The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear-cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution.

] Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo 0316 Oslo Norway [2] Natural History Museum University of Oslo 0318 Oslo Norway

] Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo 0316 Oslo Norway [2] Norwegian Institute for Nature Research 7034 Trondheim Norway

Behavioural Ecology Group Department of Systematic Zoology and Ecology Eötvös Loránd University 1117 Budapest Hungary

Bird Protection and Study Society of Serbia Radnička 20a 21000 Novi Sad Serbia

Department of Animal Ecology Evolutionary Biology Centre Uppsala University 75236 Uppsala Sweden

Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo 0316 Oslo Norway

Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE 752 36 Uppsala Sweden

Department of Evolutionary Ecology Estación Biológica de Doñana CSIC 41092 Seville Spain

Laboratory of Ornithology Department of Zoology Palacky University 77146 Olomouc Czech Republic

Museo Nacional de Ciencias Naturales CSIC 28006 Madrid Spain

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Evolution and genetic architecture of sex-limited polymorphism in cuckoos

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