Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales

Short interspersed repetitive elements (SINEs) are a kind of retroposons di spersed among the eukaryotic genomes. Previously, we isolated and character ized a new SINE family, named CHR-2, members of which are distributed in th e genomes of cetaceans, hippopotamuses, and ruminants. We analyzed systemat ically more than a hundred members of the CHR-2 SINEs, which were isolated from the genomes of cetaceans and cow, together with the additional data av ailable in the DNA databases, and showed that these SINEs are divided into at least five distinct subfamilies that share diagnostic nucleotides and/or deletions. A hybridization analysis clearly demonstrated that, among these five subfamilies, two subfamilies, named CD and CDO, are specific to cetac eans and toothed whales, respectively. We reconstruct the evolutionary hist ory of the CHR-2 SINEs during evolution of cetartiodactyl genomes.