Reversing Gene Erosion—Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data

Abstract

Abstract. In the last few years, it has become routine to use gene-order data to reconstruct phylogenies, both in terms of edge distances (parsimonious sequences of operations that transform one end point of the edge into the other) and in terms of genomes at internal nodes, on small, duplication-free genomes. Current gene-order methods break down, though, when the genomes contain more than a few hundred genes, possess high copy numbers of duplicated genes, or create edge lengths in the tree of over one hundred operations. We have constructed a series of heuristics that allow us to overcome these obstacles and reconstruct edges distances and genomes at internal nodes for groups of larger, more complex genomes. We present results from the analysis of a group of thirteen modern γproteobacteria, as well as from simulated datasets.