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

## Description of the data and file structure

This repository contains variant call data for autosomal scaffolds for five species of *Ficedula* flycatcher, and inferred recombination rates for two of the species. The variant call data are in VCF format including only single nucleotide variants, mapped to scaffolds of the collared flycatcher reference genome (v. FicAlb1.5). The data have been generated using GATK HaplotypeCaller followed by GenotypeGVCFs. Variants have been filtered for a minimum genotype quality of 30, minimum depth of 5x and maximum depth of 200x. Repeats and collapsed duplications are masked.

**VCF file name:**

final_var_sites_vcfs.tar.gz

In addition to the VCFs, callable regions of the genome are given in bed format. These data are generated from a VCF including monomorphic sites and filtered in the same way described above for vari...