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

Resolving ubiquitous model congruence in phylogenetics and its application for studying macroevolution

View ORCID ProfileSergei Tarasov, View ORCID ProfileJosef Uyeda
doi: https://doi.org/10.1101/2022.07.04.498736
Sergei Tarasov
1Finnish Museum of Natural History, Pohjoinen Raubtatiekatu 13, FI-00014 Helsinki, Finland
2National Institute for Mathematical and Biological Synthesis (NIMBioS), TN, USA
3Department of Biological Sciences, Virginia Tech 4076 Derring Hall 926 West Campus Drive Blacksburg, VA 24 061, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sergei Tarasov
  • For correspondence: sergei.tarasov@helsinki.fi
Josef Uyeda
3Department of Biological Sciences, Virginia Tech 4076 Derring Hall 926 West Campus Drive Blacksburg, VA 24 061, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Josef Uyeda
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

This paper investigates model congruence (= asymptotic unidentifiability) in phylogenetics for continuous-time Markov chains (CTMCs) that include models for DNA, protein, discrete trait evolution, and state-dependent diversification. Without exception, all CTMCs have infinite classes of congruent models. Congruent models vary in the number of parameters from one to infinity and may have drastically different evolutionary dynamics, and standard model selection criteria are not applicable to them. We classify the structure of a congruence class and show how the “best” model can be selected based on mathematical and biological reasoning. Thus, congruent models in CTMCs do not suffer from the model selection problem previously identified for the time-dependent diversification process. Moreover, we demonstrate that congruence may serve to explain some evolutionary phenomena, specifically linking macro-and microevolution. We also discuss other types of congruence that may occur in phylogenetics and ways to handle them.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/sergeitarasov/Congruent_CTMCs

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 July 05, 2022.
Download PDF
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.
Resolving ubiquitous model congruence in phylogenetics and its application for studying macroevolution
(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
Resolving ubiquitous model congruence in phylogenetics and its application for studying macroevolution
Sergei Tarasov, Josef Uyeda
bioRxiv 2022.07.04.498736; doi: https://doi.org/10.1101/2022.07.04.498736
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Resolving ubiquitous model congruence in phylogenetics and its application for studying macroevolution
Sergei Tarasov, Josef Uyeda
bioRxiv 2022.07.04.498736; doi: https://doi.org/10.1101/2022.07.04.498736

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 Areas
All Articles
  • Animal Behavior and Cognition (3688)
  • Biochemistry (7783)
  • Bioengineering (5673)
  • Bioinformatics (21267)
  • Biophysics (10574)
  • Cancer Biology (8170)
  • Cell Biology (11929)
  • Clinical Trials (138)
  • Developmental Biology (6757)
  • Ecology (10394)
  • Epidemiology (2065)
  • Evolutionary Biology (13853)
  • Genetics (9702)
  • Genomics (13063)
  • Immunology (8136)
  • Microbiology (19976)
  • Molecular Biology (7841)
  • Neuroscience (43032)
  • Paleontology (318)
  • Pathology (1278)
  • Pharmacology and Toxicology (2258)
  • Physiology (3350)
  • Plant Biology (7221)
  • Scientific Communication and Education (1311)
  • Synthetic Biology (2000)
  • Systems Biology (5533)
  • Zoology (1127)