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A Practical Guide to Phylogenetics for Nonexperts
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Maximum likelihood inference of reticulate evolutionary histories.

Yun Yu1, Jianrong Dong2, Kevin J Liu3

  • 1Departments of Computer Science and nakhleh@cs.rice.edu yy9@cs.rice.edu.

Proceedings of the National Academy of Sciences of the United States of America
|November 5, 2014
PubMed
Summary

This study introduces a new method to reconstruct complex evolutionary histories involving hybridization and incomplete lineage sorting. The approach accurately estimates reticulate evolutionary relationships, advancing phylogenetic network analysis.

Keywords:
incomplete lineage sortingmaximum likelihoodphylogenetic networksreticulate evolution

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Phylogenetics

Background:

  • Hybridization is a significant driver of evolution, adaptation, and genome diversification in many species.
  • Reconstructing reticulate evolutionary histories, which involve hybridization, remains a challenge due to limitations in current methods.

Purpose of the Study:

  • To develop a novel maximum likelihood method for inferring reticulate evolutionary histories.
  • To simultaneously account for incomplete lineage sorting in evolutionary history reconstruction.
  • To provide methods for assessing confidence in inferred reticulate evolutionary histories and their topologies.

Main Methods:

  • A maximum likelihood approach was developed to infer evolutionary histories with reticulation.
  • The method incorporates incomplete lineage sorting.
  • Confidence assessment for reticulation amount and topology was integrated.

Main Results:

  • The proposed method accurately estimates reticulate evolutionary histories on simulated datasets.
  • The method supported a hypothesis of reticulate evolutionary history in house mouse (Mus musculus) genomes.
  • The findings demonstrate the method's efficacy in real-world genomic data.

Conclusions:

  • The developed method is crucial for inferring reticulate evolutionary histories, especially with increasing evidence of hybridization in eukaryotes.
  • This work represents a significant advancement, aiming to establish phylogenetic networks as a standard model alongside phylogenetic trees.
  • The method enhances our ability to understand complex evolutionary relationships shaped by hybridization.