We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.
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Title
The Pattern of Polymorphism in Arabidopsis thaliana
Author
Nordborg, Magnus : University of Southern California Hu, Tina T. : University of Southern California Ishino, Yoko : University of Southern California Jhaveri, Jinal : University of Southern California Toomajian, Christopher : University of Southern California Zheng, Honggang : University of Southern California Bakker, Erica : University of Chicago Calabrese, Peter : University of Southern California Gladstone : University of Chicago Goyal, Rana : University of Southern California Jakobsson, Mattias : Lund University Kim, Sung : University of Southern California Morozov, Yuri : Genaissance Pharmaceuticals Padhukasahasram, Badri : University of Southern California Plagnol, Vincent : University of Southern California Rosenberg, Noah A. : University of Southern California Shah, Chitiksha : University of Southern California Wall, Jeffrey D. : University of Southern California Wang, Jue : University of Chicago Kreitman, Martin : University of Chicago Bergelson, Joy : University of Chicago
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Due to the large number of authors, only the first 20 and the University of Chicago authors are included on the above author list. Please download the article for the complete list of authors.