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Originally published as Genetics Published Articles Ahead of Print on January 19, 2009.
Genetics, Vol. 181, 1399-1413, April 2009, Copyright © 2009
doi:10.1534/genetics.108.097238
Historical Divergence and Gene Flow in the Genus Zea
Jeffrey Ross-Ibarra*,1,
Maud Tenaillon
and
Brandon S. Gaut*,2
* Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 and CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif sur Yvette, France
2 Corresponding author: Department of Ecology and Evolutionary Biology, University of California, 5205 McGaugh Hall, Irvine, CA 92697.
E-mail: bgaut{at}uci.edu
Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence—and ultimately speciation—remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticate Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last 
150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.
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