title: The pattern of polymorphism in Arabidopsis thaliana.
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.
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA. magnus@usc.edu
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
authors.forename: Tina T
authors.initials: TT
authors.lastname: Hu
authors.forename: Yoko
authors.initials: Y
authors.lastname: Ishino
authors.forename: Jinal
authors.initials: J
authors.lastname: Jhaveri
authors.forename: Christopher
authors.initials: C
authors.lastname: Toomajian
authors.forename: Honggang
authors.initials: H
authors.lastname: Zheng
authors.forename: Erica
authors.initials: E
authors.lastname: Bakker
authors.forename: Peter
authors.initials: P
authors.lastname: Calabrese
authors.forename: Jean
authors.initials: J
authors.lastname: Gladstone
authors.forename: Rana
authors.initials: R
authors.lastname: Goyal
authors.forename: Mattias
authors.initials: M
authors.lastname: Jakobsson
authors.forename: Sung
authors.initials: S
authors.lastname: Kim
authors.forename: Yuri
authors.initials: Y
authors.lastname: Morozov
authors.forename: Badri
authors.initials: B
authors.lastname: Padhukasahasram
authors.forename: Vincent
authors.initials: V
authors.lastname: Plagnol
authors.forename: Noah A
authors.initials: NA
authors.lastname: Rosenberg
authors.forename: Chitiksha
authors.initials: C
authors.lastname: Shah
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Wall
authors.forename: Jue
authors.initials: J
authors.lastname: Wang
authors.forename: Keyan
authors.initials: K
authors.lastname: Zhao
authors.forename: Theodore
authors.initials: T
authors.lastname: Kalbfleisch
authors.forename: Vincent
authors.initials: V
authors.lastname: Schulz
authors.forename: Martin
authors.initials: M
authors.lastname: Kreitman
authors.forename: Joy
authors.initials: J
authors.lastname: Bergelson
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D005787:Gene Frequency; D005828:Genetics, Population; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide