Abstract
Background.The monophyly of taxa is an important attribute of a phylogenetic tree. A lack of it may hint at shortcomings of either the tree or the current taxonomy, or can indicate cases of incomplete lineage sorting or horizontal gene transfer. Whichever is the reason, a lack of monophyly 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 packageMonoPhyallows 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 order 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 makingMonoPhya valuable tool for any researcher working with phylogenies.
Highlights
Phylogenetic trees are undoubtedly crucial for most research in ecology or evolutionary biology
Whether one is studying trait evolution (e.g., Coddington, 1988; Donoghue, 1989), diversification (e.g., Gilinsky & Good, 1991; Hey, 1992), phylogeography (Avise et al, 1987), or relatedness within a group (e.g., Czelusniak et al, 1982; Shochat & Dessauer, 1981; Sibley & Ahlquist, 1981), bifurcating trees representing hierarchically nested relationships are central to the analysis
Because phylogenies are so fundamental to the inferences we make, we need tools that enable us to examine how reconstructed relationships compare with existing assumptions, taxonomy
Summary
Phylogenetic trees are undoubtedly crucial for most research in ecology or evolutionary biology. How to cite this article Schwery and O’Meara (2016), MonoPhy: a simple R package to find and visualize monophyly issues. The new tool presented here, the R package MonoPhy, is a quick and user-friendly method for assessing monophyly of taxa in a given phylogeny.
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