Abstracts (first author)
The landscape(s) of genome divergence in Ficedula flycatchers
Unravelling the landscapes of genome divergence between individuals, populations, and species is key to understand the genomic architecture of biological diversification, and the forces driving its evolution. In the present study we make use of the recently available flycatcher genome (Ellegren et al. 2012, Nature), to study the genomic divergence between the naturally hybridizing but reproductively isolated collared flycatcher (Ficedula albicollis) and pied flycatcher (F. hypoleuca). Population genomic analysis of each 10 genomes of both species reveal a highly heterogeneous landscape of genome divergence with about 50 ‘divergence islands’ that show ~50-fold higher differentiation than the genomic background. The non-randomly distributed divergence islands are characterized by reduced nucleotide diversity, skewed allele-frequency spectra, elevated linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicating parallel episodes of selection. The high incidence of divergence islands with genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. In order to identify the molecular and evolutionary forces driving the evolution of divergence islands in Ficedula flycatchers, these insights are complemented with recent results from population genomic analyses of an additional 200 flycatcher genomes from multiple populations and species.