Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies

Large-scale chromosome rearrangements, such as fissions and fusions, are a common feature of eukaryote evolution. They can have considerable influence on the evolution of populations, yet it remains unclear exactly how rearrangements become established and eventually fix. Rearrangements could fix by genetic drift if they are weakly deleterious or neutral, or they may instead be favoured by positive natural selection. Here we compare genome assemblies of three closely related Brenthis butterfly species and characterise a complex history of fission and fusion rearrangements. An inferred demographic history of these species suggests that rearrangements became fixed in populations with large long-term effective size (Ne). However, we also find large runs of homozygosity within individual genomes and show that a model of population structure with smaller local Ne can reconcile these observations. Using a recently developed analytic framework for characterising hard selective sweeps, we find ..., , , # Data associated with: Do chromosome rearrangements fix by genetic drift or natural selection? Insights from *Brenthis* butterflies

[https://doi.org/10.5061/dryad.cnp5hqcbf](https://doi.org/10.5061/dryad.cnp5hqcbf)

These data are associated with the population genomic analyses in Mackintosh et al. (2023).

### VCFs

There are four VCF files (*vcf.gz). All of them contain filtered SNP calls.

* Samples from all three *Brenthis* species mapped to the *Fabriciana adippe* reference genome (used for demographic inference)
* *B. daphne* samples mapped to the *B. daphne* reference genome (used for ROH identification and sweep inference)
* *B. ino* samples mapped to the *B. ino* reference genome (used for ROH identification and sweep inference)
* *B. hecate* samples mapped to the *B. hecate* reference genome (used for ROH identification and sweep inference)

### Callable sites bed files

These files (*.bed) contain intervals where genotypes are callable (given coverage and indels). Each file...