ArticleSystematic biology2022
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
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- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- Leveraging Next-Generation Tools for Genetic Assessment and Demographic Monitoring in Threatened and Elusive Humboldt Martens.Evolutionary applications · 2026Article
- CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution.Systematic biology · 2026Article
- IQ-TREE 3: phylogenomic inference software using complex evolutionary models.Molecular biology and evolution · 2026Article
- A previously unrecognized class of fungal ice-nucleating proteins with bacterial ancestry.Science advances · 2026Article
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- Dating the Bacterial Tree of Life Based on Ancient Symbiosis.Systematic biology · 2025Article
- A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage.Science advances · 2025Article
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- An Alternative Self-Splicing Intron Lifecycle Revealed by Dynamic Intron Turnover in Epichloë Endophyte Mitochondrial Genomes.Molecular biology and evolution · 2025Article
- nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models.Journal of molecular evolution · 2025Article
- MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses.Molecular biology and evolution · 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
- 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
- The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex.Genome biology and evolution · 2024Article
- Revisiting the four Hexapoda classes: Protura as the sister group to all other hexapods.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Population genetics and phylogeographic history of the insular lizardEcology and evolution · 2024Article
- Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.The ISME journal · 2024Review
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
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3 authors.
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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 nonreversible 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. [Bootstrap; nonreversible models; phylogenetic inference; root estimation.].
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