THE EVOLUTION OF RIBOSOMAL DNA - DIVERGENT PARALOGUES AND PHYLOGENETIC IMPLICATIONS

Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the o ccurrence of divergent paralogues and recombinants in Gossypium, Nicot iana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed s pacer (ITS) sequences. Some of the divergent paralogues are probably r DNA pseudogenes, since they have low predicted secondary structure sta bility, high substitution rates, and many deamination-driven substitut ions at methylation sites. Under standard PCR conditions, the low stab ility paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with d imethylsulfoxide), both low- and high-stability paralogues amplified w ell. We also found recombination between divergent paralogues. For phy logenetics, divergent ribosomal paralogues can aid in reconstructing a ncestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticist s must discriminate among families of divergent paralogues and recombi nants or suffer from muddled and inaccurate organismal phylogenies.