Sonja J Prohaska, Sarah J Berkemer, Fabian Gärtner, Thomas Gatter, Nancy Retzlaff, The Students of the Graphs and Biological Networks Lab 2017, Christian Höner zu Siederdissen, and Peter F. Stadler

Paper #: 2014-04-015

Abstract.  Clusters of paralogous genes such as the famous HOX cluster of developmental transcription factors tend to evolve by stepwise duplication of its members, often involving unequal crossover. Gene conversion and possibly other mechanisms of concerted evolution further obfuscate the phylogenetic relationships. As a consequence, it is very difficult or even impossible to disentangle the detailed history of gene duplications in gene clusters. In this contribution we show that the expansion of gene clusters by unequal crossover as proposed by Walter Gehring leads to distinctive patterns of genetic distances, namely a subclass of circular split systems. Furthermore, when the gene cluster was left undisturbed by genome rearrangements, the shortest Hamiltonian paths w.r.t. genetic distances coincide with the genomic order. This observation can be used to detect ancient genomic rearrangements of gene clusters and to distinguish gene clusters whose evolution was dominated by unequal crossover within genes from those that expanded through other mechanisms.