We are in the process of assembling a molecular phylogeny that will reveal (once and for all) the evolutionary relationships of all 18,728 species within the butterfly superfamily Papilionoidea, as defined by van Nieukerken. To do this, we are using two types of sampling. To start, we are sampling one "exemplar" species from each butterfly genus (1815 total) extremely thoroughly. We are using a specially designed anchored hybrid enrichment probe set to target around 500 loci within the generalized butterfly genome. These 500 loci include 10 "standard" loci that have been used in butterfly phylogenetic research for many years. We will compare the sequence data we obtain from these exemplars, and use standardized measurements of genetic similarity to pin down the evolutionary relationships of all 1815 butterfly genera.
We will then map the rest of the 16,913 species in Papilionoidea onto this highly resolved phylogeny backbone. To expedite the process, we will use a second, simplified probe set to target only the 10 standard loci mentioned above: CAD, Wingless, COI, EF-1a, RpS5, RpS2, MDH, GAPDH, DDC and IDH. This will have the added benefit of allowing us to combine our results with sequence data generated from previous research on butterflies, which will let us estimate evolutionary relationships within each genus with a great deal of confidence!