Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals

Abstract

Using 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 implementation: rootstrap 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

Extreme genome diversity and cryptic speciation in a harmful algal bloom forming eukaryote

“…We selected 2699 single-copy orthogroups (SCOGs) present in all 15 strains for concatenation- and coalescent-based species tree analyses. Because the most closely related haptophyte species with sequenced genomes were too divergent to serve as outgroups for a nucleotide-based phylogeny, a nonreversible substitution model was used to evaluate support for different root locations on the P. parvum species tree (42). The root with the highest likelihood score caused the C-type prymnesin producers to be paraphyletic, which is a phylogenetic pattern also observed in a prior 18S rDNA phylogeny (20).…”

Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling

“…Rooted phylogenies were also inferred under the NONREV protein model (59) with 100 bootstrap replicates. The sets of rooted phylogenies and bootstrap trees were used to calculate rootstrap supports (71). We also rooted the single-gene methyltransferase (MtaB, MtsB, MtmB, MtbB, and MttB) phylogenies with MAD and MinVar.…”

Identification of a covert evolutionary pathway between two protein folds

“…However, we could not use an outgroup because it was not possible to identify a single sequence outside of our alignment that was homologous to both folds. Therefore, we combined the nonreversible model with a maximum likelihood model 79 used to calculated the loglikelihoods of the trees being rooted on every branch of the tree. Bootstrapping of 10,000 replicates was performed to obtain reliable results.…”