The butterfly family Nymphalidae contains some of the most important non-drosophilid insect model systems for evolutionary and ecological studies, yet the evolutionary history of the group has remained shrouded in mystery. We have inferred a robust phylogenetic hypothesis based on sequences of 10 genes and 235 morphological characters for exemplars of 400 of the 540 valid nymphalid genera representing all major lineages of the family. By dating the branching events, we infer that Nymphalidae originated in the Cretaceous at 90 Ma, but that the ancestors of 10–12 lineages survived the end-Cretaceous catastrophe in the Neotropical and Oriental regions. Patterns of diversification suggest extinction of lineages at the Cretaceous/Tertiary boundary (65 Ma) and subsequent elevated speciation rates in the Tertiary.

A generic-level phylogeny for the butterfly family Nymphalidae was produced by cladistic analysis of 234 characters from all life stages. The 95 species in the matrix (selected from the 213 studied) represent all important recognized lineages within this family. The analysis showed the taxa grouping into six main lineages. The basal branch is the Libytheinae, with the Danainae and Ithomiinae on the next branch. The remaining lineages are grouped into two main branches: the Heliconiinae-Nymphalinae, primarily flower-visitors (but including the fruit-attracted Coeini); and the Limenitidinae (sensu strictu), Biblidinae, and the satyroid lineage (Apaturinae, Charaxinae, Biinae, Calinaginae, Morphinae, Brassolinae, and Satyrinae), primarily fruit-attracted. Data partitions showed that the two data sets (immatures and adults) are very different, and a partitioned Bremer support analysis showed that the adult characters are the main source of conflict in the nodes of the combined analysis tree. This phylogeny includes the widest taxon coverage of any morphological study on Nymphalid butterflies to date, and supports the monophyly and relationships of most presently recognized subgroups, providing strong evidence for the presently accepted phylogenetic scheme.

Information about predation risks is critical for herbivorous insects, and natural selection favors their ability to detect predators before oviposition and to select enemy-free foliage when offspring mortality risk is high. Food plants are selected by ovipositing butterflies, and offspring survival frequently varies among plants because of variation in the presence of predators. Eunica bechina butterflies oviposit on Caryocar brasiliense, an ant-defended plant. Experiments with dried Camponotus and Cephalotes ants pinned to leaves revealed that butterflies use ant size and form as visual cues to avoid ovipositing on plant parts occupied by ants more likely to kill larval offspring. Presence of sap-sucking bugs did not affect butterfly oviposition. This is the first demonstration that visual recognition of predators can mediate egg-laying decisions by an insect herbivore and that an insect will discriminate among different species of potential predators. This unusual behavioral capability permits specialization on a risky, ant-defended food plant.

Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species^1,2. However, convincing examples of homoploid hybrid speciation remain rare because it is challenging to demonstrate that hybridization was crucial in generating reproductive isolation³. Here we combine population genomic analysis with quantitative trait locus mapping of species-specific traits to examine a case of hybrid speciation in Heliconius butterflies. We show that Heliconius elevatus is a hybrid species that is sympatric with both parents and has persisted as an independently evolving lineage for at least 180,000 years. This is despite pervasive and ongoing gene flow with one parent, Heliconius pardalinus, which homogenizes 99% of their genomes. The remaining 1% introgressed from the other parent, Heliconius melpomene, and is scattered widely across the H. elevatus genome in islands of divergence from H. pardalinus. These islands contain multiple traits that are under disruptive selection, including colour pattern, wing shape, host plant preference, sex pheromones and mate choice. Collectively, these traits place H. elevatus on its own adaptive peak and permit coexistence with both parents. Our results show that speciation was driven by introgression of ecological traits, and that speciation with gene flow is possible with a multilocus genetic architecture.