Evidence that genetic drift not adaptation drives fast-Z and large-Z effects in Ficedula flycatchers
Data files
Jan 05, 2024 version files 3.33 GB
Abstract
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.
README: Evidence that genetic drift not adaptation drives fast-Z and large-Z effects in Ficedula flycatchers
https://doi.org/10.5061/dryad.2jm63xswp
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) with the following accession numbers:
- Collared flycatcher: PRJEB22864
- Pied and snowy-browed flycatchers: PRJEB7359
- Red-breasted and taiga flycatcher: PRJEB22864