Gene Order Phylogeny via Ancestral Genome Reconstruction Under Dollo

Abstract We present a proof of principle for new kind stepwise algorithm unrooted binary gene-order phylogenies. This method incorporates simple look-ahead inspired by Dollo’s law, while simultaneously reconstructing each ancestor (sometimes referred to as hypothetical taxonomic units “HTU”). first generic version the illustrating necessary consequence Dollo characters. In concrete application we use generalized oriented gene adjacencies and maximum weight matching (MWM) reconstruct fragments monoploid ancestral genomes HTUs. is applied three flowering plant orders estimating phylogenies these in process. discuss how improve on extensive computing times that would be this handle larger trees.