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Related Experiment Videos

STRIDE: Species Tree Root Inference from Gene Duplication Events.

David M Emms1, Steven Kelly1

  • 1Department of Plant Sciences, University of Oxford, Oxford, United Kingdom.

Molecular Biology and Evolution
|October 14, 2017
PubMed
Summary

STRIDE is a new method for rooting phylogenetic trees without outgroups. It accurately infers species tree roots using gene duplication events, aiding evolutionary studies.

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Area of Science:

  • Phylogenetics and Evolutionary Biology
  • Genomics and Molecular Evolution

Background:

  • Accurate phylogenetic tree interpretation relies on correct rooting.
  • Traditional rooting methods often depend on outgroup taxa, which can be problematic.
  • Inferring the root of a species tree is crucial for understanding evolutionary history.

Purpose of the Study:

  • To introduce STRIDE, a novel, outgroup-free method for phylogenetic tree rooting.
  • To identify gene duplication events and infer species tree roots in large-scale analyses.
  • To provide a robust tool for evolutionary inference, especially when outgroups are unavailable or ambiguous.

Main Methods:

  • STRIDE identifies well-supported in-group gene duplication events from unrooted gene trees.
  • It analyzes these duplication events to infer a probability distribution for the species tree root.
Keywords:
gene duplicationphylogeneticsphylogenomicstree inference

Related Experiment Videos

  • The method employs a novel probability model to handle ambiguity in root assignment.

    • Main Results:

    • STRIDE successfully identified the correct species tree root in diverse, large-scale molecular phylogenetic datasets.
    • The method accurately represents root assignment ambiguity, particularly with limited data.
    • Application to the origin of eukaryotes provided additional support for existing hypotheses.

    Conclusions:

    • STRIDE offers a fast, effective, and outgroup-free approach for species tree root inference.
    • The method is applicable across various taxonomic groups and evolutionary timescales.
    • STRIDE enhances the reliability of phylogenetic analyses and evolutionary origin studies.