Document Type

Article

Publication Date

2019

Published In

Systematic Biology

Keywords

Bayes factor, Bayes factor calibration, Concatenation, Marginal likelihood, Phylogenetic dissonance, Phylogenetics, Phylogenomics

Abstract

With the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes to infer phylogeny of any study system. While sampling a large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the incorporation of accurate marginal likelihood estimation methods into popular Bayesian software programs, it is natural to consider using the Bayes Factor (BF) to compare different partition models in which genes within any given partition subset share both tree topology and edge lengths. We explore using marginal likelihood to assess data subset combinability when data subsets have varying levels of phylogenetic discordance due to deep coalescence events among genes (simulated within a species tree), and compare the results with our recently described phylogenetic informational dissonance index (D) estimated for each data set. BF effectively detects phylogenetic incongruence and provides a way to assess the statistical significance of D values. We use BFs to assess data combinability using an empirical data set comprising 56 plastid genes from the green algal order Volvocales. We also discuss the potential need for calibrating BFs and demonstrate that BFs used in this study are correctly calibrated.

Grant Information

This material is based upon work supported by the National Science Foundation under grant number DEB-1354146 to POL, MHC, LK, and LAL and under grant number DEB-1036448 (GrAToL) to LAL and POL. MHC’s research was also partially supported by NIH grant number GM 70335 and P01 CA142538.

DOI

10.1093/sysbio/syz007

Comments

This is a pre-copyedited, author-produced version of an article accepted for publication in Systematic Biology following peer review. The version of record is available online at https://doi.org/10.1093/sysbio/syz007.

Rights

© The Author(s) 2019. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com

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