Gene order breakpoint evidence in animal mitochondrial phylogeny

Multiple genome rearrangement methodology facilitates the inference of anim al phylogeny from gene orders on the mitochondrial genome. The breakpoint d istance is preferable to other, highly correlated but computationally more difficult, genomic distances when applied to these data. A number of theori es of metazoan evolution are compared to phylogenies reconstructed by ances tral genome optimization, using a minimal total breakpoints criterion. The notion of unambiguously reconstructed segments is introduced as a way of ex tracting the invariant aspects of multiple solutions for a given ancestral genome; this enables a detailed reconstruction of the evolution of non-tRNA mitochondrial gene order.