Evolutionary history of B1 retroposons in the genus Mus

Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one or a few evolving master gen es or by (ii) the generation of new master genes that coexist with their pr ogenitors. Individual, highly conserved, elements of the B1 SINE family wer e identified from the GenBank nucleotide database using various B1 subfamil y consensus query sequences to determine their integration times into the m ouse genome. A comparison of orthologous loci in various species of the gen us Mus demonstrated that four subfamilies of B1 elements have been amplifyi ng within the last 1-3 million years. Therefore, B1 sequences are generated by coexisting source genes. Additionally, three B1 subfamilies have been c oncurrently propagated during subspecies divergence and strain formation in Mus, indicating very recent activity of this retroposon family. The patter ns of intra- and interspecies variations of orthologous loci demonstrate th e usefulness of B1 integrations as a phylogenetic tool. A single inconsiste ncy in the phylogenetic trends was depicted by the presence of a B1 insert in an orthologous locus exclusively in M. musculus and M. pahari. However, DNA sequence analysis revealed that these were independent integrations at the same genomic site. One highly conserved B1 element that integrated at l east 4-6 million years ago suggests the possibility of occasional function for B1 integrations.