Fixation times of retroposons in the ribosomal DNA spacer of human and other primates.

We have investigated the presence/absence of two types of retroposed sequences found in human ribosomal DNA in equivalent positions in chimpanzee, gorilla, orangutan, gibbon, and rhesus monkey rDNA. These sequences are one pseudogene derived from the single-copy cdc27hs gene and seven complete Alu elements. The 2-kb pseudogene is present in the apes but not in Old World monkeys, indicating fixation in an ape ancestor. Five of the Alu elements are shared by the whole set of primates studied, indicating insertion and fixation prior to the split of the ape and Old World monkey lineages. One is absent only from the rhesus monkey rDNA, and another is absent from both gibbon and rhesus rDNA, indicating fixation at different times in primate evolutionary history. Since branching times for the primate phylogenetic tree are known from a combination of the fossil record and multiple molecular data sets, it is possible to compare Alu fixation times determined from the phylogenetic information with those calculated from Alu element mutation rates.