DOI: 10.5061/dryad.2jm63xswp
title: Evidence that genetic drift not adaptation drives fast-Z and large-Z effects in Ficedula flycatchers

description: The sex chromosomes have been hypothesized to play a key role in driving
 adaptation and speciation across many taxa. The reason for this is thought
 to be the hemizygosity of the heteromorphic part of sex chromosomes in the
 heterogametic sex, which exposes recessive mutations to natural and sexual
 selection. The exposure of recessive beneficial mutations increases their
 rate of fixation on the sex chromosomes, which results in a faster rate of
 evolution. In addition, genetic incompatibilities between sex-linked loci
 are exposed faster in the genomic background of hybrids of divergent
 lineages, which makes sex chromosomes contribute disproportionately to
 reproductive isolation. However, in birds, which show a Z/W sex
 determination system, the role of adaptation vs. genetic drift as the
 driving force of the faster differentiation of the Z chromosome (fast-Z
 effect) and the disproportionate role of the Z chromosome in reproductive
 isolation (large-Z effect) are still debated. Here, we address this debate
 in the bird genus Ficedula flycatchers based on population-level
 whole-genome sequencing data of six species. Our analysis provides
 evidence for both faster lineage sorting and reduced gene flow on the Z
 chromosome than the autosomes. However, these patterns appear to be driven
 primarily by the increased role of genetic drift on the Z chromosome,
 rather than an increased rate of adaptive evolution. Genomic scans of
 selective sweeps and fixed differences in fact suggest a reduced action of
 positive selection on the Z-chromosome. Nevertheless, it is possible that
 the faster lineage sorting of the Z chromosome due to genetic drift may
 help drive the evolution of genetic incompatibilities between species.
description: # Evidence that genetic drift not adaptation drives fast-Z and large-Z
 effects in Ficedula flycatchers
 ## Description of the data
 and file structure This repository contains variant call data for the Z
 chromosome for four species of *Ficedula* flycatcher, and one individual
 of an outgroup species. The data are in VCF format including only SNVs,
 mapped to scaffolds of the collared flycatcher reference genome. Data have
 been generated with GATK HaplotypeCaller followed by GenotypeGVCFs.
 Variants are filtered for minimum genotype quality of 30 for males and 15
 for females, and minimum depth of 5x. Repeats and collapsed duplications
 are masked, and sites with heterozygous genotypes in females are removed.
 Sites with missing data in more than 10% of individuals within any of the
 four species are also removed. VCF file name:
 var_sites.all_z_scaff.indel_rmvd.max_allele2.hard_filt.pass_only.RM.CM.minGQ.minDP.maxDP.max_miss_10_perc.vcf.gz Information on callable regions is given in BED format, which is extracted from a VCF with monomorphic sites included, filtered as described above. Callable regions file name: all_sites.all_zscaff.all_filt.missing_rmvd.callable_sites.merged.bed Sample metadata (flycatcher_sample_metadata.txt) is included providing information on the sample ID as written in the VCF file, species, sex, mapping percentage, and estimated sequencing coverage (Mean depth) 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 and snowy-browed flycatchers: PRJEB7359 * Red-breasted and taiga flycatcher: PRJEB22864