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Related Experiment Videos

Sample size for a phylogenetic inference.

G A Churchill1, A von Haeseler, W C Navidi

  • 1Department of Plant Breeding and Biometry, Cornell University, Ithaca, New York 14853.

Molecular Biology and Evolution
|July 1, 1992
PubMed
Summary
This summary is machine-generated.

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Calculating sample size for phylogenetic trees requires careful consideration of sequence data. This study found insufficient sequence data to resolve the evolutionary relationships among two archaebacteria, one eubacteria, and one eukaryote.

Area of Science:

  • Phylogenetics
  • Computational Biology
  • Molecular Evolution

Background:

  • Phylogenetic inference aims to reconstruct evolutionary relationships.
  • Accurate sample size calculations are crucial for reliable phylogenetic analysis.
  • Unrooted phylogenetic trees with four species present unique statistical challenges.

Purpose of the Study:

  • To describe sample-size calculations for inferring a nonzero central branch length in a four-species phylogeny.
  • To evaluate the impact of invariable sites on sample size requirements.
  • To assess the sufficiency of small-subunit ribosomal RNA (rRNA) sequences for resolving specific evolutionary relationships.

Main Methods:

  • Development of a statistical test using a multinomial model for character-state configurations.

Related Experiment Videos

  • Application of methods to independent binary characters from aligned nucleic acid sequences.
  • Quantification of the effect of invariable sites on sample size calculations.

    • Main Results:

    • A statistical test for inferring central branch length in a four-species phylogeny was described.
    • The inclusion of invariable sites was shown to be important and their effect on sample size was quantified.
    • Analysis of small-subunit rRNA sequences from two archaebacteria, a eubacteria, and a eukaryote indicated insufficient data for resolving the tree's branching order.

    Conclusions:

    • The provided small-subunit rRNA sequence alignment lacks sufficient information to resolve the branching order of the depicted four-species phylogeny.
    • Estimates for the number of aligned nucleotide positions needed for a powerful phylogenetic test were provided.
    • Sample size calculations are essential for robust phylogenetic inference, especially when dealing with limited sequence data.