Evolutionary applications of MIRs and SINEs

It is believed that short interspersed elements (SINEs) are irreversibly in serted into genomes. We use this concept to try to deduce the evolution of whales using sequence and hybridization studies. The observation that micro satellites are associated with SINEs lead us to screen sequences surroundin g cetacean microsatellites for artiodactyl-derived SINEs. Two sequences tha t were thought to be cetacean SINEs and the bovine SINE were aligned for co mparison to sequences flanking microsatellites from ungulates. The bovine S INE was observed only in ruminants while CetSINE1 and 2 were found in mamma ls. Hybridization studies using these three SINEs revealed that CetSINE1 wa s found in all ungulates and cetaceans with the strongest hybridization sig nal observed in the hippopotamus and beluga; CetSINE2 hybridized to all ung ulate suborders, while the bovine SINE was only observed in Ruminantia. It is proposed that these putative SINEs are not 'generic' SINEs but mammalian -wide interspersed repeats (MIRs). Caution is urged: what initially appears to be a SINE may instead be a MIR and have reduced evolutionary resolving power.