The strange phylogenies of transposable elements: are horizontal transfers the only explantation?

Analyses of the evolution of transposable elements reveal some inconsistencies when the phylogenies of such elements are compared to conventional phylogenies of the host species. Such discrepancies are generally interpreted as resulting from occasional horizontal transfers of transposable elements across species boundaries. This phenomenon has been clearly demonstrated for only a few elements and both its frequency and the mechanism by which it occurs remain unknown. Moreover, in many cases, the hypothesis of horizontal transfer must be compared with alternative evolutionary scenarios.