Reagon et al. BMC Evolutionary Biology 2010, 10:180 http://www.biomedcentral.com/1471-2148/10/180 Open Access RESEARCH ARTICLE © 2010 Reagon et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Research article Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice Michael Reagon 1 , Carrie S Thurber 1 , Briana L Gross 2 , Kenneth M Olsen 2 , Yulin Jia 3 and Ana L Caicedo* 1 Abstract Background: Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results: We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives. Conclusions: Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex. Background Among the most widespread and costly agricultural pests are the numerous weeds that have evolved from within the same complex of interfertile species as domesticated plants [1-3]. The recent and rapid evolution of these con- specific weeds also presents unique opportunities to study processes influencing adaptive population diver- gence and parallel evolution of weedy life-histories. Con- specific weeds are morphologically and ecologically divergent from domesticated and wild congener species, and are not simply transient "volunteers" of the previous season's crop [4,5]. The evolutionary success of conspe- cific weeds is often attributed to acquisition of traits asso- ciated with wild plants (e.g. dormancy), presumably selected against in crops. Conversely, these weeds also often exhibit characteristics typical of domesticated plants, (e.g. more selfing, rapid growth), which could pro- mote invasiveness in the agroecosystem. There is great interest in understanding the evolutionary mechanisms that can lead to the emergence of weedy species from the same species complexes that give rise to domesticated plants. The larger complex of interfertile species within which conspecific weeds evolve includes the crop, wild relatives, and other feral weeds [6]. Studies have shown that, in many cases, hybridization between crops and wild spe- cies can facilitate weed evolution [reviewed in [7,8]]. Alternatively, conspecific weeds may evolve from stand- ing genetic variation in wild relatives [7], or cultivated germplasm [e.g. [9]], though examples of weeds evolving directly from crops are rare. The short evolutionary time scales involved make it less likely that novel mutations are significant to weed evolution, however exceptions are known [e.g. [10]]. * Correspondence: caicedo@bio.umass.edu 1 Biology Department, University of Massachusetts, Amherst, MA 01003, USA Full list of author information is available at the end of the article