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

Evaluating intraspecific "network" construction methods using simulated sequence data: do existing algorithms

Insa Cassens1, Patrick Mardulyn, Michel C Milinkovitch

  • 1Laboratory of Evolutionary Genetics, Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, rue Jeener et Brachet 12, 6041 Gosselies, Belgium.

Systematic Biology
|July 14, 2005
PubMed
Summary

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

Chemotactic self-organization captures the dynamics of mammalian hair follicle patterning.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Stereotypical force patterns of the elephant trunk in planar reaching movements.

iScience·2026
Same author

Chemical and mechanical patterning of tortoise skin scales occur in different regions of the head.

iScience·2025
Same author

Exacerbated sonic hedgehog signalling promotes a transition from chemical pre-patterning of chicken reticulate scales to mechanical skin folding.

Open biology·2025
Same author

Regulatory and disruptive variants in the CLCN2 gene are associated with modified skin color pattern phenotypes in the corn snake.

Genome biology·2025
Same author

In vivo sonic hedgehog pathway antagonism temporarily results in ancestral proto-feather-like structures in the chicken.

PLoS biology·2025

Maximum parsimony (MP) methods can construct reticulated graphs for visualizing haplotype genealogies. A new algorithm unites equally most parsimonious trees, outperforming other network methods, especially when internal nodes are unsampled.

Area of Science:

  • Population genetics
  • Phylogenetics
  • Bioinformatics

Background:

  • Reticulated graphs visualize alternative genealogical pathways among haplotypes.
  • Maximum parsimony (MP) is often overlooked for network construction due to limitations in merging resulting trees into consensus trees.

Purpose of the Study:

  • To develop a new algorithm for uniting equally most parsimonious trees into a single reticulated graph.
  • To compare the performance of this MP-based graph construction method against purely algorithmic network approaches.

Main Methods:

  • The study proposes a novel algorithm to search tree space using the MP criterion.
  • The algorithm unites all equally most parsimonious trees into a single, possibly reticulated, graph.
  • Performance was evaluated using simulated sequence data against minimum-spanning networks, statistical parsimony, and median-joining networks.

Related Experiment Videos

Main Results:

  • The proposed MP-based graph construction method provides a good estimate of the true genealogy.
  • When internal node haplotypes are not sampled, both median-joining and MP methods yield the best genealogical estimates.
  • The minimum-spanning network algorithm demonstrated poor performance in estimating true genealogies.

Conclusions:

  • Combining equally most parsimonious trees into a single graph is a viable and effective method for inferring haplotype genealogies.
  • The MP approach, particularly when internal nodes are unsampled, offers a robust alternative to purely algorithmic network construction methods.