title: The genomic landscape of species divergence in Ficedula flycatchers.
abstract: Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.
authors.affiliation: Dept of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Hans
authors.initials: H
authors.lastname: Ellegren
authors.forename: Linnéa
authors.initials: L
authors.lastname: Smeds
authors.forename: Reto
authors.initials: R
authors.lastname: Burri
authors.forename: Pall I
authors.initials: PI
authors.lastname: Olason
authors.forename: Niclas
authors.initials: N
authors.lastname: Backström
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kawakami
authors.forename: Axel
authors.initials: A
authors.lastname: Künstner
authors.forename: Hannu
authors.initials: H
authors.lastname: Mäkinen
authors.forename: Krystyna
authors.initials: K
authors.lastname: Nadachowska-Brzyska
authors.forename: Anna
authors.initials: A
authors.lastname: Qvarnström
authors.forename: Severin
authors.initials: S
authors.lastname: Uebbing
authors.forename: Jochen B W
authors.initials: JB
authors.lastname: Wolf
mesh_terms: D000818:Animals; D044822:Biodiversity; D002503:Centromere / Q000235:genetics; D002875:Chromosomes / Q000235:genetics; D005787:Gene Frequency; D049810:Genetic Speciation; D014644:Genetic Variation; D016678:Genome / Q000235:genetics*; D023281:Genomics; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic / Q000235:genetics; D020308:Songbirds / Q000145:classification / Q000235:genetics*; D013045:Species Specificity; D016615:Telomere / Q000235:genetics