How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers.

There is an increasing awareness that selection affecting linked neutral sites strongly influences on how diversity is distributed across the genome. In particular, linked selection is likely involved in the formation of heterogenous landscapes of genetic diversity, including genomic regions with locally reduced effective population size that manifests as dips in diversity and "islands" of differentiation between closely related populations or species. Linked selection can be in the form of background selection or selective sweeps and a long-standing question in population genetics has been to unveil the relative importance of these processes. Here we analysed the theoretically expected reduction of diversity caused by linked selection in the collared flycatcher ( Ficedula albicollis ) genome and compared this with population genomic data on the distribution of diversity across the flycatcher genome. By incorporating data on recombination rate variation and the density of target sites for selection (includig both protein-coding genes and conserved non-coding elements), we found that background selection can explain most of the observed base line variation in genetic diversity. However, positive selection was necessary to explain the pronounced local diversity dips in the collared flycatcher genome. We confirmed our analytical findings by comprehensive simulations. Our study therefore demonstrates that even though both background selection and selective sweeps contribute to the heterogeneous diversity landscape seen in this avian system, they play different roles in shaping it.