Data from: A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera: Papilionidae)

Although it is widely agreed that data from multiple sources are necessary to confidently resolve phylogenetic relationships, procedures for accommodating and incorporating heterogeneity in such data remain underdeveloped. We explored the use of partitioned, model-based analyses of heterogeneous molecular data in the context of a phylogenetic study of swallowtail butterflies (Lepidoptera: Papilionidae). Despite substantial basic and applied study, phylogenetic relationships among the major lineages of this prominent group remain contentious. We sequenced 3.3 kb of mitochondrial (COI/COII α 2.3 kb) and nuclear (EF-1α 1.0 kb) DNA for 22 swallowtails, including representatives of Baroniinae, Parnassiinae, and Papilioninae, and several moth and butterfly outgroups. Parsimony encountered considerable difficulty in resolving the deepest splits among these taxa. We therefore chose two outgroups whose relationships to each other and to Papilionidae were undisputed and undertook detailed likelihood analyses of alternative topologies. Following previous studies that have demonstrated substantial heterogeneity in the evolutionary dynamics among process partitions of these genes, we estimated evolutionary parameters separately for gene-based and codon-based partitions. These values were then used as the basis for examining the likelihoods of possible resolutions and rootings under several partitioned and unpartitioned likelihood models. Partitioned models gave significantly better fits to the data than did unpartitioned models, and supported different topologies. However, the most likely topology varied from model to model. The most likely ingroup topology under the best-fitting, six partition GTR + Γ model favors a paraphyletic Parnassiinae. However, when examining the likelihoods of alternative rootings of this tree relative to rootings of the classical hypothesis two rootings of the latter emerge as most likely. Of these two, the most likely rooting is within the Papilioninae, although a rooting between Baronia and the remaining Papilionidae is only nonsignificantly less likely