title: Time scales of divergence and speciation among natural populations and subspecies of Arabidopsis lyrata (Brassicaceae).
abstract: OBJECTIVE
  Plant populations that face new environments adapt and diverge simultaneously, and both processes leave footprints in their genetic diversity. Arabidopsis lyrata is an excellent species for studying these processes. Pairs of populations and subspecies of A. lyrata represent different stages of divergence. These populations are also known to be locally adapted and display various stages of emerging reproductive isolation.
  
  
  METHODS
  We used nucleotide diversity data from 19 loci to estimate divergence times and levels of diversity among nine A. lyrata populations. Traditional distance-based methods and model-based clustering analysis were used to supplement pairwise coalescence-based analysis of divergence.
  
  
  RESULTS
  Estimated divergence times varied from 130,000 generations between North American and European subspecies to 39,000 generations between central European and Scandinavian populations. In concordance with previous studies, the highest level of diversity was found in Central Europe and the lowest in North America and a diverged Russian Karhumäki population. Local adaptation among Northern and central European populations has emerged during the last 39,000 generations. Populations that are reproductively isolated by prezygotic mechanisms have been separated for a longer time period of ∼70,000 generations but still have shared nucleotide polymorphism.
  
  
  CONCLUSIONS
  In A. lyrata, reproductively isolated populations started to diverge ∼70,000 generations ago and more closely related, locally adapted populations have been separate lineages for ∼39,000 generations. However, based on the posterior distribution of divergence times, the processes leading to reproductive isolation and local adaptation are likely to temporally coincide.
authors: Department of Biology, University of Oulu, Finland. tanja.pyhajarvi@oulu.fi
authors: Tanja
authors: T
authors: Pyhäjärvi
authors: Esa
authors: E
authors: Aalto
authors: Outi
authors: O
authors: Savolainen
mesh_terms: D000222:Adaptation, Physiological; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D016000:Cluster Analysis; D018744:DNA, Plant / Q000235:genetics; D004777:Environment; D005060:Europe; D056426:Genetic Loci; D049810:Genetic Speciation; D014644:Genetic Variation; D005828:Genetics, Population; D008969:Molecular Sequence Data; D010802:Phylogeny; D012098:Reproduction; D060047:Reproductive Isolation; D017422:Sequence Analysis, DNA; D013997:Time Factors; D014481:United States
chemical_list: D018744:DNA, Plant