Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction

Abstract

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods.

TreeCluster: Massively scalable transmission clustering using phylogenetic trees

“…Each replicate dataset was aligned using MAFFT [6], and phylogenetic trees were inferred under the General Time Reversible (GTR) + Γ model using FastTree 2 [7]. Polytomies were then randomly resolved with 0-length branches using the ape R package, the trees were midpoint-rooted using FastRoot [8], and Shimodaira-Hasegawa-like (SH-like) branch support values were computed using FastTree 2.…”

Log Transformation Improves Dating of Phylogenies

“…First, the current formulation of LogDate assumes a rooted phylogenetic tree, whereas most inferred trees are unrooted. Rooting phylogenies is a non-trivial problem and can also be done based on principles of minimizing rate variation [21]. Similar to LSD, LogDate can be generalized to unrooted trees by rooting the tree on each branch, solving the optimization problem for each root, and choosing the root that minimizes the (w)LogDate objective function.…”

HIV Care Prioritization using Phylogenetic Branch Length

“…from the pol region), rooted using an outgroup or clock-based methods (e.g. midpoint or MinVar-root, Mai et al (2017)). ProACT simply orders samples in order of incident branch length of their associated virus, and it breaks ties based on incident branch lengths of parent nodes, then those of grandparent nodes, etc.…”

“…For each simulated sequence dataset, using FastTree 2 (Price et al, 2010), a phylogenetic tree was inferred under the GTR+Γ model from the sequences obtained in the first 9 years of the simulation. These trees were then MinVar-rooted using FastRoot (Mai et al, 2017), and ProACT was run on the resulting trees.…”

“…A phylogenetic tree was inferred from the MSA under the GTR+Γ model using FastTree 2 (Price et al, 2010), and the resulting tree was MinVar-rooted using FastRoot (Mai et al, 2017). For each decile, using TreeSwift (Moshiri, 2018), the full tree was pruned to only contain samples obtained up to the end of that decile.…”