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

Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot

View ORCID ProfileJuan Antonio Balbuena, View ORCID ProfileÓscar Alejandro Pérez-Escobar, View ORCID ProfileCristina Llopis-Belenguer, View ORCID ProfileIsabel Blasco-Costa
doi: https://doi.org/10.1101/481846
Juan Antonio Balbuena
1Ecology and Evolution of Symbionts Lab, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Official P.O. Box 22085, 46071 Valencia, Spain. E-mail:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Juan Antonio Balbuena
  • For correspondence: j.a.balbuena@uv.es j.a.balbuena@uv.es
Óscar Alejandro Pérez-Escobar
2Identification and Naming Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, U.K
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Óscar Alejandro Pérez-Escobar
Cristina Llopis-Belenguer
1Ecology and Evolution of Symbionts Lab, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Official P.O. Box 22085, 46071 Valencia, Spain. E-mail:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Cristina Llopis-Belenguer
  • For correspondence: j.a.balbuena@uv.es
Isabel Blasco-Costa
3Department of Invertebrates, Natural History Museum of Geneva, P.O. Box 6134, CH-1211 Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Isabel Blasco-Costa
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

Symbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals and nodes that maximize phylogenetic congruence. By means of simulations, we show that the output value produced is inversely proportional to the number and proportion of cospeciation events employed to build simulated tanglegrams. In addition, with time-calibrated trees, Random TaPas is also efficient at distinguishing cospeciation from pseudocospeciation. Random TaPas can handle large tanglegrams in affordable computational time and incorporates phylogenetic uncertainty in the analyses. We demonstrate its application with two real examples: Passerine birds and their feather mites, and orchids and bee pollinators. In both systems, Random TaPas revealed low cophylogenetic signal, but mapping its variation onto the tanglegram pointed to two different coevolutionary processes. We suggest that the recursive partitioning of the tanglegram buffers the effect of phylogenetic nonindependence occurring in current global-fit methods and therefore Random TaPas is more reliable than regular global-fit methods to identify host-symbiont associations that contribute most to cophylogenetic signal. Random TaPas can be implemented in the public-domain statistical software R with scripts provided herein. A User’s Guide is also available at GitHub.

Footnotes

  • The most significant change in this revised version concerns the way the frequencies of the host-symbiont associations are computed. The Random TaPas algorithm favors the sapling of one-to-one associations that potentially can lead to an over-representation of their occurrence in the percentile set. To avoid this, we have resorted to generate a null model based on the frequencies of each association in the whole frequency distribution. So we compute a residual Ri= Frequency actually observed in percentile – Expected frequency from the null model that measures whether the association is represented more or less frequently than expected by chance. So we expect large positive and negative residuals to represent congruent and incongruent associations, respectively. We now recommend this strategy to deal with systems with multiple host-symbiont associations, whereas the original Random Tapas is still appropriate for the less frequent one-to-one association systems.

  • https://github.com/Ligophorus/RandomTaPas

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 28, 2019.
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.
Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot
(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
Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot
Juan Antonio Balbuena, Óscar Alejandro Pérez-Escobar, Cristina Llopis-Belenguer, Isabel Blasco-Costa
bioRxiv 481846; doi: https://doi.org/10.1101/481846
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot
Juan Antonio Balbuena, Óscar Alejandro Pérez-Escobar, Cristina Llopis-Belenguer, Isabel Blasco-Costa
bioRxiv 481846; doi: https://doi.org/10.1101/481846

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 (3609)
  • Biochemistry (7585)
  • Bioengineering (5533)
  • Bioinformatics (20825)
  • Biophysics (10344)
  • Cancer Biology (7995)
  • Cell Biology (11653)
  • Clinical Trials (138)
  • Developmental Biology (6617)
  • Ecology (10224)
  • Epidemiology (2065)
  • Evolutionary Biology (13639)
  • Genetics (9557)
  • Genomics (12856)
  • Immunology (7930)
  • Microbiology (19568)
  • Molecular Biology (7675)
  • Neuroscience (42182)
  • Paleontology (308)
  • Pathology (1259)
  • Pharmacology and Toxicology (2208)
  • Physiology (3271)
  • Plant Biology (7058)
  • Scientific Communication and Education (1295)
  • Synthetic Biology (1953)
  • Systems Biology (5433)
  • Zoology (1119)