DOI: 10.5061/dryad.q2bvq83nw
title: The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome

description: 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.
description: Variant call data are provided for four species of
 <em>Ficedula</em> 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.
description: # 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 variable sites. **Callable regions file name:**
 all_sites.all_non_zscaff.all_filt.missing_rmvd.non_z_scaff.callable_sites.merged.bed Recombination rates estimated with LDhelmet are given between adjacent SNP pairs and summarized for 200kb windows for collared flycatcher and taiga flycatcher. SNP-pair rates are population-scaled, and provide the average value across 5 independent runs of LDhelmet separately for two different runs of statistical phasing. The window-based estimates are rescaled into cM/Mb by using the collared flycatcher pedigree-based recombination map, and have been filtered for extreme outliers. Window-based estimates are given mapped to scaffolds and translated to chromosomes. **SNP-pair recombination rate files:** taig.snp_recom.pop_scaled.txt coll.snp_recom.pop_scaled.txt **Scaffold level recombination rate files:** taig.ld_recom_converted.w200k_s200k.txt coll.ld_recom_converted.w200k_s200k.txt **Chromosome level recombination rate files:** taig.ld_recom_converted.w200k_s200k.chrompos.txt coll.ld_recom_converted.w200k_s200k.chrompos.txt Sample metadata is included providing information on the sample ID as written in the VCF file, species, sex, mapping percentage, and estimated sequencing coverage for each sample. ## Sharing/Access information Sequencing data from which the VCF is derived is publicly available on the European nucleotide archive (ENA; [http://www.ebi.ac.uk/ena) ](http://www.ebi.ac.uk/ena)with the following accession numbers: * Collared flycatcher: PRJEB22864 * Pied flycatcher and snowy-browed flycatcher: PRJEB7359 * Red-breasted flycatcher and taiga flycatcher: PRJEB43825 ## Code/Software Scripts used for analyses are available on GitHub (