Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models

Abstract

AO_SCPLOWBSTRACTC_SCPLOWUsing time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the rootstrap, which provides information on the statistical support for any given root position. Availability and implementationrootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage http://www.iqtree.org/doc/Rootstrap. In addition, a python script is available at https://github.com/suhanaser/Rootstrap. [phylogenetic inference, root estimation, bootstrap, non-reversible models]