A non-LTR retroelement extinction in Spermophilus tridecemlineatus.

The typical mammalian genome is dominated by two types of transposable elements (TEs), the autonomous and non-autonomous non-LTR retrotransposons, i.e. LINEs and SINEs, and with few exceptions there is a sole active LINE family (L1). During an ongoing investigation of TEs in rodents we determined that overall transposon activity has been steadily declining in Spermophilus tridecemlineatus. More specifically, the typically ubiquitous L1 activity of mammals has decreased drastically within the last 26MY. Indeed, only three L1 insertions with intact ORF1 sequences were readily identifiable and no intact ORF2 sequences were identified. The last L1 and SINE insertions date to ~5.3MYA and 4MYA, respectively. Based on our inability to computationally identify recently inserted L1 elements we suggest that S. tridecemlineatus is experiencing a quiescence or extinction of non-LTR retrotransposon activity. Such a finding represents only the fourth instance of a loss of non-LTR retrotransposon activity identified in mammals and, as such, represents an important additional data point to guide our understanding of LINE dynamics in eutherians.