title: Taming the wild: resolving the gene pools of non-model Arabidopsis lineages.
abstract: BACKGROUND
  Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses.
  
  
  RESULTS
  Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins.
  
  
  CONCLUSIONS
  Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.
authors.affiliation: Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany. nora.hohmann@cos.uni-heidelberg.de.
authors.forename: Nora
authors.initials: N
authors.lastname: Hohmann
authors.affiliation: Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany. roswitha.schmickl@cos.uni-heidelberg.de.|Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic. roswitha.schmickl@cos.uni-heidelberg.de.
authors.forename: Roswitha
authors.initials: R
authors.lastname: Schmickl
authors.affiliation: Department of Life Sciences, Cheng-Kung University, Tainan, Taiwan. tychiang@mail.ncku.edu.tw.
authors.forename: Tzen-Yuh
authors.initials: TY
authors.lastname: Chiang
authors.affiliation: Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic. kubesovm@gmail.com.|Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic. kubesovm@gmail.com.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Lučanová
authors.affiliation: Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic. filip.kolar@gmail.com.|Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic. filip.kolar@gmail.com.
authors.forename: Filip
authors.initials: F
authors.lastname: Kolář
authors.affiliation: Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic. karol.marhold@savba.sk.|Institute of Botany Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, SK-845 23, Slovakia. karol.marhold@savba.sk.
authors.forename: Karol
authors.initials: K
authors.lastname: Marhold
authors.affiliation: Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany. marcus.koch@cos.uni-heidelberg.de.
authors.forename: Marcus A
authors.initials: MA
authors.lastname: Koch
mesh_terms: D017360:Arabidopsis / Q000145:classification* / Q000166:cytology / Q000235:genetics*; D005075:Biological Evolution; D002736:Chloroplasts / Q000235:genetics; D060146:Ecotype; D051456:Gene Flow; D005788:Gene Pool; D014644:Genetic Variation; D054628:Genome, Chloroplast; D018895:Microsatellite Repeats; D058974:Phylogeography