title: Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex.
abstract: Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.
authors: Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.
authors: Nagarjun
authors: N
authors: Vijay
authors: Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.|Department of Zoology, Population Genetics, Stockholm University, Stockholm SE-106 91, Sweden.
authors: Christen M
authors: CM
authors: Bossu
authors: Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.
authors: Jelmer W
authors: JW
authors: Poelstra
authors: Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.
authors: Matthias H
authors: 0000-0001-9302-798X
authors: MH
authors: Weissensteiner
authors: Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.
authors: Alexander
authors: A
authors: Suh
authors: Laboratory of Evolutionary Zoology and Genetics, Institute of Biology and Soil Science, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia.
authors: Alexey P
authors: AP
authors: Kryukov
authors: Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.|Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Grosshaderner Street 2, Planegg-Martinsried 82152, Germany.
authors: Jochen B W
authors: JB
authors: Wolf
mesh_terms: D000818:Animals; D046368:Crows / Q000235:genetics*; D005260:Female; D051456:Gene Flow; D049810:Genetic Speciation; D016678:Genome; D005843:Geography; D006824:Hybridization, Genetic; D008297:Male; D009693:Nucleic Acid Hybridization; D010641:Phenotype; D010858:Pigmentation; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics; D060047:Reproductive Isolation