Classification of the cosmopolitan butterfly genus Danaus (Nymphalidae: Danainae) is revised at subgeneric, specific and subspecific levels, combining for the first time mitochondrial and nuclear DNA sequence information with morphological data. Tree topologies based on the nuclear genome (allozymes, pheromone components, the morphology of all life history stages and nuclear DNA sequences), on the one hand, and mitochondrial DNA, on the other, are incongruent and challenge the current taxonomy of the genus. Although earlier classifications, based on adult morphology alone, are, in general, well supported by an analysis of total evidence, the mitochondrial phylogeny shows that the species D. chrysippus and its subgenus Anosia are deeply paraphyletic. Subspecies dorippus of D. chrysippus is the basal clade of the genus and is reinstated as the species D. dorippus. The former species D. plexaure is demoted to a subspecies of D. eresimus. The specific status of D. erippus, as distinct from D. plexippus, is tentatively supported. On the strength of the new data, division of the monophyletic genus Danaus s.l. into three subgenera Danaus s.s., Salatura and Anosia is unsustainable and is abandoned. Of the 15 terminal clades (taxa) of Danaus s.l. included in the study, 11 are species that broadly conform to the biological species concept. (The West Indian species D. cleophile, missing from our analysis, is the twelfth species). The remaining terminal clades are subspecies of D. chrysippuscomb. nov. and D. dorippusstat. rev. Two sympatric Neotropical species, D. eresimus and D. gilippus, are morphologically distinct and sexually isolated but have nearly identical mitochondrial genomes. In contrast, two partially sympatric Palaeotropical species, D. chrysippus and D. dorippus, are cryptic species that share structural morphology and hybridize but have highly differentiated mitochondrial genomes. D. dorippus is polymorphic for two anciently diverged haplotypes and its history has possibly involved recombinational speciation and/or hybridism
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