Estimating true evolutionary distances between genomes

Abstract

Evolution operates on whole genomes by operations that change the order and strandedness of genes within the genomes. This type of data presents new opportunities for discoveries about deep evolutionary rearrangement events, provided that sufficiently accurate methods can be developed to reconstruct evolutionary trees in these models [3, 6, 7, 15, 17]. A necessary component of any such method is the ability to accurately estimate true evolutionary distances between two genomes, which is the number of rearrangement events that took place in the evolutionary history between them. We present a new technique called IEBP, for estimating the true evolutionary distance between two genomes, whether signed or unsigned, circular or linear, and for any relative probabilities of rearrangement event classes. The method is highly accurate, as our simulation study shows. This simulation study also shows that the distance estimation technique improves the accuracy of the phylogenetic trees reconstructed by the popular distance-based method, neighbor joining [1, 20].