Ribosomal DNA: Molecular Evolution and Phylogenetic Inference

Abstract

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. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. 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. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

“…Like ribosomal RNAs, spliceosomal RNAs are subject to concerted evolution [28,68,21], i.e., one observes that paralogous sequences in the same species are more similar than orthologous sequences of different species. Multiple molecular mechanisms may account for this phenomenon: gene conversion, repeated unequal crossover, and gene amplification (frequent duplications and losses within family), see [40] for a review.…”

Molecular evidence that Heligmosomoides polygyrus from laboratory mice and wood mice are separate species

“…Additional material of related Heligmosomoides and Heligmosomum species was also included. This dual molecular approach combines the advantages, and overcomes some of the disadvantages, of focussing on just nuclear or mitochondrial DNA (see Hillis and Dixon, 1991 ;Mayer and Soltis, 1999 ;Avise, 2000). It does not, however, clarify precise species boundaries without a statistically defined framework (Sites and Marshall, 2004).…”

Evolutionary patterns of non-coding RNAs

“…In Escherichia coli, for instance, there are seven operons encoding rRNAs 16S, 23S, and 5S [31]. Typical Eukaryotes contain tandemly repeated arrays of rRNAs genes each of which contains three of the four ribosomal RNA components separated by two "internally transcribed spacers" (18S/ITS1/5.8S/ITS2/28S) [155]. In most species the fourth rRNA gene, 5S rRNA, is also contained in this array, while it sometimes is dispersed throughout the genome (as in Schizosaccharomyces pombe, [441]), organized in its own tandem arrays (as in soybeans [128]), or both (as in humans [252]).…”

“…In most species the fourth rRNA gene, 5S rRNA, is also contained in this array, while it sometimes is dispersed throughout the genome (as in Schizosaccharomyces pombe, [441]), organized in its own tandem arrays (as in soybeans [128]), or both (as in humans [252]). For each of these genes, however, the rDNA sequences that are represented in fully processed rRNA are essentially identical in most organisms, i.e., rRNA genes are subject to concerted evolution [155,361,121]. This is the tendency of the different genes in a gene family or gene cluster to evolve "in concert".…”