Stability of rearrangement measures in the comparison of genome sequences

Abstract. We present data-analytic and statistical tools for studying rates of rearrangement of whole genomes and to assess the stability of these methods with changes in the level of resolution of the genomic data. We construct data sets on the numbers of conserved syntenies and conserved segments shared by pairs of animal genomes at different levels of resolution. We fit these data to an evolutionary tree and find the rates of rearrangement on various evolutionary lineages. We doc-ument the lack of clocklike behaviour of rearrangement processes, the independence of translocation and inversion rates, and the level of res-olution beyond which translocations rates are lost in noise due to other processes.