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

The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments

I B Jakobsen1, S R Wilson, S Easteal

  • 1Human Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra, Australia. ingrid@jcsmr.anu.edu.au

Molecular Biology and Evolution
|May 1, 1997
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

Clinical impact of CEUS on non-characterizable observations and observations with intermediate probability of malignancy on CT/MRI in patients at risk for HCC.

Abdominal radiology (New York)·2024
Same author

Continuing benefits of the Montreal Protocol and protection of the stratospheric ozone layer for human health and the environment.

Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology·2024
Same author

Changes in tropospheric air quality related to the protection of stratospheric ozone in a changing climate.

Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology·2023
Same author

Environmental effects of stratospheric ozone depletion, UV radiation, and interactions with climate change: UNEP Environmental Effects Assessment Panel, Update 2021.

Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology·2022
Same author

Environmental effects of stratospheric ozone depletion, UV radiation, and interactions with climate change: UNEP Environmental Effects Assessment Panel, Update 2020.

Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology·2021
Same author

Environmental effects of stratospheric ozone depletion, UV radiation and interactions with climate change: UNEP Environmental Effects Assessment Panel, update 2019.

Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology·2020

The partition matrix visually analyzes nucleotide sequence evolution, revealing reticulate patterns. This tool helps identify evolutionary events like gene conversion and recombination in complex sequence regions.

Area of Science:

  • Bioinformatics
  • Molecular Evolution
  • Computational Biology

Background:

  • Comparative analysis of nucleotide sequences is crucial for understanding evolutionary relationships.
  • Reticulate evolution, involving processes like gene conversion and recombination, complicates traditional phylogenetic analyses.
  • Identifying regions with divergent evolutionary histories requires specialized analytical tools.

Purpose of the Study:

  • To introduce and demonstrate the utility of the partition matrix as a graphical tool for analyzing nucleotide sequence evolution.
  • To provide a method for visually assessing changes in evolutionary history along aligned sequences.
  • To aid in the interpretation of reticulate evolution and identify underlying genetic events.

Main Methods:

  • Generation of a partition matrix by assessing the consistency of informative sites with inferred binary partitions.

Related Experiment Videos

  • Maintaining the linear order of sites to visualize changes in support or conflict with partitions.
  • Proposing suitable ordering schemes for partitions to enhance visual interpretation.

    • Main Results:

    • The partition matrix effectively visualizes the distribution of sites supporting or conflicting with phylogenetic partitions.
    • Demonstrated application in interpreting the evolution of the pseudoautosomal boundary region in primates.
    • The method allows for the identification of regional differences in evolutionary history.

    Conclusions:

    • The partition matrix is a valuable exploratory tool for comparative nucleotide sequence analysis, especially for regions with reticulate evolution.
    • It helps avoid misinterpreting complex evolutionary histories as single phylogenies.
    • Facilitates the identification of gene conversion and recombination events, forming a basis for further formal analysis.