Phylogenetic reconstruction with gene rearrangements and gene losses

Reconstructing phylogenies from gene-order data has become very attractive in the research of evolution these years. So far, most methods can only treat genomes with equal gene contents with each gene appearing exactly once in each genome. In this paper, we propose a new distance measurement for genomes with inversions and insertions/deletions that comply with triangle inequality. Based on this distance, we develop a new method to solve the median problem of unequal gene content, which are used to reconstruct both phylogenies and ancestral genomes. We test our method on simulated datasets under various conditions and the experimental results show that our distance measurement can produce more accurate phylogenetic trees compared with other popular methods for unequal genomes. Also our median algorithm produces remarkably more accurate ancestral genomes than the only unequal genome median solver that is currently available.