LINE-1 (L1) lineages in the mouse

Recently, a rapidly amplifying family of mouse LINE-1 (L1) has been identif ied and named T-F. The evolutionary context surrounding the derivation of t he T-F family was examined through phylogenetic analysis of sequences in th e 3' portion of the repeat. The Mus musculus domesticus T-F family was foun d to be the terminal subfamily of the previously identified L1Md4 lineage. The L1Md4 lineage joins the other prototypical mouse LINE-1 lineage (the L1 MdA2 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 fami ly from Al. m. domesticus was found to join to the previously reported M. s pretus Ms475 and Ms7024 LINE-1 families at just 0.5 MYA, indicating horizon tal transfer. The T-F family from M. m. domesticus was then found to be eve n 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 l ibrary. This lineage, in contrast to the spretus T-F lineage, does join dom esticus at about 1 MYA, as would be expected in the absence of horizontal t ransfer. A third major family was also found that splits off from the L1Md4 lineage shortly after its departure from the L1MdA2 lineage. The new famil y, named the Z family, was found to contain the de novo LINE-1 inserts caus ing 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 mo re numerous than the reported number of 5' ends, suggesting that T-F may no t be subjected to the 90% truncation pattern typical of LINE-1 as a whole.