors.forename: Edward S
authors.initials: ES
authors.lastname: Buckler
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616 Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Hufford
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616 The Center for Population Biology and the Genome Center, University of California, Davis, California 95616 rossibarra@ucdavis.edu.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Ross-Ibarra
mesh_terms: D000064:Acclimatization / Q000235:genetics; D000222:Adaptation, Physiological / Q000235:genetics*; D019143:Evolution, Molecular; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation; D023281:Genomics; D006239:Haplotypes; D008954:Models, Biological; D009154:Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D003313:Zea mays / Q000235:genetics* / Q000502:physiology*
keywords: convergent evolution; highland adaptation; maize; population genomics