Subspecies chrysippus, dorippus and alcippus of the butterfly Danaus chrysippus differ at three biallelic colour gene loci. They have partially vicariant distributions, but their ranges overlap over a substantial part of central and East Africa, where hybridism is commonplace. We now report that the West African subspecies alcippus differs from other subspecies, not only in nuclear genotype but also in mitochondrial haplotype in both allopatry and sympatry. The maintenance of concordant nuclear and cytoplasmic genetic differences in sympatry, and in the face of hybridisation, is prima facie evidence for sexual isolation. Other evidence that suggests alcippus may be isolated from chrysippus and dorippus include differences in sex ratio (SR), heterozygote deficiency at one site and deduced differences in patterns of migration. We suggest that, within the hybrid zone, differential infection of subspecies by a male-killing Spiroplasma bacterium causes SR differences that restrict female choice, triggering rounds of heterotypic mating and consequent heterozygote excess that is largely confined to females. The absence of these phenomena from hybrid populations that test negative for Spiroplasma supports the hypothesis. The incomplete sexual isolation and partial vicariance of alcippus suggests that it is a nascent species
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