Echoes from the Past: What Ancient Genomic Insertions say about the Phylogeny of Species

Methods to reconstruct evolutionary histories have been developing successively over the last 150 years, with the main aim being to gain resourceful insights into our history and those of related or distant species. Nevertheless, critical phylogenetic zones continuously resist any attempt at resolution. Comparing mutual morphologies, forms, and structures to resolve the relationships of species found their boundaries in the limited number of these characters and in their sensitivities to convergence. Molecular data are able to overcome numerous of these limitations, but their intrinsically low level of character complexity also means that they are prone to homoplasy, a molecular effect comparable to phenotypic convergence. With the current increasing availability of fully sequenced genomes, more and more investigations encompass the analyses of full genomes, but still do not fully resolve an organism's evolutionary history. To avoid the problems of homoplasy, we and others have turned to a virtually homoplasy-free marker system, the ancestral genomic insertions of transposable elements (TEs) to resolve evolutionary trees. This methodology compensates for the shortcomings of other systems, but requires high throughput computational and experimental screenings and very critical analyses of orthology. Even when this marker system does not deliver consistent evolutionary patterns, the inconsistencies themselves provide a unique tool to detect the effects of incomplete lineage sorting or hybridization and thereby to more easily distinguish true polytomy from dichotomous speciation events. Selected, optimized search strategies to find phylogenetically informative retrotransposon markers enable us to reap valuable historical information from this unique marker system.