Data from: Whole-chromosome hitchhiking driven by a male-killing endosymbiont

Neo-sex chromosomes are found in many taxa, but the forces driving their
emergence and spread are poorly understood. The female-specific neo-W
chromosome of the African monarch (or queen) butterfly Danaus chrysippus
presents an intriguing case study because it is restricted to a single
‘contact zone’ population, involves a putative colour patterning
supergene, and co-occurs with infection by the the male-killing
endosymbiont Spiroplasma. We investigated the origin and evolution of this
system using whole genome sequencing. We first identify the ‘BC
supergene’, a broad region of suppressed recombination across nearly half
a chromosome, which links two colour patterning loci. Association analysis
suggests that the genes yellow and arrow in this region control the
forewing colour pattern differences between D. chrysippus subspecies. We
then show that the same chromosome has recently formed a neo-W that has
spread through the contact zone within ~2200 years. We also assembled the
genome of the male-killing Spiroplasma, and find that it shows perfect
genealogical congruence with the neo-W, suggesting that the neo-W has
hitchhiked to high frequency as the male killer has spread through the
population. The complete absence of female crossing-over in the
Lepidoptera causes whole-chromosome hitchhiking of a single neo-W
haplotype, carrying a single allele of the BC supergene, and dragging
multiple non-synonymous mutations to high frequency. This has created a
population of infected females that all carry the same recessive colour
patterning allele, making the phenotypes of each successive generation
highly dependent on uninfected male immigrants. Our findings show how
hitchhiking can occur between the unlinked genomes of host and
endosymbiont, with dramatic consequences.