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A Practical Guide to Phylogenetics for Nonexperts
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Defining phylogenetic networks using ancestral profiles.

Allan Bai1, Péter L Erdős2, Charles Semple1

  • 1School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand.

Mathematical Biosciences
|January 16, 2021
PubMed
Summary
This summary is machine-generated.

Phylogenetic networks, which model reticulate evolution, are not always uniquely determined by their ancestral profiles. This study shows that

Keywords:
Accumulation phylogeniesAncestral profilesOrchard networksPath-tuplesTree-child networks

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Area of Science:

  • Evolutionary Biology
  • Computational Biology
  • Phylogenetics

Background:

  • Phylogenetic trees are limited in representing reticulate evolution.
  • Rooted phylogenetic networks offer a more complete ancestral relationship model.
  • Ancestral profiles (path counts) are used for network reconstruction.

Purpose of the Study:

  • To investigate the uniqueness of orchard networks based on ancestral profiles.
  • To identify necessary conditions for unique phylogenetic network reconstruction.
  • To explore uniqueness under relaxed conditions for orchard networks.

Main Methods:

  • Analysis of ancestral profiles in rooted phylogenetic networks.
  • Mathematical investigation of 'orchard networks' and 'stack-free' properties.
  • Comparison of uniqueness claims with and without the stack-free restriction.

Main Results:

  • The 'stack-free' property is necessary for the unique determination of orchard networks by ancestral profiles.
  • Orchard networks are unique up to high in-degree vertex resolution when the stack-free restriction is lifted.
  • The ancestral profile alone does not generally guarantee a unique phylogenetic network.

Conclusions:

  • The stack-free condition is crucial for unique reconstruction of orchard networks.
  • Relaxing the stack-free condition leads to a different form of uniqueness in orchard networks.
  • Understanding network structure is key to accurate evolutionary history reconstruction.