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 accommoda ting and incorporating heterogeneity in such data remain underdeveloped. We explored the use of partitioned, model-based analyses of heterogeneous mol ecular data in the context of a phylogenetic study of swallowtail butterfli es (Lepidoptera: Papilionidae). Despite substantial basic and applied study , phylogenetic relationships among the major lineages of this prominent gro up remain contentious. We sequenced 3.3 kb of mitochondrial and nuclear DNA (2.3 kb of cytochrome oxidase I and II and 1.0 kb of elongation factor-1 a lpha, respectively) from 22 swallowtails, including representatives of Baro niinae, Parnassiinae, and Papilioninae, and from several moth and butterfly outgroups. Using parsimony, we encountered considerable difficulty in reso lving the deepest splits among these taxa. We therefore chose two outgroups with undisputed relationships to each other and to Papilionidae and undert ook detailed likelihood analyses of alternative topologies. Following from previous studies that have demonstrated substantial heterogeneity in the ev olutionary dynamics among process partitions of these genes, we estimated e volutionary 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 unpartitio ned likelihood models. Partitioned models gave markedly better fits to the data than did unpartitioned models and supported different topologies. Howe ver, the most likely topology varied from model to model. The most likely i ngroup topology under the best-fitting, six-partition GTR + Gamma model fav ors a paraphyletic Parnassiinae. However, when examining the likelihoods of alternative rootings of this tree relative to rootings of the classical hy pothesis, two rootings of the latter emerge as most likely. Of these two, t he most likely rooting is within the Papilioninae, although a rooting betwe en Baronia and the remaining Papilionidae is only nonsignificantly less lik ely.