Jove
Visualize
Contact Us

Related Experiment Videos

Combining data sets with different phylogenetic histories.

J J Wiens1

  • 1Section of Amphibians and Reptiles, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania 15213-4080, USA. wiensj@clpgh.org

Systematic Biology
|June 18, 2002
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

Is geographic variation within species related to macroevolutionary patterns between species?

Journal of evolutionary biology·2015
Same author

Ecological radiation with limited morphological diversification in salamanders.

Journal of evolutionary biology·2012
Same author

Crest evolution in newts: implications for reconstruction methods, sexual selection, phenotypic plasticity and the origin of novelties.

Journal of evolutionary biology·2011
Same author

Bridging the gap between community ecology and historical biogeography: niche conservatism and community structure in emydid turtles.

Molecular ecology·2009
Same author

Testing for evolutionary trade-offs in a phylogenetic context: ecological diversification and evolution of locomotor performance in emydid turtles.

Journal of evolutionary biology·2007
Same author

War of the Iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards.

Systematic biology·2002
Same journal

Diversification dynamics in the global radiation of gobies.

Systematic biology·2026
Same journal

Correction to: nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.

Systematic biology·2026
Same journal

Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae).

Systematic biology·2026
Same journal

An evolving view of phylogenetic biogeography.

Systematic biology·2026
Same journal

Modeling Site-and-Branch-Heterogeneity with GFmix.

Systematic biology·2026
Same journal

Coalescent-based branch length estimation improves dating of species trees.

Systematic biology·2026
See all related articles
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

Phylogenetic analysis combining data sets with different evolutionary histories requires careful methods. A new approach partitions data, performs separate analyses, and resolves conflicts to improve species tree accuracy.

Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic analyses often combine multiple data sets.
  • Discrepancies in evolutionary histories between data sets (e.g., gene trees vs. species trees) pose challenges for data combination.
  • Existing methods for handling data heterogeneity have limitations.

Purpose of the Study:

  • To propose and evaluate a new methodology for phylogenetic analysis when data sets have partially conflicting evolutionary histories.
  • To improve the accuracy of species tree reconstruction in the presence of localized historical mismatches.

Main Methods:

  • Partitioning data to detect differing phylogenetic histories.
  • Performing separate phylogenetic analyses on data subsets.

Related Experiment Videos

  • Combining data while flagging strongly contested regions as unresolved until supported by a majority of data sets.
  • Computer simulations to test the proposed methodology.

    • Main Results:

    • Combined analysis can exceed the accuracy of separate analyses when historical mismatches are small and estimates are imperfect.
    • Combined analysis accurately estimates species trees in regions with shared history but poorly estimates in regions with conflicting history.
    • The proposed method offers a nuanced approach to data combination, outperforming global heterogeneity tests and taxon excision in specific scenarios.

    Conclusions:

    • A novel methodology effectively addresses localized conflicts in phylogenetic data, improving species tree estimation.
    • This approach balances the benefits of combined and separate analyses, providing more reliable phylogenetic inferences.
    • The method is robust even with imperfect data and small historical divergences, offering a practical solution for complex phylogenetic problems.