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The pattern of polymorphism in Arabidopsis thaliana

Nordborg, M; Hu, TT; Ishino, Y; Jhaveri, J; Toomajian, C; Zheng, HG; Bakker, E; Calabrese, P; Gladstone, J and Goyal, R, et al. (2005) In PLoS Biology 3(7). p.1289-1299
Abstract
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... (More)
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. (Less)
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PLoS Biology
volume
3
issue
7
pages
1289 - 1299
publisher
Public Library of Science
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  • wos:000230759000016
  • scopus:22744434580
ISSN
1544-9173
DOI
10.1371/journal.pbio.0030196
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English
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yes
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52f61d57-ee43-4e75-96dc-1678df3a0039 (old id 231943)
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2007-10-05 11:15:09
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@article{52f61d57-ee43-4e75-96dc-1678df3a0039,
  abstract     = {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.},
  author       = {Nordborg, M and Hu, TT and Ishino, Y and Jhaveri, J and Toomajian, C and Zheng, HG and Bakker, E and Calabrese, P and Gladstone, J and Goyal, R and Jakobsson, Mattias and Kim, S and Morozov, Y and Padhukasahasram, B and Plagnol, V and Rosenberg, NA and Shah, C and Wall, JD and Wang, J and Zhao, KY and Kalbfleisch, T and Schulz, V and Kreitman, M and Bergelson, J},
  issn         = {1544-9173},
  language     = {eng},
  number       = {7},
  pages        = {1289--1299},
  publisher    = {Public Library of Science},
  series       = {PLoS Biology},
  title        = {The pattern of polymorphism in Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1371/journal.pbio.0030196},
  volume       = {3},
  year         = {2005},
}