An ancient retrovirus-like element contains hot spots for SINE insertion

Vertebrate retrotransposons have been used extensively for phylogenetic ana lyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumul ated over time in orthologous copies of that insert or by determining the p resence or absence of that specific element at a particular site. The prese nce of specific copies has been deemed to be an essentially homoplasy-free phylogenetic character because the probability of multiple independent inse rtions into any one site has been believed to be nil. Mys elements are a ty pe of LTR-containing retrotransposon present in Sigmodontine rodents. In th is study we have shown that one particular insert, mys-9, is an extremely o ld insert present in multiple species of the genus Peromyscus. We have foun d that different copies of this insert show a surprising range of sizes, du e primarily to a continuing series of SINE (short interspersed element) ins ertions into this locus. We have identified two hot spots for SINE insertio n within mys-9 and at each hot spot have found that two independent SINE in sertions have occurred at identical sites. These results have major repercu ssions for phylogenetic analyses based on SINE insertions, indicating the n eed for caution when one concludes that the existence of a SINE at a specif ic locus in multiple individuals is indicative of common ancestry. Athough independent insertions at the same locus may be rare, SINE insertions are n ot homoplasy-free phylogenetic markers.