Evolution of nucleic acids (original) (raw)
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Molecular Biology and Evolution
Ribosomal RNAs have secondary structures that are maintained by internal Watson-Crick pairing. Through analysis of chordate, arthropod, and plant 5s ribosomal RNA sequences, we show that Darwinian selection operates on these nucleotide sequences to maintain functionally important secondary structure. Insect phylogenies based on nucleotide positions involved in pairing and the production of secondary structure are incongruent with those constructed on the basis of positions that are not. Furthermore, phylogeny reconstruction using these nonpairing bases is concordant with other, morphological data.
Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology - COMP BIOCHEM PHYSIOL B BIOCHEM MOL BIOL, 1982
The molecular weights and the integrity of the principal rRNA species derived from the large and the small ribosomal subunit (respectively, L-rRNA and S-rRNA) of several species of Protostomia and Protozoa have been investigated. 2. Using gel electrophoresis in formamide, the molecular weights of protostomian L-rRNA species have been found to range from 1.30 × 10 6 (Annelida) to 1.61 x 10 6 (Diptera); those of the S-rRNA's cover the range 0.65 × 10 6 (Annelida~0.81 x 10 6 (Diptera). 3. Both rRNA components have incurred extensive changes among the Protozoa; the L-rRNA ranges in weight from 1.35 x 106 (T. pyriformis) to 1.57 x 10 6 (A. castellanii) and the S-rRNA from 0.70 x 10 6 of T. pyriformis to 0.85 x 106 of A. eastellanii and E. 9racilis. 4. The L-rRNA components of all the species investigated are discontinuous molecules endowed with a latent median break; depending on whether the nick is located at the centre of the L-rRNA chain, or lies off-centre, the molecular weight of the S-rRNA equals that of either both, or only one, of the two fragments composing the L-rRNA.
The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications
1997
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 occurrence of divergent paralogues and recombinant.2 in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low-and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and ~.
Journal of Molecular Biology, 1969
Polyacrylamide gel electrophoresis was used to analyse the rapidly labelled RNA in Xenopus Levis cultured kidney cells. The ribosomal precursor was identified by its base composition and found to have a molecular weight of 2.5 to 2.6 x 106. This is O-3 to 0.4 x lo6 greater than the sum of the weights of the ribosomal RNA. This excess of non-ribosomal RNA has a high content of G+C and is assumed to be lost during processing. The precursor in plant tissues was shown to be similar to that in Xenqnus. A relatively long-lived intermediate in the processing was found in Xenopus and plants, which had a molecular weight of 0.1 x lo6 greater than the heavy ribosomal RNA; it was assumed to be a precursor to the latter. These amounts of excess non-ribosomal RNA are much smaller than in the mammalian 45 and 32 s precursors. It is concluded that the very high molecular weight precursors which contain about 40% of excess RNA are peculiar to the mammals. The results are correlated with other work on the ribosomal DNA and on the structures of the nucleolar core.
Ribosomal RNA genes and hominoid phylogeny
Molecular Biology and Evolution
Sequences totaling 3,500 bases from the 28s rRNA gene and from one of the ribosomal internal transcribed spacers (ITSl) have been determined for human, chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus). Analyses of the rRNA alignments show (1) a clustering of substitutions in the "variable regions" of the 28s gene, (2) a 1.5-3-fold increase in divergence in the transcribed spacer over that in the exon, and (3) that human and chimpanzee are the most closely related pair, in agreement with the results of Miyamoto et al., Sibley and Ahlquist, and Caccone and Powell.
Rates and patterns of base change in the small subunit ribosomal RNA gene
Genetics, 1993
The small subunit ribosomal RNA gene (srDNA) has been used extensively for phylogenetic analyses. One common assumption in these analyses is that substitution rates are biased toward transitions. We have developed a simple method for estimating relative rates of base change that does not assume rate constancy and takes into account base composition biases in different structures and taxa. We have applied this method to srDNA sequences from taxa with a noncontroversial phylogeny to measure relative rates of evolution in various structural regions of srRNA and relative rates of the different transitions and transversions. We find that: (1) the long single-stranded regions of the RNA molecule evolve slowest, (2) biases in base composition associated with structure and phylogenetic position exist, and (3) the srDNAs studied lack a consistent transition/transversion bias. We have made suggestions based on these findings for refinement of phylogenetic analyses using srDNA data.