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Multipronged Phenotyping Approaches to Characterize Sugarcane Root Systems
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An empirical test of the midpoint rooting method.

Pablo N Hess1, Claudia A DE Moraes Russo1

  • 1Laboratório de Biodiversidade Molecular, Departamento de Genética, Instituto de Biologia, CCS, Bloco A, Av Pau Brasil 211, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, RJ 21941-S70, Brazil.

Biological Journal of the Linnean Society. Linnean Society of London
|April 15, 2020
PubMed
Summary

Midpoint rooting (MPR) offers a valuable alternative for rooting phylogenetic trees when a suitable outgroup is unavailable. This study demonstrates MPR

Keywords:
molecular clockoutgroup rootingoutgroupsphylogenetic treessystematicsunrooted trees

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Area of Science:

  • Phylogenetics
  • Evolutionary Biology
  • Computational Biology

Background:

  • Phylogenetic tree rooting is crucial for evolutionary inference.
  • The outgroup method is standard but relies on identifying appropriate outgroup taxa.
  • Midpoint rooting (MPR) is an alternative but its accuracy is not well-established.

Purpose of the Study:

  • To empirically evaluate the success rate of midpoint rooting (MPR) in accurately placing the root of phylogenetic trees.
  • To compare MPR's performance against the established outgroup method.

Main Methods:

  • Tested MPR on 50 datasets from 33 published papers by removing original outgroups.
  • Rooted trees using MPR and compared the resulting root position to the original outgroup-derived root.
  • Categorized datasets based on outgroup composition and consistency.

Main Results:

  • MPR achieved a 54% success rate with single outgroup taxa.
  • Success rates increased to 82% with inconsistent multiple outgroups and 94% with consistent multiple outgroups.
  • MPR's success correlates positively with the consistency of the outgroup root.

Conclusions:

  • Midpoint rooting (MPR) is a reliable method for rooting phylogenetic trees, especially when outgroups are problematic.
  • The accuracy of MPR is enhanced when the underlying phylogenetic signal supports a consistent root.
  • MPR provides a valuable tool for phylogenetic analysis in diverse evolutionary scenarios.