Polytypy and systematics: diversification of Papilio swallowtail butterflies in the biogeographically complex Indo-Australian Region

A long-standing problem in evolutionary biology and systematics is defining patterns of diversification and speciation, which is compounded by allopatric distributions of polytypic taxa in biogeographically fragmented landscapes. In this paper we revisit this enduring systematic challenge using Mormon swallowtail butterflies (Papilio subgenus Menelaides)--an evolutionary and genetic model system. Menelaides is speciose and intensively sampled, with nearly 260 years of systematic study complicated by polytypy resulting from discontinuous morphological variation. This variation is structured by the mainland-island matrix of the geologically complex Indo-Australian Region, where drawing species boundaries has been difficult. We sampled variation across the biogeographic range of Menelaides, covering 97% of currently recognized species and nearly half of all subspecies. We generated a well-supported mito-nuclear phylogeny, on which we delineated species based on two species delimitation methods (GMYC and mPTP) and strongly supported reciprocal monophyly. These analyses showed that the true species diversity in this group may be up to 25% greater than traditional taxonomy suggests, and prompts extensive taxonomic restructuring. Biogeographic analyses showed that Menelaides have diversified largely in allopatry in Indo-Australian subregions by repeated dispersals across key biogeographic barriers. These results provide critical insights into the diversification process in this morphologically diverse and taxonomically complicated model group. These results will also be informative in future studies on systematics, biogeography, speciation and morphological diversification in the Indo-Australian Region--arguably the most complex geological land/seascape in the world.