This article is available from: http://www.biomedcentral.com/1471-2164/9/219[Background] Transposable elements are selfish genetic sequences which only occasionally provide useful functions to their host species. In addition, models of mobile element evolution assume a second type of selfishness: elements of different familes do not cooperate, but they independently fight for their survival in the host genome.[Results] We show that recombination events among distantly related Athila retrotransposons have led to the generation of new Athila lineages. Their pattern of diversification suggests that Athila elements survive in Arabidopsis by a combination of selfish replication and of amplification of highly diverged copies with coding potential. Many Athila elements are non-autonomous but still conserve intact open reading frames which are under the effect of negative, purifying natural selection.[Conclusion] The evolution of these mobile elements is far more complex than hitherto assumed. Strict selfish replication does not explain all the patterns observed.Research supported by grant 200720I021 (Proyectos intramurales especiales, CSIC. Spain).Peer reviewed