DOI: 10.5061/dryad.cnp5hqcbf
title: Data from: Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies

description: 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 that chromosome fusions are not enriched for evidence of
 past sweeps compared to other regions of the genome. Nonetheless, one
 chromosome fusion in the B. daphne genome is associated with a
 valley of diversity where genealogical branch lengths are distorted,
 consistent with a selective sweep. Our results suggest that drift is a
 stronger force in these populations than suggested by overall genetic
 diversity, but that the fixation of strongly underdominant rearrangements
 remains unlikely. Additionally, although chromosome fusions do not
 typically exhibit signatures of selective sweeps, a single example raises
 the possibility that natural selection may sometimes play a role in their
 fixation.
description: # 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 is associated with one of the VCF files above. The bed file for demographic inference only contains 4D sites, whereas the bed files for sweep inference only contain intergenic sites. ### 3D-SFS These files (*.obs) contain the three-dimensional SFS for *B. daphne, B. ino* and *B. hecate*. One contains the unfolded spectra (DSFS) and the other the folded spectra (MSFS). They are in the format expected by fastsimcoal2. ### Blockwise SFS Each file (*.formatted_blocks.tsv) contains a blockwise SFS for 1 Mb around a chromosome fusion in B. daphne, B. ino* or *B. hecate*, or, alternatively, the bSFS across an entire chromosome.* This is the input for the sweep inference. ### Inferred selective sweeps These files (*sweeps.tsv) contain results of the inferred selective sweeps, either around fusion points of from loci sampled elsewhere in the genome. ### ROH summary A tsv file giving a summary of ROH in each *Brenthis* individual.