The evolution of modern lineages of mouse L1 elements

There are three known families of L1 elements in the Mus genome, V, F, and A. An individual L1 element is classified as a member of one of these families based on which of three different types of transcription promoters is at its 5' end. Initial evidence suggested that the only actively transposing L1 elements in the modern mouse genome were a young subfamily of A-type elements. That belief was overturned when a transposing F subfamily, T(F), was discovered. We used molecular phylogenetic methods to investigate the emergence of the two currently transposing L1 lineages, young A's and T(F)'s. Both of these subfamilies appear to be direct descendants from a specific clade of F-type L1's. Our results imply that recombination between L1 sequences occurred in the lineage from which the T(F) subfamily evolved. We also found that phylogenetic analysis of a L1 3' untranslated region (UTR) is diagnostic for the promoter type at the 5' end of the sequence and, therefore, for the family to which it belongs. As part of this investigation, we developed a set of full-length L1 sequences, which may serve as a general reference set for phylogenetic analyses in Mus. Our analyses included 21 full-length L1 elements from the GenBank nonredundant database that had not been phylogenetically analyzed previously.