A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera: Papilionidae). Syst. Biol

Abstract.—Although it is widely agreed that data from multiple sources are necessary to condently resolve phylogenetic relationships, procedures for accommodating and incorporating heterogeneity in such data remain underdeveloped.Weexplored theuseofpartitioned, model-based analyses ofhetero-geneous molecular data in the context of a phylogenetic study of swallowtail butteries (Lepidoptera: Papilionidae). Despite substantial basic and applied study, phylogenetic relationships among the ma-jor lineages of this prominent group 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®, respectively) from 22 swallowtails, including representatives of Baroniinae, Parnassiinae, and Papilioninae, and from several moth and buttery outgroups. Using parsimony, we encountered considerable difculty in resolving the deepest splits among these taxa. We therefore chose two outgroups with undisputed relationships to each other and to Papilionidae and undertook detailed likelihood analyses of alter-native topologies. Following from 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 an