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 famil ies based on which of three different types of transcription promoters is a t 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 el ements. That belief was overturned when a transposing F subfamily, T-F, was discovered. We used molecular phylogenetic methods to investigate the emer gence of the two currently transposing L1 lineages, young A's and T-F's. Bo th of these subfamilies appear to be direct descendants from a specific cla de of F-type L1's. Our results imply that recombination between L1 sequence s occurred in the lineage from which the T-F subfamily evolved. We also fou nd that phylogenetic analysis of a L1 3' untranslated region (UTR) is diagn ostic for the promoter type at the 5' end of the sequence and, therefore, f or the family to which it belongs. As part of this investigation, we develo ped a set of full-length L1 sequences, which may serve as a general referen ce set for phylogenetic analyses in Mus. Our analyses included 21 full-leng th L1 elements from the GenBank nonredundant database that had not been phy logenetically analyzed previously.