How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction.

@article{Hancock2000HowSS,
  title={How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction.},
  author={John M. Hancock and A P Vogler},
  journal={Molecular phylogenetics and evolution},
  year={2000},
  volume={14 3},
  pages={
          366-74
        }
}
We analyzed the type and frequency of mutational changes in hypervariable rRNA regions, using the highly length-variable region V4 of the small subunit rRNA locus of tiger beetles (Cicindelidae) as an example. Phylogenetic analysis of indels in closely related species showed that (1) most indels are single nucleotides (usually A or T and sometimes G) or di-nucleotides of A and T. These occur at numerous foci, and they exhibit a strong bias for duplication of 5' single and di-nucleotide motifs… 
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Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium.
A secondary structural model of the 28S rRNA expansion segments D2 and D3 for Chalcidoid wasps (Hymenoptera: Chalcidoidea).
TLDR
An annotated secondary structural model for the D2, D3 expansion segments of the 28S ribosomal (rRNA)-encoding gene region will prove useful in assigning positional nucleotide homology for phylogeny reconstruction in these and closely related apocritan taxa.
Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA.
TLDR
Two-dimensional and three-dimensional variability maps of the rRNAs showed that the substitution rates are generally low near the centre of the ribosome, where the nucleotides essential for its function are situated, and that they increase towards the surface.
The cyanobacterial tRNA(Leu) (UAA) intron: evolutionary patterns in a genetic marker.
TLDR
It is proposed that both slipped strand mispairing during replication and homologous recombination among different loci in the genome are important processes causing variation between introns.
Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes.
TLDR
Mapping of indels onto known protein structures demonstrated that structural cores are markedly less tolerant to indels than are loop regions, and both insertions and deletions are more common in higher G+C content sequences.
Molecular evolution of the trnLUAA intron in bryophytes
Evolution of transcript structure and base composition of rDNA expansion segment D3 in ticks
TLDR
The distribution of sequence differences, biased substitution, and conservation of transcript conformation in D3 suggest selective constraint.
UNUSUALLY LONG HYPTIOTES (ARANEAE, ULOBORIDAE) SEQUENCE FOR SMALL SUBUNIT (18S) RIBOSOMAL RNA SUPPORTS SECONDARY STRUCTURE MODEL UTILITY IN SPIDERS
TLDR
Thermodynamic modeling of the H. gertschi inserts suggests they are largely self-complementary, extending the stem portions of the variable regions of the eukaryotic 18S genes.
Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes
TLDR
A tree alignment based approach is introduced that is suitable for working with multiple genomes and that emphasizes the concept of indel history, and is able to refute a previous claim that indel rates are approximately fixed even when the mutation rate changes, and allows us to show that indels events are not neutral.
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References

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TLDR
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TLDR
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TLDR
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