The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome

Recombination is a central evolutionary process that reshuffles combinations of alleles along chromosomes and consequently, is expected to influence the efficacy of direct selection via Hill-Robertson interference. Additionally, the indirect effects of selection on neutral genetic diversity are expected to show a negative relationship with recombination rate, as background selection and genetic hitchhiking are stronger when recombination rate is low. However, owing to the limited availability of recombination rate estimates across divergent species, the impact of evolutionary changes in recombination rate on genomic signatures of selection remains largely unexplored. To address this question, we estimate recombination rate in two Ficedula flycatcher species, the taiga flycatcher (F. albicilla) and collared flycatcher (F. albicollis). We show that recombination rate is strongly correlated with signatures of indirect selection and that evolutionary changes in recombination rate between species have observable impacts on this relationship. Conversely, signatures of direct selection on coding sequences show little to no relationship with recombination rate, even when restricted to genes where recombination rate is conserved between species. Thus, using measures of indirect and direct selection that bridge micro- and macro-evolutionary timescales, we demonstrate that the role of recombination rate and its dynamics varies for different signatures of selection.

Methods
Variant call data are provided for four species of Ficedula flycatcher from whole genome re-sequencing data. Variant calling was performed with GATK v4. All-sites variant calling was performed, and callable sites determined from this are provided as a bed file. VCF files are provided for variant sites only. 

Recombination rate data for taiga flycatcher and collared flycatcher are provided, estimated from patterns of linkage disequilibrium using LD-helmet and converted to cM/Mb based on the collared flycatcher linkage map.