Ribosomal DNA: Molecular Evolution and Phylogenetic Inference

  title={Ribosomal DNA: Molecular Evolution and Phylogenetic Inference},
  author={David M. Hillis and Michael T. Dixon},
  journal={The Quarterly Review of Biology},
  pages={411 - 453}
Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. [] Key Result An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence.

Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins.

To standardize the set of protein-coding loci assayed in bacterial genomes, over 100 widely distributed genes were examined to identify sets of universal primers for use in the PCR amplification of protein coding regions that are common to virtually all bacteria.

Amplification of mitochondrial small subunit ribosomal DNA of polypores and its potential for phylogenetic analysis

Phylogenetic relationships were resolved quite efficiently by mt SSU rDNA sequences, and they proved to be more useful in phylogenetic reconstruction of Ganoderma than nuclear internal transcribed spacer (ITS) r DNA sequences.

Evolution and phylogenetic information content of the ribosomal DNA repeat unit in the Blattodea (Insecta).

Ribosomal ITS sequences and plant phylogenetic inference.

The phylogenetic potential of entire 26S rDNA sequences in plants.

The patterns of molecular evolution of entire 26S rDNA sequences and their impact on phylogeny retrieval are explored, exhibiting less cryptic sequence simplicity, a lower frequency of insertion and deletion, and greater phylogenetic potential.

Computational discovery and analysis of rDNA sequence heterogeneity in yeast

Initial simulations show the distribution of pSNPs varies depending upon the balance between mutations and concerted evolutionary events, and provide a framework to investigate the mechanisms involved in altered rDNA dynamics in various cellular processes.

Sequence variation within the rRNA gene loci of 12 Drosophila species.

The 28S gene was found to contain fewer variants than the 18S gene despite evolving 2.5-fold faster, and it is postulate that the fewer variants in the28S gene is due to localized gene conversion or DNA repair triggered by the activity of retrotransposable elements that are specialized for insertion into the 28S genes of these species.

Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects

The information is summarized about the structure and utility of the phylogenetically informative spacer regions of the rDNA, namely internal- and external transcribedSpacer regions as well as the intergenic spacer (IGS).

Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda

Conditionally Neutral Phylogenetic Markers of Major Taxa: A New Aspect of the Evolution of Macromolecules

The nature of these markers of ancient taxa, paradoxical from the perspective of neutral evolution, is discussed, as well as their importance for establishing monophyly of both new large-scale taxonomic groups of invertebrates and some major taxa of Nematoda.



Phylogenetic evidence for the acquisition of ribosomal RNA introns subsequent to the divergence of some of the major Tetrahymena groups.

Complete small subunit ribosomal RNA gene sequences from 13 species of Tetrahymena are determined and the absolute number of nucleotide differences between the sequences was used to construct a phylogenetic tree to indicate that the intron character has been acquired independently in different species at a stage later than the branching out of the species.

16S ribosomal DNA amplification for phylogenetic study

By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them.

Partial phylogeny of the unicellular eukaryotes based on rapid sequencing of a portion of 28S ribosomal RNA.

Using a rapid rRNA sequencing technique, the sequence of the 400 nucleotides located at the 5' end of the large subunit rRNA molecule from eight species of unicellular eukaryotes (protists) is determined, suggesting a very ancient origin for organelles containing a 9 + 2 microtubular arrangement.

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.

A protocol is described for rapidly generating large blocks of 16S rRNA sequence data without isolation of the 16 S rRNA or cloning of its gene, and its phylogenetic usefulness is evaluated by examination of several 17S rRNAs whose gene sequences are known.

Ribosomal RNA in Vertebrates: Evolution and Phylogenetic Applications

It is recognized that the pursuits of molecular systematics and molecular evolution are mutually informing and patterns of sequence change over thousands and millions of years can be inferred only by comparing sequences among taxa whose divergences span.

A Commentary on the Use of Ribosomal DNA in Systematic Studies

The same characteristics which make rDNA attractive may also introduce difficulties, and it strikes us as improbable that closely related species can become differentially fixed for NTS restriction site patterns without exhibiting both within and between individual polymorphism during at least some stage of the divergence process.


This analysis suggests that R. sylvatica of North America is more closely related to the R. temporaria group of Eurasia than to other North American Rana, and this demonstrates that restriction site mapping of rDNA arrays provides a useful molecular technique for the examination of historical evolutionary questions across considerable periods of time.