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.

[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.

[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.

[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.

[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.

Natural Environment Research Council : NE/S007407/1. Natural Environment Research Council : NE/L011522/1. European Research Council : ModelGenomLand 757648.

[ROH summary] A tsv file giving a summary of ROH in each Brenthis individual.

Peer reviewed