The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

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Model systems not only allow scientists to investigate complex processes that are difficult to study in nonmodel organisms but also serve to focus community efforts and resources, significantly advancing research. Arabidopsis (Arabidopsis thaliana) has served as a plant model system for almost 30 years and is widely considered the preeminent model plant. The success of Arabidopsis-related research has been driven not only by key features common to any model organism but also by the collaborative environment built by the Arabidopsis community. A decade after the Arabidopsis genome sequence was published, the development of model plants follows a different trajectory. In the past, the development of extensive resources and a large user community happened first and then sequencing the genome followed. Today, however, an organism is selected as a potential model and genome sequencing occurs prior to or concurrent with the development of experimental tools and a user community. Arabidopsis research has provided many scientific breakthroughs (Flavell, 2009). However, its utility as a model is limited to a certain extent when investigating monocot-specific processes.Within the monocots, grasses provide the vast majority of human calories and are increasingly utilized as a sustainable source of energy. Traits including cell wall composition, plant architecture, grain properties,