Expected Gene Order Distances and Model Selection in Bacteria

Abstract

The most parsimonous distances calculated in pairwise gene order comparisons cannot accurately reflect the true number of events separating two species, unless the number of changes are few. Better is to use the expected distances. In this study we recapitulate previous results and derive new expected distances for models that have gained support in other studies, such as, symmetrical reversal distances and short reversals. Further, we investigate the patterns of dotplots between species of bacteria with the purpose of model selection in gene order problems. We find several categories of data which can be explained by carefully weighing the contributions of reversals, transpositions, symmetric reversals, single gene transpositions, and single gene reversals.