Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis

View ORCID ProfileAndrew F. Magee, Sarah K. Hilton, William S. DeWitt
doi: https://doi.org/10.1101/2020.11.17.387365
Andrew F. Magee
1Department of Biology, University of Washington, Seattle, USA
3Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Andrew F. Magee
  • For correspondence: andyfmagee@gmail.com
Sarah K. Hilton
2Department of Genome Sciences, University of Washington, Seattle, USA
3Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
William S. DeWitt
2Department of Genome Sciences, University of Washington, Seattle, USA
3Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

Likelihood-based phylogenetic inference posits a probabilistic model of character state change along branches of a phylogenetic tree. These models typically assume statistical independence of sites in the sequence alignment. This is a restrictive assumption that facilitates computational tractability, but ignores how epistasis, the effect of genetic background on mutational effects, influences the evolution of functional sequences. We consider the effect of using a misspecified site-independent model on the accuracy of Bayesian phylogenetic inference in the setting of pairwise-site epistasis. Previous work has shown that as alignment length increases, tree reconstruction accuracy also increases. Here, we present a simulation study demonstrating that accuracy increases with alignment size even if the additional sites are epistatically coupled. We introduce an alignment-based test statistic that is a diagnostic for pair-wise epistasis and can be used in posterior predictive checks.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/WSDeWitt/phyload/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted November 17, 2020.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis
Andrew F. Magee, Sarah K. Hilton, William S. DeWitt
bioRxiv 2020.11.17.387365; doi: https://doi.org/10.1101/2020.11.17.387365
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis
Andrew F. Magee, Sarah K. Hilton, William S. DeWitt
bioRxiv 2020.11.17.387365; doi: https://doi.org/10.1101/2020.11.17.387365

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (2533)
  • Biochemistry (4977)
  • Bioengineering (3486)
  • Bioinformatics (15232)
  • Biophysics (6910)
  • Cancer Biology (5395)
  • Cell Biology (7753)
  • Clinical Trials (138)
  • Developmental Biology (4539)
  • Ecology (7159)
  • Epidemiology (2059)
  • Evolutionary Biology (10234)
  • Genetics (7517)
  • Genomics (9794)
  • Immunology (4863)
  • Microbiology (13234)
  • Molecular Biology (5144)
  • Neuroscience (29465)
  • Paleontology (203)
  • Pathology (838)
  • Pharmacology and Toxicology (1466)
  • Physiology (2142)
  • Plant Biology (4756)
  • Scientific Communication and Education (1013)
  • Synthetic Biology (1338)
  • Systems Biology (4014)
  • Zoology (768)