ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2015
New substitution models for rooting phylogenetic trees.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- Article
- Phylogenomic Testing of Root Hypotheses.Genome biology and evolution · 2023Article
- Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method.Life (Basel, Switzerland) · 2022Article
- Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals.Systematic biology · 2022Article
- An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.Genome biology and evolution · 2021Article
- Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life.Molecular biology and evolution · 2021Article
- Origin of the Phosphoprotein Phosphatase (PPP) sequence family in Bacteria: Critical ancestral sequence changes, radiation patterns and substrate binding features.BBA advances · 2021Article
- Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.Clinical microbiology reviews · 2020Review
- Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria).Protoplasma · 2020Review
- Article
- Phylogenomics provides robust support for a two-domains tree of life.Nature ecology & evolution · 2020Article
- From pairs of most similar sequences to phylogenetic best matches.Algorithms for molecular biology : AMB · 2020Article
- Investigating the Origins of Membrane Phospholipid Biosynthesis Genes Using Outgroup-Free Rooting.Genome biology and evolution · 2019Article
- Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons.Frontiers in immunology · 2019Article
- Genomic diversity, lifestyles and evolutionary origins of DPANN archaea.FEMS microbiology letters · 2019Review
- Genome size evolution in the Archaea.Emerging topics in life sciences · 2018Article
- A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.Nature biotechnology · 2018Article
- Reconstruction of the sialylation pathway in the ancestor of eukaryotes.Scientific reports · 2018Article
- STRIDE: Species Tree Root Inference from Gene Duplication Events.Molecular biology and evolution · 2017Article
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6 authors.
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Abstract
The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made.
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