An Empirical Comparison of Phylogenetic Methods on Chloroplast Gene Order Data in Campanulaceae

The first heuristic for reconstructing phylogenetic trees from gene order data was introduced by Blanchette et al.. It sought to reconstruct the breakpoint phylogeny and was applied to a variety of datasets. We present a new heuristic for estimating the breakpoint phylogeny which, although not polynomial-time, is much faster in practice than BPAnalysis. We use this heuristic to conduct a phylogenetic analysis of chloroplast genomes in the flowering plant family Campanulaceae. We also present and discuss the results of experimentation on this real dataset with three methods: our new method, BPAnalysis, and the neighbor-joining method, using breakpoint distances, inversion distances, and inversion plus transposition distances.