Biological Sciences Division
Published May 24, 2005 | Version v1
Journal article Open

The Pattern of Polymorphism in Arabidopsis thaliana

Creators

  • 1. University of Southern California
  • 2. University of Chicago
  • 3. Lund University
  • 4. Genaissance Pharmaceuticals

Description

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.

Notes

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.

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Additional details

Identifiers

DOI
10.1371/journal.pbio.0030196
Other
oai:uchicago.tind.io:10861

UChicago Information

Division(s)
Biological Sciences Division
Department(s)
Ecology and Evolution