ArticlePloS one2017
Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Triplet-based species tree estimation: Sensitivity to gene tree rooting (or lack thereof).PLoS computational biology · 2026Article
- Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US.Scientific data · 2026Article
- krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.Genome biology · 2026Article
- Functionally distinct core microbes of Tricholoma matsutake revealed by cross-study analysis.Microbiome · 2026Article
- Phylogenetic reconciliation provides new insights into the evolutionary diversification of the glutamine synthetase gene family in seed plants.The FEBS journal · 2026Article
- Adaptation of Fe-S Cluster Assembly to Rising OResearch square · 2026Article
- eggNOG v7: phylogeny-based orthology predictions and functional annotations.Nucleic acids research · 2026Article
- Patterns of Recombination in Coronaviruses.International journal of molecular sciences · 2025Article
- Genomic diversity and tracing ofMicrobial genomics · 2025Article
- Classification of polyphenol oxidases shows ancient gene duplication leading to two distinct enzyme types.iScience · 2025Article
- Unraveling the Ancient Introgression History ofInternational journal of molecular sciences · 2025Article
- Application of a Quantitative Real-Time PCR Assay for Early Detection ofTransboundary and emerging diseases · 2025Article
- Resolving phylogenetic conflicts in Pandanales: the dual roles of gene flow and whole-genome duplication.Frontiers in plant science · 2025Article
- Order of amino acid recruitment into the genetic code resolved by last universal common ancestor's protein domains.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Characterisation of the genetic diversity of citrus viroid VII using amplicon sequencing.Archives of virology · 2024Article
- Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model.Systematic biology · 2024Article
- Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains.bioRxiv : the preprint server for biology · 2024Article
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- Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites.Journal of integrative bioinformatics · 2024Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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