Tempo and mode of evolution of a primate-specific retrotransposon belonging to the LINE 1 family

L1P_MA2 is a primate-specific subfamily of L1 retrotransposons. The consensus sequence of this element differs from the canonical L1 consensus by the presence of a 3800-bp region in 5' (L1M1_J). Part of this region has been proposed to be involved in a dystrophin mutation affecting the correct splicing of the gene and causing an X-linked dilated cardiomyopathy. In consideration of the potential involvement in splicing regulation of this element and also because of its atypical structure, we investigated its evolutionary history by analyzing the inter- and intraspecific divergence of L1P_MA2 sequences in various species of primates. The resulting phylogenetic trees show long terminal branches and short basal internodes, as expected for a rapid event of diversification that occurred in the past. The phylogenetic analysis and the intraspecific divergence estimates revealed a pattern of evolution for this element similar in all primates with the exception of lemurs, thus suggesting that the major wave of expansion of L1P_MA2 in primate genomes occurred after the divergence between Prosimiae and Anthropoidea. These results clearly indicate that a phylogenetic approach is more appropriate than methods based on sequence data from a single species, when investigating time and mode of evolution of retro-elements.