Mating cues evolve rapidly and can contribute to species formation and maintenance. However, little is known about how sexual signals diverge and how this variation integrates with other barrier loci to shape the genomic landscape of reproductive isolation. Here, we elucidate the genetic basis of UV iridescence, a courtship signal that differentiates the males of Colias eurytheme butterflies from a sister species, allowing females to avoid costly heterospecific matings. Anthropogenic range expansion of the two incipient species established a large zone of secondary contact across the eastern US with strong signatures of genomic admixtures spanning all autosomes. In contrast, Z chromosomes are highly differentiated between the two species, supporting a disproportionate role of sex chromosomes in speciation known as the large-X effect. Within this chromosome-wide reproductive barrier, cis-regulatory variation of bric a brac (bab) drives the male UV-iridescence polymorphism between the two species. Bab is expressed in all non-UV scales, and butterflies of either species or sex acquire widespread ectopic iridescence following its CRISPR knock-out, demonstrating that Bab functions as a suppressor of UV-scale differentiation that potentiates mating cue divergence. These results provide new insights into the diversification of sexual signals and the species concept.

This is the Dryad repository for the paper "A genetic switch for male UV-iridescence in an incipient species pair of sulphur butterflies"

It contains population genetic data generated from WGS reads found on SRA at PRJNA663300 and PRJNA719421, as well as linkage data and code used to perform linkage analysis. 

# written by JJ Hanly, 4/20/2021 (joe.hanly@gmail.com)

Contents: 

1. bab.gff3 # GFF annotation of the gene bab, including annotations for linkage markers and recombination breakpoints
2. Colias_scaffold_lengths.txt # table containing the name, length and orientation of every scaffold in the Colias eurytheme genome
3. genotypePlotting_AnnotatedCode.r # includes the code used to filter and plot the genotype plots from Fig 1 and Fig S5, using r module written by Jim Whiting.
4. loess.txt # recombination rate in cM per Mb in 100kb windows with a slide of 10kb, generated using r/MareyMap
5. Manhattan_SVB_function.R # function written by Steven Van Belleghem used to plot Manhattan plots. 
6. PopgenStats.txt #table containing all population genetic statistics and lod scores in sliding windows. 
7. variang_calling_pipeline.txt # commands used to call variants with GATK. 
8. LinkageMap.txt # linkage map data for Colias hybrid broods
9. UVLinkageAnalysisCode.r # code used to plot figure 1 LOD plot. 
10. bab_pp.fa # Alignments of Bab protein coding sequences from the Colias eurytheme x philodice population (Buckeystown, MD, USA) 
11. bab_nuc.fa # Alignments of bab nucleotide sequence from the Colias eurytheme x philodice population (Buckeystown, MD, USA) 
12. CeurXCphi_2bRADseq_samples.xlsx: table of all individuals from broods 49,75 and 79, plus parents and phenotype scoring