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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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.
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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.
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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
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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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TLDR
Sequence variation in the middle part of the small-subunit rRNA was studied for representatives of the major groups in the family Cicindelidae, finding a much expanded segment in variable region V4 that was not found in other groups of beetles and leaves open the possibility that this expansion segment can be used for phylogeny reconstruction within subgroups.
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TLDR
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TLDR
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