title: Inferring the demographic history of European Ficedula flycatcher populations.
abstract: BACKGROUND
  Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher.
  
  
  RESULTS
  We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations.
  
  
  CONCLUSIONS
  Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, SE-752 36, Sweden. niclas.backstrom@ebc.uu.se
authors.forename: Niclas
authors.initials: N
authors.lastname: Backström
authors.forename: Glenn-Peter
authors.initials: GP
authors.lastname: Saetre
authors.forename: Hans
authors.initials: H
authors.lastname: Ellegren
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D005060:Europe; D051456:Gene Flow; D005787:Gene Frequency; D049810:Genetic Speciation; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D006824:Hybridization, Genetic; D007438:Introns; D008957:Models, Genetic; D010641:Phenotype; D017422:Sequence Analysis, DNA; D020308:Songbirds / Q000145:classification / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial