MONOPHYLETIC ORIGIN OF ALU ELEMENTS IN PRIMATES

To get insight into the early evolution of the primate Alu elements, w e characterized sequences of these repeats from the Malagasy prosimian s, lemurs (Lemuridae) and sifakas (Indriidae), as well as from galagos (Lorisidae). These sequences were compared with the oldest Alu specie s known from the human genome: dimeric Alu J and S and free Alu monome rs. Our analysis indicates that about 60 Myr ago, before the prosimian divergence, free left and right monomers formed an Alu heterodimer co nnected by a 19-nucleotide-long A-rich linker. The resulting elements successfully propagated in diverging primate lineages until about simi lar to 20 Myr ago, conserving similar sequence features and essentiall y the same Alu RNA secondary structure. We suggest that until that tim e the same ''retropositional niche'', molecular machinery making possi ble the proliferation by retroposition, constrained the evolution of A lu elements in extant primate species. These constraints became subseq uently relaxed. In the Malagasy prosimians the dimeric Alu continued t o amplify after acquiring a 34- to 36-nucleotide extension of their li nker segment, whereas in the galago genome the ''retropositional niche '' was occupied by novel short elements.