DOI: 10.5061/dryad.4b8gthtcc
title: A genetic switch for male UV-iridescence in an incipient species pair

description: 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.
description: This is the Dryad repository for the paper "A genetic switch
 for male UV-iridescence in an incipient species pair of sulphur
 butterflies"<br> <br> 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<br> 2. Colias_scaffold_lengths.txt # table containing
 the name, length and orientation of every scaffold in the Colias eurytheme
 genome<br> 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.<br> 4. loess.txt # recombination rate
 in cM per Mb in 100kb windows with a slide of 10kb, generated using
 r/MareyMap<br> 5. Manhattan_SVB_function.R # function written by
 Steven Van Belleghem used to plot Manhattan plots. <br> 6.
 PopgenStats.txt #table containing all population genetic statistics and
 lod scores in sliding windows. <br> 7. variang_calling_pipeline.txt
 # commands used to call variants with GATK. <br> 8. LinkageMap.txt #
 linkage map data for Colias hybrid broods<br> 9.
 UVLinkageAnalysisCode.r # code used to plot figure 1 LOD plot. <br>
 10. bab_pp.fa # Alignments of Bab protein coding sequences from the Colias
 eurytheme x philodice population (Buckeystown, MD, USA) <br> 11.
 bab_nuc.fa # Alignments of bab nucleotide sequence from the Colias
 eurytheme x philodice population (Buckeystown, MD, USA) <br> 12.
 CeurXCphi_2bRADseq_samples.xlsx: table of all individuals from broods
 49,75 and 79, plus parents and phenotype scoring