MonoPhy: A simple R package to find and visualize monophyly issues
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology
- Keywords
- phylogeny, evolution, monophyly, R package, taxonomy, rogue taxa, tree conflict
- Copyright
- © 2015 Schwery et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2015. MonoPhy: A simple R package to find and visualize monophyly issues. PeerJ PrePrints 3:e1600v1 https://doi.org/10.7287/peerj.preprints.1600v1
Abstract
Background. The monophyly of taxa is an important attribute of a phylogenetic tree, as a lack of it may hint at shortcomings of either the tree or the current taxonomy and can misguide subsequent analyses. While monophyly is conceptually simple, it is manually tedious and time consuming to assess on modern phylogenies of hundreds to thousands of species. Results. The R package MonoPhy allows assessment and exploration of monophyly of taxa in a phylogeny. It can assess the monophyly of genera using the phylogeny only, and with an additional input file, any other desired higher taxa or unranked groups can be checked as well. Conclusion. Summary tables, easily subsettable results and several visualization options allow quick and convenient exploration of monophyly issues, thus making MonoPhy a valuable tool for any researcher working with phylogenies.
Author Comment
This paper describes an R package to assess monophyly of taxonomic groups in a given phylogeny, and to explore the underlying causes of non-monophyly. A current stable version is accessible on CRAN, including a detailed tutorial. It is submitted for review to PeerJ Computer Science.
Supplemental Information
Supplementary Information: Commands for Examples (MonoPhy)
The commented R commands to run the examples from the main article, along with the detailed results.
Monophyly plot of the genera of Ericaceae
Fig. S1: Monophyly plot of the genera of Ericaceae, with branches of the tree coloured by monophyly status. We see clearly how e.g.Orthilia invades Pyrola and how Vaccinium has two outliers.
Monophyly plot of the genera of Embryophyta, collapsed
Fig. S2: Monophyly plot of the genera of Embryophyta, with branches of the tree coloured by monophyly status, just as in Figure 1. Monophyletic groups were collapsed to one branch to save space.
Monophyly plot of the genera of Embryophyta, uncollapsed
Fig. S3: Monophyly plot of the genera of Embryophyta, with branches of the tree coloured by monophyly status, just as in Figure 1. Monophyletic groups were not collapsed to one branch.
Intruder plot of the genera of Embryophyta
Fig. S4: Intruder plot of the genera of Embryophyta, with branches of the tree coloured by monophyly status (monophyletic gray, non-monophyletic black) and intruders and outliers coloured according to their genus. Monophyletic groups were not collapsed to one branch.
MonoPhy results of Embryophyta
Tab. S1:MonoPhy result table for the genera of Ericaceae.