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Data from: Rewinding the ratchet: Rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence

Cite this dataset

Mackintosh, Alexander; Decroly, Thomas; Lohse, Konrad; Vila, Roger (2024). Data from: Rewinding the ratchet: Rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence [Dataset]. Dryad. https://doi.org/10.5061/dryad.fj6q57435

Abstract

Natural selection is less efficient in the absence of recombination. As a result, non-recombining sequences, such as sex chromosomes, tend to degenerate over time. Although the outcomes of recombination arrest are typically observed after many millions of generations, recent neo-sex chromosomes can give insight into the early stages of this process. Here we investigate the evolution of neo-sex chromosomes in the Spanish marbled white butterfly, Melanargia ines, where a Z-autosome fusion has turned the homologous autosome into a non-recombining neo-W chromosome. We show that these neo-sex chromosomes are likely limited to the Iberian population of M. ines, and that they arose around the time when this population split from North-African populations, around 1.5 million years ago. Recombination arrest of the neo-W chromosome has led to an excess of premature stop codons and frameshift mutations, and reduced gene expression compared to the neo-Z chromosome. Surprisingly, we identified two regions of 1 Mb at one end of the neo-W that are both less diverged from the neo-Z and less degraded than the rest of the chromosome, suggesting a history of rare but repeated genetic exchange between the two neo-sex chromosomes. These plateaus of neo-sex chromosome divergence suggest that neo-W degradation can be locally reversed by rare recombination between neo-W and neo-Z chromosomes.

README: Data from: Rewinding the ratchet: rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence

https://doi.org/10.5061/dryad.fj6q57435

These data are associated with the population genomic analyses in Decroly et al. (2024).

Repeat intervals

The file melanargia_ines.PT_MI_8.v2_0.sequences.red_repeats.bed contains intervals of the genome identified as repeats using the software Red (Girgis, 2015).

Gene annotation

The file melanargia_ines.PT_MI_8.v2_0.sequences.red_repeats.augustus.gt.gff3 contains a gene annotation generated with braker2.1.5 (Hoff et al. 2019).

VCF

The file melanargia_ines.vcf.gz contains filtered variant calls for 15 individuals sampled throughout Iberia and the Maghreb (see Decroly et al. 2024 for details).

Callable intervals

The file melanargia_ines.callable.bed.gz contains intervals of the genome where genotypes are callable in a specific subset of individuals (see Decroly et al. 2024 for details).

Funding

European Research Council, ModelGenomLand