Nordborg, M; Hu, TT; Ishino, Y; Jhaveri, J; Toomajian, C; Zheng, H; ... Bergelson, J; + view all Nordborg, M; Hu, TT; Ishino, Y; Jhaveri, J; Toomajian, C; Zheng, H; Bakker, E; Calabrese, P; Gladstone, J; Goyal, R; Jakobsson, M; Kim, S; Morozov, Y; Padhukasahasram, B; Plagnol, V; Rosenberg, NA; Shah, C; Wall, JD; Wang, J; Zhao, K; Kalbfleisch, T; Schulz, V; Kreitman, M; Bergelson, J; - view fewer (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology , 3 (7) , Article e196 . 10.1371/journal.pbio.0030196.
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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.
|Title:||The pattern of polymorphism in Arabidopsis thaliana.|
|Open access status:||An open access publication. A version is also available from UCL Discovery.|
|Additional information:||© 2005 Nordborg et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. PMCID: PMC1135296|
|Keywords:||Arabidopsis, Gene Frequency, Genetics, Population, Polymorphism, Genetic, Polymorphism, Single Nucleotide|
|UCL classification:||UCL > School of Life and Medical Sciences > Faculty of Life Sciences > Biosciences (Division of) > Genetics, Evolution and Environment > UCL Genetics Institute|
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