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

Biases in phylogenetic estimation can be caused by random sequence segments.

Edward Susko1, Mathew Spencer, Andrew J Roger

  • 1Genome Atlantic, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5. susko@mathstat.dal.ca

Journal of Molecular Evolution
|July 27, 2005
PubMed
Summary

Random sequences in phylogenetic analysis can cause complex biases, attracting or repelling taxa based on overlap. Researchers should test analyses with and without potentially problematic sequences to ensure accurate branching patterns.

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

GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics.

bioRxiv : the preprint server for biology·2026
Same author

Modeling Site-and-Branch-Heterogeneity with GFmix.

Systematic biology·2026
Same author

IQ-TREE 3: phylogenomic inference software using complex evolutionary models.

Molecular biology and evolution·2026
Same author

Comparing partition and mixture models with akaike information criteria.

Systematic biology·2026
Same author

The LECA had a conventional kinetochore and the kinetoplastid kinetochore is a derived feature - a critical evaluation of Akiyoshi, 2025.

Journal of cell science·2026
Same author

Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes.

Current biology : CB·2025

Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Fully or partially random sequences can arise from sequence misalignment or rapid site evolution, particularly in deep divergence analyses.
  • Such random sequences can occur in subsets of taxa or specific sites within alignments.
  • These phenomena complicate the accurate estimation of evolutionary relationships.

Purpose of the Study:

  • To investigate the impact of fully or partially random sequences on the estimation of four-taxon phylogenies.
  • To understand how random sequences influence phylogenetic inference and introduce biases.
  • To identify conditions under which random sequences lead to attraction or repulsion biases.

Main Methods:

  • Simulations were used to model the effects of random sequences on phylogenetic tree estimation.

Related Experiment Videos

  • Analysis focused on scenarios with varying proportions and overlap of random sites/sequences.
  • The study examined the relationship between random sequences and branch lengths, specifically long-branch attraction and repulsion.

    • Main Results:

    • A single random sequence added to a three-taxon alignment tends to group with the longest branch.
    • Approximately 50% of random sites can induce a long-branch repulsion bias, while a minority can cause long-branch attraction.
    • When multiple sequences are partially random, biases depend on the overlap of random sites, leading to attraction or repulsion that persists with increasing sequence length.

    Conclusions:

    • Random sequences and sites introduce complex, non-intuitive biases into phylogenetic inference.
    • The degree of randomness and overlap significantly influences attraction and repulsion phenomena.
    • It is recommended to perform phylogenetic analyses with and without potentially saturated or misaligned sites to validate inferred branching patterns.