Interaction of process partitions in phylogenetic analysis: An example from the swallowtail butterfly genus Papilio

In this study, we explored how the concept of the process partition may be applied to phylogenetic analysis. Sequence data were gathered from 23 speci es and subspecies of the swallowtail butterfly genus Papilio, as well as fr om two outgroup species from the genera Eurytides and Pachliopta. Sequence data consisted of 1,010 bp of the nuclear protein-coding gene elongation fa ctor-1 alpha (EF-1 alpha) as well as the entire sequences (a total of 2,211 bp) of the mitochondrial protein-coding genes cytochrome oxidase I and cyt ochrome oxidase II (COI and COII). In order to examine the interaction betw een the nuclear and mitochondrial partitions in a combined analysis. we use d a method of visualizing branch support as a function of partition weight ratios. We demonstrated how this method may be used to diagnose error at di fferent levels of a tree in a combined maximum-parsimony analysis. Further, we assessed patterns of evolution within and between subsets of the data b y implementing a multipartition maximum-likelihood model to estimate evolut ionary parameters fur various putative process partitions. COI third positi ons have an estimated average substitution rate more than 15 times that of EF-1 alpha, while COII third positions have an estimated average substituti on rate more than 22 times that of EF-1 alpha. Ultimately, we found that al though the mitochondrial and nuclear data were not significantly incongruen t, homoplasy in the fast-evolving mitochondrial data confounded the resolut ion of basal relationships in the combined unweighted parsimony analysis de spite the fact that there was relatively strong support for the relationshi ps in the nuclear data. We conclude that there may be shortcomings to the m ethods of "total evidence" and "conditional combination" because they may f ail to detect or accommodate the type of confounding bias we found in our d ata.