Rapid evolution of a young L1 (LINE-1) clade in recently speciated Rattus taxa

L1 elements are retrotransposons that have been replicating and evolving in mammalian genomes since before the mammalian radiation. Rattus norvegicus shares the young L1(m1vi2) clade only with its sister taxon, Rattus cf moluccarius. Here we compared the L1(m1vi2) clade in these recently diverged species and found that it evolved rapidly into closely related but distinct clades: the L1(m1vi2-rm) clade (or subfamily), characterized here from R. cf moluccarius, and the L1(m1vi2-rn) clade, originally described in R. norvegicus. In addition to other differences, these clades are distinguished by a cluster of amino acid replacement substitutions in ORF I. Both rat species contain the L1(m1vi2-rm) clade, but the L1(m1vi2-rn) clade is restricted to R. norvegicus. Therefore, the L1(m1vi2-rm) clade arose prior to the divergence of R. norvegicus and R. cf moluccarius, and the L1(m1vi2-rn) clade amplified after their divergence. The total number of L1(m1vi2-rm) elements in R. cf moluccarius is about the same as the sum of the L1(m1vi2-rm) and L1(m1vi2-rn) elements in R. norvegicus. The possibility that L1 amplification is in some way limited so that the two clades compete for replicative supremacy as well as the implications of the other distinguishing characteristic of the L1(m1vi2-rn) and L1(m1vi2-rm) clades are discussed.