DNA “Fossils” and Phylogenetic Analysis

The L1 element (LINE-1, long interspersed repeated DNA) is the mammalian version of the non-long terminal repeat class of transposable elements that replicate via an RNA intermediate (retrotransposons)(1). Every modern mammalian species studied to date contains a distinctive L1 family consisting of tens of thousands of members, which are interspersed throughout the genome. Despite their distinctiveness, all full-length mammalian L1 elements share the same organization: a 5′-UTR, 1 which includes a regulatory sequence; ORF I, which encodes a protein of unknown function; ORF II, which encodes an RT(2); and a 3′-UTR that contains a G-rich polypurine:polypyrimidine tract and terminates in an A-rich sequence (Fig.