title: The scale of population structure in Arabidopsis thaliana.
abstract: The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Platt
authors.forename: Matthew
authors.initials: M
authors.lastname: Horton
authors.forename: Yu S
authors.initials: YS
authors.lastname: Huang
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Alison E
authors.initials: AE
authors.lastname: Anastasio
authors.forename: Ni Wayan
authors.initials: NW
authors.lastname: Mulyati
authors.forename: Jon
authors.initials: J
authors.lastname: Agren
authors.forename: Oliver
authors.initials: O
authors.lastname: Bossdorf
authors.forename: Diane
authors.initials: D
authors.lastname: Byers
authors.forename: Kathleen
authors.initials: K
authors.lastname: Donohue
authors.forename: Megan
authors.initials: M
authors.lastname: Dunning
authors.forename: Eric B
authors.initials: EB
authors.lastname: Holub
authors.forename: Andrew
authors.initials: A
authors.lastname: Hudson
authors.forename: Valérie
authors.initials: V
authors.lastname: Le Corre
authors.forename: Olivier
authors.initials: O
authors.lastname: Loudet
authors.forename: Fabrice
authors.initials: F
authors.lastname: Roux
authors.forename: Norman
authors.initials: N
authors.lastname: Warthmann
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Luz
authors.initials: L
authors.lastname: Rivero
authors.forename: Randy
authors.initials: R
authors.lastname: Scholl
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
authors.forename: Joy
authors.initials: J
authors.lastname: Bergelson
authors.forename: Justin O
authors.initials: JO
authors.lastname: Borevitz
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics*; D003433:Crosses, Genetic; D005843:Geography; D006239:Haplotypes / Q000235:genetics; D006579:Heterozygote; D007178:Inbreeding; D011157:Population Dynamics