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Related Experiment Videos

Rooting phylogenetic trees with distant outgroups: a case study from the commelinoid monocots.

Sean W Graham1, Richard G Olmstead, Spencer C H Barrett

  • 1Department of Biological Sciences, University of Alberta, Edmonton, Canada. swgraham@ualberta.ca

Molecular Biology and Evolution
|September 25, 2002
PubMed
Summary

Phylogenetic rooting experiments reveal that chloroplast genes from closely related species retain signals for determining the root position of the pickerelweed family (Pontederiaceae). Real outgroups provide more reliable rooting information than random sequences.

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Area of Science:

  • Phylogenetics
  • Molecular Evolution
  • Plant Systematics

Background:

  • Determining the root of a phylogenetic tree is crucial for understanding evolutionary relationships.
  • Chloroplast genes are widely used in plant phylogenetics due to their conserved nature and presence in multiple copies.
  • The pickerelweed family (Pontederiaceae) is a group of flowering plants with complex evolutionary histories.

Purpose of the Study:

  • To investigate the reliability of phylogenetic rooting using chloroplast genes from closely related taxa.
  • To compare the rooting signal of real outgroup sequences with that of artificial, completely divergent sequences.
  • To assess the factors influencing rooting discriminatory power, such as branch length and outgroup relatedness.

Main Methods:

  • Phylogenetic rooting experiments were conducted using two chloroplast genes from commelinoid monocot taxa.

Related Experiment Videos

  • Real outgroup sequences were compared with artificial sequences designed to have lost all phylogenetic signal.
  • Rooting preferences and penalties for suboptimal roots were analyzed using parsimony and likelihood-based methods.

    • Main Results:

    • Chloroplast genes from close relatives of Pontederiaceae retain measurable rooting signals.
    • Artificial outgroups preferentially root on long terminal branches, unlike real outgroups.
    • Real outgroups require a greater rooting penalty for suboptimal roots, indicating nonrandom signal, but discrimination among optimal roots is limited.
    • Likelihood-based tests reject equally good rootings and eliminate half of the least optimal candidates.
    • Adding genes or outgroups, especially closely related ones, improves rooting discriminatory power.

    Conclusions:

    • Phylogenetic signal for rooting is retained in chloroplast genes of closely related taxa.
    • Real outgroups provide more reliable rooting information than random sequences, though discrimination among optimal roots can be challenging.
    • Rooting discriminatory power is enhanced by using more closely related outgroups and additional genes.