PT  - JOURNAL ARTICLE
AU  - Shohei Takuno
AU  - Peter Ralph
AU  - Kelly Swarts
AU  - Rob J. Elshire
AU  - Jeffrey C. Glaubitz
AU  - Edward S. Buckler
AU  - Matthew B. Hufford
AU  - Jeffrey Ross-Ibarra
TI  - Independent molecular basis of convergent highland adaptation in maize
AID  - 10.1101/013607
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 013607
4099  - http://biorxiv.org/content/early/2015/06/09/013607.short
4100  - http://biorxiv.org/content/early/2015/06/09/013607.full
AB  - 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.