Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Estimating the reliability of evolutionary trees.

D Penny1, M Hendy

  • 1Department of Botany and Zoology, Massey University, Palmerston North, New Zealand.

Molecular Biology and Evolution
|September 1, 1986
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

IsProchlorothrix hollandica the best choice as a prokaryotic model for higher plant Chla/b photosynthesis?

Photosynthesis research·2013
Same author

Progress with methods for constructing evolutionary trees.

Trends in ecology & evolution·2011
Same author

Recovering evolutionary trees under a more realistic model of sequence evolution.

Molecular biology and evolution·2009
Same author

Genomics and the irreducible nature of eukaryote cells.

Science (New York, N.Y.)·2006
Same author

The MinMax Squeeze: guaranteeing a minimal tree for population data.

Molecular biology and evolution·2004
Same author

Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study.

Systematic biology·2003
Same journal

Population Epigenetics: Deciphering DNA Methylation Diversity and its Implications for Health, Disease, and Evolution.

Molecular biology and evolution·2026
Same journal

Genomic signature of repeated transitions to diurnality in spiders.

Molecular biology and evolution·2026
Same journal

Phylogenomic blind spots: The limits of UCE and BUSCO loci in the presence of gene flow.

Molecular biology and evolution·2026
Same journal

seqLens: Optimizing Language Models for Genomic Predictions.

Molecular biology and evolution·2026
Same journal

The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts.

Molecular biology and evolution·2026
Same journal

800 million years of co-evolution in the green plant lineage - the case of LEUNIG and SEUSS transcriptional co-regulators.

Molecular biology and evolution·2026
See all related articles

This study introduces a method to assess the reliability of evolutionary phylogenetic trees using real protein sequence data. It demonstrates that weighting slowly changing nucleotide positions improves tree accuracy and estimates reliability for evolutionary relationships.

Area of Science:

  • Molecular Evolution
  • Bioinformatics
  • Phylogenetics

Background:

  • Phylogenetic trees are crucial for understanding evolutionary relationships.
  • Assessing the reliability of trees derived from real biological data is challenging.
  • Previous methods often relied on simulated data, limiting real-world applicability.

Purpose of the Study:

  • To estimate the accuracy and reliability of phylogenetic trees using authentic mammalian protein sequence data.
  • To develop a method for quantifying the reliability of inferred evolutionary trees.
  • To determine the minimum data required for a reliable phylogenetic reconstruction.

Main Methods:

  • Utilized six protein sequences from 11 mammalian taxa.
  • Employed a tree comparison metric to evaluate tree similarity with increasing nucleotide data subsets.

Related Experiment Videos

  • Calculated the ratio of observed to expected incompatibilities at each nucleotide position to predict evolutionary changes.
  • Applied differential weighting to nucleotide positions based on their evolutionary rate.

    • Main Results:

    • The ratio of observed to expected incompatibilities effectively predicts changes needed for the most-parsimonious tree.
    • Weighting slowly evolving positions enhances the convergence of minimal length trees towards the true evolutionary tree.
    • A reasonable estimate of final tree reliability can be achieved, especially with combined sequence data.
    • The rodent-primate-lagomorph trichotomy and the position of the dog were identified as less certain aspects of the inferred tree.

    Conclusions:

    • It is feasible to estimate the reliability of phylogenetic trees constructed from real sequence data.
    • Weighting nucleotide positions by evolutionary rate improves tree accuracy and reliability.
    • Publishing evolutionary trees without an assessment of their reliability is not scientifically rigorous.