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Assessing Combinability of Phylogenomic Data Using Bayes Factors.

Suman Neupane1,2, Karolina Fučíková3, Louise A Lewis2

  • 1Department of Biological Sciences, Virginia Tech University, 4076 Derring Hall, 926 West Campus Drive, Blacksburg, VA 24061, USA.

Systematic Biology
|February 7, 2019
PubMed
Summary

Bayes Factors (BF) can now assess phylogenetic incongruence in large genomic datasets. This method effectively evaluates data subset combinability, improving phylogenetic resolution and uncovering evolutionary relationships.

Keywords:
Bayes factorBayes factor calibrationconcatenationmarginal likelihoodphylogenetic dissonancephylogeneticsphylogenomics

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Area of Science:

  • Genomics
  • Phylogenetics
  • Evolutionary Biology

Background:

  • High-throughput sequencing enables using hundreds of genes for phylogenetic inference.
  • Conflicting evolutionary histories among genes pose challenges for accurate phylogenetic reconstruction.
  • Bayesian software now incorporates accurate marginal likelihood estimation.

Purpose of the Study:

  • To explore the use of Bayes Factor (BF) for comparing partition models in phylogenetics.
  • To assess data subset combinability using marginal likelihood when evolutionary histories vary.
  • To compare BF results with the phylogenetic informational dissonance index (D).

Main Methods:

  • Utilized marginal likelihood estimation within Bayesian frameworks.
  • Simulated deep coalescence events to create phylogenetic discordance among genes.
  • Applied Bayes Factor (BF) to assess data combinability and phylogenetic incongruence.
  • Calculated the phylogenetic informational dissonance index (D) for comparison.

Main Results:

  • Bayes Factor (BF) effectively detects phylogenetic incongruence.
  • BF provides a statistically significant assessment of phylogenetic informational dissonance (D) values.
  • BF successfully assessed data combinability in an empirical dataset of 56 plastid genes from Volvocales.
  • Demonstrated that the BFs used in this study are correctly calibrated.

Conclusions:

  • Bayes Factor (BF) is a valuable tool for evaluating phylogenetic incongruence and data subset combinability.
  • Marginal likelihood estimation offers a robust approach to handling conflicting gene histories in phylogenetics.
  • The study validates the use of BF in analyzing complex genomic datasets for evolutionary studies.