title: Early eukaryote evolution based on mitochondrial gene order breakpoints.
abstract: 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 breakpoints"; this solution can then be incorporated into a routine for estimating optimal 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 problem 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 groupings which have been proposed and, conversely, confirming the usefulness of the breakpoint method as a phylogenetic tool even for small genomes.
authors: Centre de recherches mathématiques, Université de Montréal, Québec. sankoff@crm.umontreal.ca
authors: D
authors: D
authors: Sankoff
authors: D
authors: D
authors: Bryant
authors: M
authors: M
authors: Deneault
authors: B F
authors: BF
authors: Lang
authors: G
authors: G
authors: Burger
mesh_terms: D005075:Biological Evolution; D019295:Computational Biology; D004272:DNA, Mitochondrial / Q000235:genetics*; D005057:Eukaryotic Cells; D008957:Models, Genetic; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial