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© The Willi Hennig Society 2012.

Explanations for the high species diversity of the Indo‐Australian Archipelago are often challenged by the region’s complex climatic and geological histories. Here, we investigated the evolutionary history of swallowtail butterflies of the Papilio subgenus Achillides, comprising up to 25 recognized species and about 100 subspecies distributed across the Indo‐Australian Archipelago. To estimate the relative contributions of factors influencing their biodiversity, we used DNA sequences to infer the phylogeny and species limits of 22 species including most of their subspecies. We recovered a highly resolved and well‐supported phylogeny for the subgenus, and clarified some taxonomic ambiguities at the species level. The corresponding DNA‐based species phylogeny was then employed to reconstruct their historical biogeography using relaxed‐clock and parametric‐based …