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Updated: Sep 27, 2025
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The ITS2 Database
Published on: March 12, 2012
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Compensatory Base Changes and Varying Phylogenetic Effects on Angiosperm ITS2 Genetic Distances
Ruixin Cao1, Shuyan Tong1, Tianjing Luan1
1Marine College, Shandong University, 180 Wenhua Xilu, Weihai 264209, China.
Plants (Basel, Switzerland)
|April 12, 2022
Summary
Compensatory base changes (CBCs) in ribosomal internal transcribed spacer 2 (ITS2) can inflate genetic distance estimates. This study provides a threshold for accounting for CBCs, improving phylogenetic accuracy for angiosperm lineages.
Area of Science:
- Molecular Biology
- Phylogenetics
- Bioinformatics
Background:
- Ribosomal internal transcribed spacer 2 (ITS2) is a popular genetic marker for phylogenetic analysis.
- Compensatory base changes (CBCs) coevolving in ITS2 secondary structures can distort genetic distance estimations.
- The precise impact of CBCs on ITS2 genetic distances remains unclear.
Purpose of the Study:
- To investigate the effect of CBCs on ITS2 genetic distance estimation in angiosperms.
- To develop criteria for assessing the applicability of phylogenetic analyses in the presence of CBCs.
- To provide an empirical threshold for considering CBCs before ITS2 phylogenetic analyses.
Main Methods:
- Screening of ITS2 sequences from 5677 angiosperm genera.
- Phylogenetic analysis incorporating secondary structure prediction and structure-based alignment.
- Comparative estimation of ITS2 genetic distances using DNA and RNA substitution models.
- Partitioning of ITS2 sequences into paired (stems) and unpaired (loops) regions.
Main Results:
- CBCs were found to inflate ITS2 genetic distances, with deviations potentially reaching 180% when substitution rates in stems are high.
- The impact of CBCs on genetic distance was minor when the substitution rate ratio between stems and loops was below two.
- Conventional DNA models remain applicable for recent lineages with minimal CBC occurrence.
Conclusions:
- CBCs significantly influence ITS2 genetic distance estimations, posing challenges for phylogenetic reconstructions.
- An empirical threshold for CBCs is proposed to guide the appropriate use of ITS2 in phylogenetic studies.
- Understanding CBC effects is crucial for accurate phylogenetic analyses using the ITS2 marker.
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