title: R-gene variation across Arabidopsis lyrata subspecies: effects of population structure, selection and mating system.
abstract: BACKGROUND
  Examining allelic variation of R-genes in closely related perennial species of Arabidopsis thaliana is critical to understanding how population structure and ecology interact with selection to shape the evolution of innate immunity in plants. We finely sampled natural populations of Arabidopsis lyrata from the Great Lakes region of North America (A. l. lyrata) and broadly sampled six European countries (A. l. petraea) to investigate allelic variation of two R-genes (RPM1 and WRR4) and neutral genetic markers (Restriction Associated DNA sequences and microsatellites) in relation to mating system, phylogeographic structure and subspecies divergence.
  
  
  RESULTS
  Fine-scale sampling of populations revealed strong effects of mating system and population structure on patterns of polymorphism for both neutral loci and R-genes, with no strong evidence for selection. Broad geographic sampling revealed evidence of balancing selection maintaining polymorphism in R-genes, with elevated heterozygosity and diversity compared to neutral expectations and sharing of alleles among diverged subspecies. Codon-based tests detected both positive and purifying selection for both R-genes, as commonly found for animal immune genes.
  
  
  CONCLUSIONS
  Our results highlight that combining fine and broad-scale sampling strategies can reveal the multiple factors influencing polymorphism and divergence at potentially adaptive genes such as R-genes.
authors.affiliation: Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. james.buckley@env.ethz.ch.|Current address: Center for Adaptation to a Changing Environment, ETH Zurich, Zurich, 8092, Switzerland. james.buckley@env.ethz.ch.
authors.forename: James
authors.initials: J
authors.lastname: Buckley
authors.affiliation: Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Kilbride
authors.affiliation: School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK.|Current address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR47UH, UK.
authors.forename: Volkan
authors.initials: V
authors.lastname: Cevik
authors.affiliation: School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK.
authors.forename: Joana G
authors.initials: JG
authors.lastname: Vicente
authors.affiliation: School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK.
authors.forename: Eric B
authors.initials: EB
authors.lastname: Holub
authors.affiliation: Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
authors.forename: Barbara K
authors.initials: BK
authors.lastname: Mable
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D006239:Haplotypes; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
chemical_list: D029681:Arabidopsis Proteins; C095014:RPM1 protein, Arabidopsis; C532021:WRR4 protein, Arabidopsis
keywords: Arabidopsis lyrata; Bacterial disease; Disease resistance; Heterozygosity; Inbreeding; Mating system; Oomycete; Selection