Hologenomic speciation: synergy between a male‐killing bacterium and sex‐linkage creates a ‘magic trait’ in a butterfly hybrid zone

Danaus chrysippus (L.) in Africa comprises four substantially isolated semispecies that are migratory and hybridize on a seasonal basis throughout the eastern and central part of the continent. In the hybrid zone (but not elsewhere), the butterfly is commonly host to a male killing endosymbiotic bacterium, Spiroplasma sp., which principally infects one semispecies, Danaus chrysippus chrysippus in Kenya. A W‐autosome mutation, inherited strictly matrilinearly, links B and C colour gene loci, which have thus gained sex‐linkage in chrysippus. We have monitored variation in sex ratio and genotype at the A and C colour gene loci for two extended periods of 18 months (2004–5) and 12 months (2009–10) in adults reared from wild eggs laid on trap plants in Kasarani, near Nairobi, Kenya. Additionally, in 2009–10, all surviving adult butterflies were screened for Spiroplasma infection. The hybridizing Kasarani population is highly atypical in three respects, and has apparently been so for some 30 years: first, the sex ratio is permanently female‐biased (as expected), although subject to seasonal fluctuation, being lowest (male/female) when D. c. chrysippus (cc) peaks and highest when Danaus chrysippus dorippus (CC) predominates; second, the population is invariably dominated by Cc heterozygotes of both sexes but especially females; and third, cc males are always scarce because they are systematically eliminated by male killing, whereas the CC genotype is male‐biased. It is this imbalance of sex versus genotype that determines the massive departure from Hardy–Weinberg equilibrium in the population, in part because cc females have little choice but to pair with C‐ males. We suggest that: first, Cc hybrids of both sexes fail to disperse in the company of either parental semispecies; second, Spiroplasma positive females carrying the W‐autosome mutation have a selective advantage over females that lack the translocation; third, the endoparasite and the translocation create a ‘magic trait’ linkage group that underlies hologenomic reproductive isolation between two emerging species, D. c. chrysippus and D. c. dorippus; and, fourth, that the predominance of males in dorippus suggests that individuals must be protected by a male‐killing suppressor gene. By contrast to the C locus, Aa heterozygotes are in substantial and permanent deficit, suggesting either assortative mating between AA (chrysippus and dorippus) and aa (Danaus chrysippus alcippus), or heterozygote unfitness, or both. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 92–109.