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A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

New substitution models for rooting phylogenetic trees.

Tom A Williams¹, Sarah E Heaps², Svetlana Cherlin²

¹Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK tom.williams2@ncl.ac.uk.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences

|September 2, 2015

Summary

This summary is machine-generated.

New phylogenetic models can infer the root position of evolutionary trees without an outgroup. These models place the root of life within bacteria, not eukaryotes or archaea, advancing evolutionary biology.

Keywords:

phylogenetics substitution models tree of life

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Area of Science:

Evolutionary biology
Phylogenetics
Computational biology

Background:

Phylogenetic tree rooting is crucial for biological interpretation but standard models lack root position information.
Outgroup rooting is a common method, but can be challenging or unavailable.

Purpose of the Study:

To introduce and evaluate novel phylogenetic models for root inference.
To apply these models to fundamental questions in evolutionary biology, including the tree of life and archaeal radiation.

Main Methods:

Description of two new models relaxing stationarity and reversibility assumptions.
Comparison of model performance on a classic phylogenetic test case.
Application of models to analyze alignments for the tree of life and archaeal radiation.

Main Results:

The new models successfully inferred root positions without outgroups.
Analyses excluded eukaryotes and Archaea as the root of the tree of life, suggesting a bacterial origin.
Root of the archaeal radiation was excluded from several major clades, aligning with other methods.

Conclusions:

Non-reversible and non-stationary models are effective tools for rooting phylogenetic trees.
These models provide valuable insights into deep evolutionary history and complement existing methods.
Further research can build upon these models to refine our understanding of evolutionary relationships.