title: Divergence in gene expression within and between two closely related flycatcher species.
abstract: Relatively little is known about the character of gene expression evolution as species diverge. It is for instance unclear if gene expression generally evolves in a clock-like manner (by stabilizing selection or neutral evolution) or if there are frequent episodes of directional selection. To gain insights into the evolutionary divergence of gene expression, we sequenced and compared the transcriptomes of multiple organs from population samples of collared (Ficedula albicollis) and pied flycatchers (F. hypoleuca), two species which diverged less than one million years ago. Ordination analysis separated samples by organ rather than by species. Organs differed in their degrees of expression variance within species and expression divergence between species. Variance was negatively correlated with expression breadth and protein interactivity, suggesting that pleiotropic constraints reduce gene expression variance within species. Variance was correlated with between-species divergence, consistent with a pattern expected from stabilizing selection and neutral evolution. Using an expression PST approach, we identified genes differentially expressed between species and found 16 genes uniquely expressed in one of the species. For one of these, DPP7, uniquely expressed in collared flycatcher, the absence of expression in pied flycatcher could be associated with a ≈20-kb deletion including 11 of 13 exons. This study of a young vertebrate speciation model system expands our knowledge of how gene expression evolves as natural populations become reproductively isolated.
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Severin
authors.initials: S
authors.lastname: Uebbing
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Axel
authors.initials: A
authors.lastname: Künstner
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Hannu
authors.initials: H
authors.lastname: Mäkinen
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Niclas
authors.initials: N
authors.lastname: Backström
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Paulina
authors.initials: P
authors.lastname: Bolivar
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Reto
authors.initials: R
authors.lastname: Burri
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Dutoit
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Carina F
authors.initials: CF
authors.lastname: Mugal
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Alexander
authors.initials: A
authors.lastname: Nater
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Bronwen
authors.identifier: 0000-0002-3032-4095
authors.initials: B
authors.lastname: Aken
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Fergal J
authors.initials: FJ
authors.lastname: Martin
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Stephen M J
authors.initials: SM
authors.lastname: Searle
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Hans
authors.initials: H
authors.lastname: Ellegren
mesh_terms: D000818:Animals; D005075:Biological Evolution; D005260:Female; D015870:Gene Expression; D040961:Genetic Drift; D058685:Genetic Pleiotropy; D005828:Genetics, Population; D008297:Male; D008957:Models, Genetic; D012641:Selection, Genetic; D020308:Songbirds / Q000145:classification* / Q000235:genetics; D013045:Species Specificity; D013548:Sweden
keywords: Ficedula; collared flycatcher; gene regulation; pied flycatcher; speciation; transcriptomics