Early eukaryote evolution based on mitochondrial gene order breakpoints

The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders, For three genomes this is done by solving the "median problem for breakpoin ts"; this solution can then be incorporated into a routine for estimating o ptimal gene orders for all the ancestral genomes in a fixed phylogeny. For the difficult (and most prevalent) case where the genomes contain partially different sets of genes, we present a general heuristic for the median pro blem for induced breakpoints. A fixed-phylogeny optimization based on this is applied in a phylogenetic study of a set of completely sequenced protist mitochondrial genomes, confirming some of the recent sequence-based groupi ngs which have been proposed and, conversely, confirming the usefulness of the breakpoint method as a phylogenetic tool even for small genomes.