SINE insertions in cladistic analyses and the phylogenetic affiliations ofTarsius bancanus to other primates

Transpositions of Alu sequences, representing the most abundant primate sho rt interspersed elements (SINE), were evaluated as molecular cladistic mark ers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR anal yzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns ex hibited longer fragments for the anthropoids (New World and Old World monke ys) and T. bancanus whereas shorter fragments were detected for the strepsi rhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occu rred independently in the same intron on the lineages leading both to the c ommon ancestor of anthropoids and to T. bancanus, albeit at different nucle otide positions. Our results demonstrate the efficiency and possible pitfal ls of SINE transpositions used as molecular cladistic markers in tracing ba ck a divergence point in primate evolution over 40 million years old. The t hree Alu insertions characterized underpin the monophyly of haplorhine prim ates (Anthropoidea and Tarsioidea) from a novel perspective.