LINE-1 (L1) lineages in the mouse

Recently, a rapidly amplifying family of mouse LINE-1 (L1) has been identified and named T-F. The evolutionary context surrounding the derivation of the T-F family was examined through phylogenetic analysis of sequences in the 3' portion of the repeat. The Mus musculus domesticus T-F family was found to be the terminal subfamily of the previously identified L1Md4 lineage. The L1Md4 lineage joins the other prototypical mouse LINE-1 lineage (the L1MdA2 lineage) approximately 1 MYA at about the time of the common ancestor of M. m. domesticus, Mus spicilegus, and Mus spretus. However, the T-F family from Al. m. domesticus was found to join to the previously reported M. spretus Ms475 and Ms7024 LINE-1 families at just 0.5 MYA, indicating horizontal transfer. The T-F family from M. m. domesticus was then found to be even more recently related to LINE-1's from another species, Al. spicilegus. A separate spretus A2 lineage was found through a directed search of a PCR library. This lineage, in contrast to the spretus T-F lineage, does join domesticus at about 1 MYA, as would be expected in the absence of horizontal transfer. A third major family was also found that splits off from the L1Md4 lineage shortly after its departure from the L1MdA2 lineage. The new family, named the Z family, was found to contain the de novo LINE-1 inserts causing the beige and riled mutations. Whether the split with the Z family was before or after the recombination that introduced the F-type promoters and defined the inception of T-F as a lineage is unclear. In enumerating copies of the various LINE-1 families, we found that T-F 3' ends were not much more numerous than the reported number of 5' ends, suggesting that T-F may not be subjected to the 90% truncation pattern typical of LINE-1 as a whole.