Estimation of the true evolutionary distance under the INFER model

Abstract

Genome rearrangements are evolutionary events that shuffle genomic architectures. Usually the rearrangement distance between two genomes is estimated as the minimal number of rearrangements needed to transform one genome into another, which is usually referred to as the parsimony assumption. Since in reality the parsimony assumption may or may not hold, the question arises of estimating the true evolutionary distance (i.e., the actual number of genome rearrangements between the genomes of two species). While several methods for solving this problem have been developed, all of them have their own disadvantages. In the current paper we consider a very general model and provide a flexible estimator as well as the limits of applicability for the most popular estimation methods, such as the maximum parsimony method.