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Estimating phylogenetic trees for rapid radiations is challenging. Using a single-taxon outgroup often leads to incorrect rooting, while no outgroup provided the most accurate ingroup recovery in simulations.

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Area of Science:

  • Evolutionary biology
  • Computational phylogenetics

Background:

  • Rapid radiations, characterized by short internal and long external branches, pose challenges for phylogenetic tree estimation.
  • Accurate phylogenetic tree rooting is crucial for understanding evolutionary relationships.

Purpose of the Study:

  • To evaluate the performance of various phylogenetic methods in estimating trees for rapid radiations.
  • To assess the impact of different outgroup strategies on phylogenetic tree accuracy.

Main Methods:

  • Simulation study using diverse phylogenetic methods including maximum likelihood, neighbor-joining, and parsimony.
  • Testing different outgroup sizes (single-taxon vs. two-taxon) and no outgroup rooting strategies.
  • Analysis of tree topology biases and rooting accuracy with varying sequence lengths.

Main Results:

  • Maximum likelihood, neighbor-joining, and parsimony methods showed biases towards specific tree topologies.
  • Single-taxon outgroups frequently resulted in incorrect ingroup phylogenies.
  • Uncorrected parsimony with single-taxon outgroups selected incorrect trees more often than the correct tree, even with long sequences.
  • Two-taxon outgroups improved accuracy over single-taxon outgroups, but no outgroup yielded the most accurate ingroup recovery.

Conclusions:

  • Phylogenetic methods can exhibit topological biases when modeling rapid radiations.
  • Outgroup selection significantly impacts phylogenetic tree accuracy, with single-taxon outgroups being particularly problematic.
  • For rapid radiations, omitting an outgroup may be the most reliable strategy for accurate ingroup phylogeny reconstruction.