Evidence that genetic drift not adaptation drives fast-Z and large-Z effects in Ficedula flycatchers

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 addre..., , , # 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 for...