title: Extensive recent secondary contacts between four European white oak species.
abstract: Historical trajectories of tree species during the late Quaternary have been well reconstructed through genetic and palaeobotanical studies. However, many congeneric tree species are interfertile, and the timing and contribution of introgression to species divergence during their evolutionary history remains largely unknown. We quantified past and current gene flow events between four morphologically divergent oak species (Quercus petraea, Q. robur, Q. pyrenaica, Q. pubescens), by two independent inference methods: diffusion approximation to the joint frequency spectrum (∂a∂i) and approximate Bayesian computation (ABC). For each pair of species, alternative scenarios of speciation allowing gene flow over different timescales were evaluated. Analyses of 3524 single nucleotide polymorphisms (SNPs) randomly distributed in the genome, showed that these species evolved in complete isolation for most of their history, but recently came into secondary contact, probably facilitated by the most recent period of postglacial warming. We demonstrated that: there was sufficient genetic differentiation before secondary contact for the accumulation of barriers to gene flow; and current European white oak genomes are a mosaic of genes that have crossed species boundaries and genes impermeable to gene flow.
authors.affiliation: BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France.
authors.forename: Thibault
authors.initials: T
authors.lastname: Leroy
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.
authors.forename: Camille
authors.initials: C
authors.lastname: Roux
authors.affiliation: BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Villate
authors.affiliation: BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Bodénès
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Romiguier
authors.affiliation: Instituto de Biologia Experimental e Tecnológica, iBET, Apartado 12, Oeiras, 2780-901, Portugal.|Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszynska street, Poznań, PL-60-479, Poland.
authors.forename: Jorge A P
authors.initials: JA
authors.lastname: Paiva
authors.affiliation: Institut de Genomique (IG), Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, 91057, France.
authors.forename: Carole
authors.initials: C
authors.lastname: Dossat
authors.affiliation: Institut de Genomique (IG), Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, 91057, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
authors.affiliation: BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Plomion
authors.affiliation: BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Kremer
mesh_terms: D001499:Bayes Theorem; D005060:Europe; D049810:Genetic Speciation; D014644:Genetic Variation; D016013:Likelihood Functions; D010802:Phylogeny; D025341:Principal Component Analysis; D029963:Quercus / Q000235:genetics*; D013045:Species Specificity
keywords: 
  Quercus
  ; interglacial recolonization; reproductive isolation; secondary contact; speciation