Phylogenomics: Retroposed Elements as Archives for Evolutionary History

Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades. However, long or rapid evolutionary periods as well as directional mutation pressure can produce molecular homoplasies, similar characteristics lacking common ancestors.
Retroposed elements, by contrast, integrate randomly into genomes with negligible probabilities of the same element integrating independently into orthologous positions in different species. Thus, presence/absence analyses of these elements are a superior strategy for molecular systematics.