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Ribosomal DNA: molecular evolution and phylogenetic inference.

D M Hillis1, M T Dixon

  • 1Department of Zoology, University of Texas, Austin 78712.

The Quarterly Review of Biology
|December 1, 1991
PubMed
Summary

Ribosomal DNA (rDNA) sequences offer a versatile tool for understanding evolutionary history across all life forms. Analysis of rDNA gene regions provides insights into phylogenetic relationships at various divergence levels.

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Area of Science:

  • Molecular Evolution
  • Phylogenetics
  • Genomics

Background:

  • Ribosomal DNA (rDNA) sequences are widely used for inferring phylogenetic relationships across diverse organisms.
  • The evolutionary rates, copy number, and concerted evolution of rDNA contribute to its utility in systematic studies.
  • Previous studies have demonstrated the power of rDNA sequence comparisons for understanding evolutionary history.

Purpose of the Study:

  • To identify specific regions within nuclear and mitochondrial ribosomal RNA (rRNA) genes suitable for phylogenetic analysis at different evolutionary timescales.
  • To develop primer sequences for amplifying the entire nuclear rDNA array using the polymerase chain reaction (PCR).
  • To assess the utility of rDNA sequences for resolving phylogenetic problems across the entire spectrum of life.

Main Methods:

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  • Alignment and comparison of ribosomal DNA (rDNA) sequences from various organisms.
  • Analysis of nuclear and mitochondrial rRNA gene sequences to identify regions informative for different divergence levels.
  • Design of "universal" primer sequences for PCR amplification of nuclear rDNA arrays, complementing existing mitochondrial primers.

Main Results:

  • Specific regions within small and large subunit nuclear rDNA and organellar rRNA genes are identified as optimal for resolving Precambrian, Paleozoic/Mesozoic, and Cenozoic divergences, respectively.
  • Development of PCR primers enables comprehensive amplification of the nuclear rDNA array.
  • rDNA sequence analysis, despite secondary structure and concerted evolution constraints, remains a powerful tool for phylogenetic inference.

Conclusions:

  • Ribosomal DNA sequences provide a robust and versatile molecular marker for phylogenetic studies across all taxonomic levels.
  • The strategic selection of rDNA regions and the use of PCR-based amplification facilitate detailed evolutionary analyses.
  • This approach offers a framework for addressing systematic questions throughout the tree of life.